10mh
|
transferase-DNA |
X-ray (2.55 Å) |
Sheikhnejad G, Brank A, Christman JK, Goddard A,
Alvarez E, Ford Jr H, Marquez VE, Marasco CJ, Sufrin JR,
O'gara M, Cheng X |
(1999) "Mechanism
of inhibition of DNA (cytosine C5)-methyltransferases
by oligodeoxyribonucleotides containing
5,6-dihydro-5-azacytosine." J.Mol.Biol.,
285, 2021-2034. doi: 10.1006/jmbi.1998.2426.
|
Ternary structure of hhai methyltransferase with adohcy
and hemimethylated DNA containing
5,6-dihydro-5-azacytosine at the target . SNAP output
|
173d
|
DNA-antibiotic |
X-ray (3.0 Å) |
Kamitori S, Takusagawa F |
(1994) "Multiple Binding Modes of Anticancer Drug
Actinomycin D: X-Ray, Molecular Modeling, and
Spectroscopic Studies of D(Gaagcttc)2-Actinomycin D
Complexes and its Host DNA." J.Am.Chem.Soc.,
116, 4154. doi: 10.1021/JA00089A002.
|
Multiple binding modes of anticancer drug actinomycin
d: x-ray, molecular modeling, and spectroscopic studies
of d(gaagcttc)2-actinomycin d complexes and its host
DNA . SNAP output
|
185d
|
DNA-antibiotic |
NMR |
Addess KJ, Feigon J |
(1994) "Sequence
Specificity of Quinoxaline Antibiotics. 1. Solution
Structure of a 1:1 Complex between Triostin a and
[D(Gacgtc)]2 and Comparison with the Solution Structure
of the [N-Mecys3,N-Mecys7]Tandem-[D(Gatatc)]2
Complex." Biochemistry,
33, 12386. doi: 10.1021/BI00207A005.
|
Sequence specificity of quinoxaline antibiotics. 1.
solution structure of a 1:1 complex between triostin a
and [d(gacgtc)]2 and comparison with the solution
structure of the [n-mecys3,
n-mecys7]tandem-[d(gatatc)]2 complex . SNAP output
|
193d
|
DNA-antibiotic |
NMR |
Chen H, Patel DJ |
(1995) "Solution
Structure of a Quinomycin Bisintercalator-DNA
Complex." J.Mol.Biol.,
246, 164. doi: 10.1006/JMBI.1994.0074.
|
Solution structure of a quinomycin bisintercalator-DNA
complex . SNAP
output
|
1a02
|
transcription-DNA |
X-ray (2.7 Å) |
Chen L, Glover JN, Hogan PG, Rao A, Harrison SC |
(1998) "Structure
of the DNA-binding domains from NFAT, Fos and Jun bound
specifically to DNA." Nature,
392, 42-48. doi: 10.1038/32100.
|
Structure of the DNA binding domains of nfat, fos and
jun bound to DNA . SNAP
output
|
1a0a
|
transcription-DNA |
X-ray (2.8 Å) |
Shimizu T, Toumoto A, Ihara K, Shimizu M, Kyogoku Y,
Ogawa N, Oshima Y, Hakoshima T |
(1997) "Crystal
structure of PHO4 bHLH domain-DNA complex: flanking
base recognition." EMBO J.,
16, 4689-4697. doi: 10.1093/emboj/16.15.4689.
|
Phosphate system positive regulatory protein pho4-DNA
complex . SNAP
output
|
1a1f
|
transcription-DNA |
X-ray (2.1 Å) |
Elrod-Erickson M, Benson TE, Pabo CO |
(1998) "High-resolution
structures of variant Zif268-DNA complexes:
implications for understanding zinc finger-DNA
recognition." Structure,
6, 451-464. doi: 10.1016/S0969-2126(98)00047-1.
|
Dsnr (zif268 variant) zinc finger-DNA complex (gacc
site) . SNAP output
|
1a1g
|
transcription-DNA |
X-ray (1.9 Å) |
Elrod-Erickson M, Benson TE, Pabo CO |
(1998) "High-resolution
structures of variant Zif268-DNA complexes:
implications for understanding zinc finger-DNA
recognition." Structure,
6, 451-464. doi: 10.1016/S0969-2126(98)00047-1.
|
Dsnr (zif268 variant) zinc finger-DNA complex (gcgt
site) . SNAP output
|
1a1h
|
transcription-DNA |
X-ray (1.6 Å) |
Elrod-Erickson M, Benson TE, Pabo CO |
(1998) "High-resolution
structures of variant Zif268-DNA complexes:
implications for understanding zinc finger-DNA
recognition." Structure,
6, 451-464. doi: 10.1016/S0969-2126(98)00047-1.
|
Qgsr (zif268 variant) zinc finger-DNA complex (gcac
site) . SNAP output
|
1a1i
|
transcription-DNA |
X-ray (1.6 Å) |
Elrod-Erickson M, Benson TE, Pabo CO |
(1998) "High-resolution
structures of variant Zif268-DNA complexes:
implications for understanding zinc finger-DNA
recognition." Structure,
6, 451-464. doi: 10.1016/S0969-2126(98)00047-1.
|
Radr (zif268 variant) zinc finger-DNA complex (gcac
site) . SNAP output
|
1a1j
|
transcription-DNA |
X-ray (2.0 Å) |
Elrod-Erickson M, Benson TE, Pabo CO |
(1998) "High-resolution
structures of variant Zif268-DNA complexes:
implications for understanding zinc finger-DNA
recognition." Structure,
6, 451-464. doi: 10.1016/S0969-2126(98)00047-1.
|
Radr (zif268 variant) zinc finger-DNA complex (gcgt
site) . SNAP output
|
1a1k
|
transcription-DNA |
X-ray (1.9 Å) |
Elrod-Erickson M, Benson TE, Pabo CO |
(1998) "High-resolution
structures of variant Zif268-DNA complexes:
implications for understanding zinc finger-DNA
recognition." Structure,
6, 451-464. doi: 10.1016/S0969-2126(98)00047-1.
|
Radr (zif268 variant) zinc finger-DNA complex (gacc
site) . SNAP output
|
1a1l
|
transcription-DNA |
X-ray (2.3 Å) |
Elrod-Erickson M, Benson TE, Pabo CO |
(1998) "High-resolution
structures of variant Zif268-DNA complexes:
implications for understanding zinc finger-DNA
recognition." Structure,
6, 451-464. doi: 10.1016/S0969-2126(98)00047-1.
|
Zif268 zinc finger-DNA complex (gcac site) . SNAP output
|
1a1v
|
hydrolase-DNA |
X-ray (2.2 Å) |
Kim JL, Morgenstern KA, Griffith JP, Dwyer MD,
Thomson JA, Murcko MA, Lin C, Caron PR |
(1998) "Hepatitis
C virus NS3 RNA helicase domain with a bound
oligonucleotide: the crystal structure provides
insights into the mode of unwinding."
Structure, 6, 89-100. doi:
10.1016/S0969-2126(98)00010-0.
|
Hepatitis c virus ns3 helicase domain complexed with
single stranded sDNA . SNAP output
|
1a31
|
isomerase-DNA |
X-ray (2.1 Å) |
Redinbo MR, Stewart L, Kuhn P, Champoux JJ, Hol
WG |
(1998) "Crystal
structures of human topoisomerase I in covalent and
noncovalent complexes with DNA." Science,
279, 1504-1513. doi: 10.1126/science.279.5356.1504.
|
Human reconstituted DNA topoisomerase i in covalent
complex with a 22 base pair DNA duplex . SNAP output
|
1a35
|
isomerase-DNA |
X-ray (2.5 Å) |
Redinbo MR, Stewart L, Kuhn P, Champoux JJ, Hol
WG |
(1998) "Crystal
structures of human topoisomerase I in covalent and
noncovalent complexes with DNA." Science,
279, 1504-1513. doi: 10.1126/science.279.5356.1504.
|
Human topoisomerase i-DNA complex . SNAP output
|
1a36
|
isomerase-DNA |
X-ray (2.8 Å) |
Stewart L, Redinbo MR, Qiu X, Hol WG, Champoux
JJ |
(1998) "A model
for the mechanism of human topoisomerase I."
Science, 279, 1534-1541. doi:
10.1126/science.279.5356.1534.
|
Topoisomerase i-DNA complex . SNAP output
|
1a3q
|
transcription-DNA |
X-ray (2.1 Å) |
Cramer P, Larson CJ, Verdine GL, Muller CW |
(1997) "Structure
of the human NF-kappaB p52 homodimer-DNA complex at 2.1
A resolution." EMBO J.,
16, 7078-7090. doi: 10.1093/emboj/16.23.7078.
|
Human nf-kappa-b p52 bound to DNA . SNAP output
|
1a66
|
transcription-DNA |
NMR |
Zhou P, Sun LJ, Dotsch V, Wagner G, Verdine GL |
(1998) "Solution
structure of the core NFATC1/DNA complex."
Cell(Cambridge,Mass.), 92,
687-696. doi: 10.1016/S0092-8674(00)81136-8.
|
Solution NMR structure of the core nfatc1-DNA complex,
18 structures . SNAP
output
|
1a6b
|
viral protein-DNA |
NMR |
Schuler W, Dong C, Wecker K, Roques BP |
(1999) "NMR
structure of the complex between the zinc finger
protein NCp10 of Moloney murine leukemia virus and the
single-stranded pentanucleotide d(ACGCC): comparison
with HIV-NCp7 complexes." Biochemistry,
38, 12984-12994. doi: 10.1021/bi990378d.
|
NMR structure of the complex between the zinc finger
protein ncp10 of moloney murine leukemia virus and a
sequence of the psi-packaging domain of hiv-1, 20
structures . SNAP
output
|
1a6y
|
transcription-DNA |
X-ray (2.3 Å) |
Zhao Q, Khorasanizadeh S, Miyoshi Y, Lazar MA,
Rastinejad F |
(1998) "Structural
elements of an orphan nuclear receptor-DNA
complex." Mol.Cell, 1,
849-861. doi: 10.1016/S1097-2765(00)80084-2.
|
Reverba orphan nuclear receptor-DNA complex . SNAP output
|
1a73
|
hydrolase-DNA |
X-ray (1.8 Å) |
Flick KE, Jurica MS, Monnat Jr RJ, Stoddard BL |
(1998) "DNA
binding and cleavage by the nuclear intron-encoded
homing endonuclease I-PpoI." Nature,
394, 96-101. doi: 10.1038/27952.
|
Intron-encoded endonuclease i-ppoi complexed with DNA .
SNAP output
|
1a74
|
hydrolase-DNA |
X-ray (2.2 Å) |
Flick KE, Jurica MS, Monnat Jr RJ, Stoddard BL |
(1998) "DNA
binding and cleavage by the nuclear intron-encoded
homing endonuclease I-PpoI." Nature,
394, 96-101. doi: 10.1038/27952.
|
I-ppol homing endonuclease-DNA complex . SNAP output
|
1aay
|
transcription-DNA |
X-ray (1.6 Å) |
Elrod-Erickson M, Rould MA, Nekludova L, Pabo CO |
(1996) "Zif268
protein-DNA complex refined at 1.6 A: a model system
for understanding zinc finger-DNA interactions."
Structure, 4, 1171-1180. doi:
10.1016/S0969-2126(96)00125-6.
|
Zif268 zinc finger-DNA complex . SNAP output
|
1ahd
|
DNA binding protein-DNA |
NMR |
Billeter M, Qian YQ, Otting G, Muller M, Gehring W,
Wuthrich K |
(1993) "Determination
of the nuclear magnetic resonance solution structure of
an Antennapedia homeodomain-DNA complex."
J.Mol.Biol., 234, 1084-1097.
doi: 10.1006/jmbi.1993.1661.
|
Determination of the NMR solution structure of an
antennapedia homeodomain-DNA complex . SNAP output
|
1ais
|
transcription-DNA |
X-ray (2.1 Å) |
Kosa PF, Ghosh G, DeDecker BS, Sigler PB |
(1997) "The 2.1-A
crystal structure of an archaeal preinitiation complex:
TATA-box-binding protein/transcription factor (II)B
core/TATA-box." Proc.Natl.Acad.Sci.USA,
94, 6042-6047. doi: 10.1073/pnas.94.12.6042.
|
Tata-binding protein-transcription factor
(ii)b-tata-box complex from pyrococcus woesei .
SNAP output
|
1akh
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Li T, Jin Y, Vershon AK, Wolberger C |
(1998) "Crystal
structure of the MATa1/MATalpha2 homeodomain
heterodimer in complex with DNA containing an
A-tract." Nucleic Acids Res.,
26, 5707-5718. doi: 10.1093/nar/26.24.5707.
|
Mat a1-alpha2-DNA ternary complex . SNAP output
|
1am9
|
transcription-DNA |
X-ray (2.3 Å) |
Parraga A, Bellsolell L, Ferre-D'Amare AR, Burley
SK |
(1998) "Co-crystal
structure of sterol regulatory element binding protein
1a at 2.3 A resolution." Structure,
6, 661-672. doi: 10.1016/S0969-2126(98)00067-7.
|
Human srebp-1a bound to ldl receptor promoter .
SNAP output
|
1an2
|
transcription-DNA |
X-ray (2.9 Å) |
Ferre-D'Amare AR, Prendergast GC, Ziff EB, Burley
SK |
(1993) "Recognition
by Max of its cognate DNA through a dimeric b/HLH/Z
domain." Nature, 363,
38-45. doi: 10.1038/363038a0.
|
Recognition by max of its cognate DNA through a dimeric
b-hlh-z domain . SNAP
output
|
1an4
|
transcription-DNA |
X-ray (2.9 Å) |
Ferre-D'Amare AR, Pognonec P, Roeder RG, Burley
SK |
(1994) "Structure
and function of the b/HLH/Z domain of USF."
EMBO J., 13, 180-189.
|
Structure and function of the b-hlh-z domain of usf .
SNAP output
|
1aoi
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Luger K, Mader AW, Richmond RK, Sargent DF, Richmond
TJ |
(1997) "Crystal
structure of the nucleosome core particle at 2.8 A
resolution." Nature, 389,
251-260. doi: 10.1038/38444.
|
Complex between nucleosome core particle
(h3,h4,h2a,h2b) and 146 bp long DNA fragment . SNAP output
|
1apl
|
DNA binding protein-DNA |
X-ray (2.7 Å) |
Wolberger C, Vershon AK, Liu B, Johnson AD, Pabo
CO |
(1991) "Crystal
structure of a MAT alpha 2 homeodomain-operator complex
suggests a general model for homeodomain-DNA
interactions." Cell(Cambridge,Mass.),
67, 517-528. doi: 10.1016/0092-8674(91)90526-5.
|
Crystal structure of a mat-alpha2 homeodomain-operator
complex suggests a general model for homeodomain-DNA
interactions . SNAP
output
|
1au7
|
transcription-DNA |
X-ray (2.3 Å) |
Jacobson EM, Li P, Leon-del-Rio A, Rosenfeld MG,
Aggarwal AK |
(1997) "Structure
of Pit-1 POU domain bound to DNA as a dimer: unexpected
arrangement and flexibility." Genes Dev.,
11, 198-212.
|
Pit-1 mutant-DNA complex . SNAP output
|
1awc
|
transcription-DNA |
X-ray (2.15 Å) |
Batchelor AH, Piper DE, de la Brousse FC, McKnight
SL, Wolberger C |
(1998) "The
structure of GABPalpha/beta: an ETS domain- ankyrin
repeat heterodimer bound to DNA." Science,
279, 1037-1041. doi: 10.1126/science.279.5353.1037.
|
Mouse gabp alpha-beta domain bound to DNA . SNAP output
|
1az0
|
hydrolase-DNA |
X-ray (2.0 Å) |
Perona JJ, Martin AM |
(1997) "Conformational
transitions and structural deformability of EcoRV
endonuclease revealed by crystallographic
analysis." J.Mol.Biol.,
273, 207-225. doi: 10.1006/jmbi.1997.1315.
|
Ecorv endonuclease-DNA complex . SNAP output
|
1azp
|
DNA binding protein-DNA |
X-ray (1.6 Å) |
Robinson H, Gao YG, McCrary BS, Edmondson SP, Shriver
JW, Wang AH |
(1998) "The
hyperthermophile chromosomal protein Sac7d sharply
kinks DNA." Nature, 392,
202-205. doi: 10.1038/32455.
|
Hyperthermophile chromosomal protein sac7d bound with
kinked DNA duplex . SNAP
output
|
1azq
|
DNA binding protein-DNA |
X-ray (1.94 Å) |
Robinson H, Gao YG, McCrary BS, Edmondson SP, Shriver
JW, Wang AH |
(1998) "The
hyperthermophile chromosomal protein Sac7d sharply
kinks DNA." Nature, 392,
202-205. doi: 10.1038/32455.
|
Hyperthermophile chromosomal protein sac7d bound with
kinked DNA duplex . SNAP
output
|
1b01
|
gene regulation-DNA |
X-ray (2.56 Å) |
Gomis-Ruth FX, Sola M, Acebo P, Parraga A, Guasch A,
Eritja R, Gonzalez A, Espinosa M, del Solar G, Coll
M |
(1998) "The
structure of plasmid-encoded transcriptional repressor
CopG unliganded and bound to its operator."
EMBO J., 17, 7404-7415. doi:
10.1093/emboj/17.24.7404.
|
Transcriptional repressor copg-DNA complex . SNAP output
|
1b3t
|
protein-DNA |
X-ray (2.2 Å) |
Bochkarev A, Bochkareva E, Frappier L, Edwards
AM |
(1998) "The 2.2 A
structure of a permanganate-sensitive DNA site bound by
the Epstein-Barr virus origin binding protein,
EBNA1." J.Mol.Biol., 284,
1273-1278. doi: 10.1006/jmbi.1998.2247.
|
Ebna-1 nuclear protein-DNA complex . SNAP output
|
1b69
|
integrase-DNA |
NMR |
Wojciak JM, Connolly KM, Clubb RT |
(1999) "NMR
structure of the Tn916 integrase-DNA complex."
Nat.Struct.Biol., 6, 366-373.
doi: 10.1038/7603.
|
The solution structure of tn916 integrase n-terminal
domain-DNA complex . SNAP output
|
1b72
|
protein-DNA |
X-ray (2.35 Å) |
Piper DE, Batchelor AH, Chang CP, Cleary ML,
Wolberger C |
(1999) "Structure
of a HoxB1-Pbx1 heterodimer bound to DNA: role of the
hexapeptide and a fourth homeodomain helix in complex
formation." Cell(Cambridge,Mass.),
96, 587-597. doi: 10.1016/S0092-8674(00)80662-5.
|
Pbx1, homeobox protein hox-b1-DNA ternary complex .
SNAP output
|
1b8i
|
transcription-DNA |
X-ray (2.4 Å) |
Passner JM, Ryoo HD, Shen L, Mann RS, Aggarwal
AK |
(1999) "Structure
of a DNA-bound Ultrabithorax-Extradenticle homeodomain
complex." Nature, 397,
714-719. doi: 10.1038/17833.
|
Structure of the homeotic ubx-exd-DNA ternary complex .
SNAP output
|
1b94
|
hydrolase-DNA |
X-ray (1.9 Å) |
Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin
GS |
(1999) "Structural
analysis of a mutational hot-spot in the EcoRV
restriction endonuclease: a catalytic role for a main
chain carbonyl group." Nucleic Acids Res.,
27, 3438-3445. doi: 10.1093/nar/27.17.3438.
|
Restriction endonuclease ecorv with calcium . SNAP output
|
1b95
|
hydrolase-DNA |
X-ray (2.05 Å) |
Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin
GS |
(1999) "Structural
analysis of a mutational hot-spot in the EcoRV
restriction endonuclease: a catalytic role for a main
chain carbonyl group." Nucleic Acids Res.,
27, 3438-3445. doi: 10.1093/nar/27.17.3438.
|
Analysis of a mutational hot-spot in the ecorv
restriction endonuclease: a catalytic role for a main
chain carbonyl group . SNAP output
|
1b96
|
hydrolase-DNA |
X-ray (2.3 Å) |
Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin
GS |
(1999) "Structural
analysis of a mutational hot-spot in the EcoRV
restriction endonuclease: a catalytic role for a main
chain carbonyl group." Nucleic Acids Res.,
27, 3438-3445. doi: 10.1093/nar/27.17.3438.
|
Analysis of a mutational hot-spot in the ecorv
restriction endonuclease: a catalytic role for a main
chain carbonyl group . SNAP output
|
1b97
|
hydrolase-DNA |
X-ray (1.9 Å) |
Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin
GS |
(1999) "Structural
analysis of a mutational hot-spot in the EcoRV
restriction endonuclease: a catalytic role for a main
chain carbonyl group." Nucleic Acids Res.,
27, 3438-3445. doi: 10.1093/nar/27.17.3438.
|
Analysis of a mutational hot-spot in the ecorv
restriction endonuclease: a catalytic role for a main
chain carbonyl group . SNAP output
|
1bbx
|
DNA binding protein-DNA |
NMR |
Agback P, Baumann H, Knapp S, Ladenstein R, Hard
T |
(1998) "Architecture
of Nonspecific Protein-DNA Interactions in the
Sso7D-DNA Complex." Nat.Struct.Biol.,
5, 579-584. doi: 10.1038/836.
|
Non-specific protein-DNA interactions in the sso7d-DNA
complex, NMR, 1 structure . SNAP output
|
1bc7
|
transcription-DNA |
X-ray (2.01 Å) |
Mo Y, Vaessen B, Johnston K, Marmorstein R |
(1998) "Structures
of SAP-1 bound to DNA targets from the E74 and c-fos
promoters: insights into DNA sequence discrimination by
Ets proteins." Mol.Cell,
2, 201-212. doi: 10.1016/S1097-2765(00)80130-6.
|
Serum response factor accessory protein 1a (sap-1)-DNA
complex . SNAP
output
|
1bc8
|
transcription-DNA |
X-ray (1.93 Å) |
Mo Y, Vaessen B, Johnston K, Marmorstein R |
(1998) "Structures
of SAP-1 bound to DNA targets from the E74 and c-fos
promoters: insights into DNA sequence discrimination by
Ets proteins." Mol.Cell,
2, 201-212. doi: 10.1016/S1097-2765(00)80130-6.
|
Structures of sap-1 bound to DNA sequences from the e74
and c-fos promoters provide insights into how ets
proteins discriminate between related DNA targets .
SNAP output
|
1bdh
|
transcription-DNA |
X-ray (2.7 Å) |
Glasfeld A, Schumacher MA, Choi KY, Zalkin H, Brennan
RG |
(1996) "A Positively Charged Residue Bound in the
Minor Groove Does not Alter the Bending of a DNA Duplex."
J.Am.Chem.Soc., 118,
13073-13074. |
Purine repressor mutant-hypoxanthine-palindromic
operator complex . SNAP
output
|
1bdi
|
transcription-DNA |
X-ray (3.0 Å) |
Glasfeld A, Schumacher MA, Choi KY, Zalkin H, Brennan
RG |
(1996) "A Positively Charged Residue Bound in the
Minor Groove Does not Alter the Bending of a DNA Duplex."
J.Am.Chem.Soc., 118,
13073-13074. |
Purine repressor mutant-hypoxanthine-palindromic
operator complex . SNAP
output
|
1bdt
|
gene regulation-DNA |
X-ray (2.5 Å) |
Schildbach JF, Karzai AW, Raumann BE, Sauer RT |
(1999) "Origins
of DNA-binding specificity: role of protein contacts
with the DNA backbone."
Proc.Natl.Acad.Sci.USA, 96,
811-817. doi: 10.1073/pnas.96.3.811.
|
Wild type gene-regulating protein arc-DNA complex .
SNAP output
|
1bdv
|
gene regulation-DNA |
X-ray (2.8 Å) |
Schildbach JF, Karzai AW, Raumann BE, Sauer RT |
(1999) "Origins
of DNA-binding specificity: role of protein contacts
with the DNA backbone."
Proc.Natl.Acad.Sci.USA, 96,
811-817. doi: 10.1073/pnas.96.3.811.
|
Arc fv10 cocrystal . SNAP output
|
1bf4
|
DNA-binding protein-DNA |
X-ray (1.6 Å) |
Gao YG, Su SY, Robinson H, Padmanabhan S, Lim L,
McCrary BS, Edmondson SP, Shriver JW, Wang AH |
(1998) "The
crystal structure of the hyperthermophile chromosomal
protein Sso7d bound to DNA."
Nat.Struct.Biol., 5, 782-786.
doi: 10.1038/1822.
|
Chromosomal DNA-binding protein sso7d-d(gcgaacgc)
complex . SNAP
output
|
1bf5
|
gene regulation-DNA |
X-ray (2.9 Å) |
Chen X, Vinkemeier U, Zhao Y, Jeruzalmi D, Darnell Jr
JE, Kuriyan J |
(1998) "Crystal
structure of a tyrosine phosphorylated STAT-1 dimer
bound to DNA." Cell(Cambridge,Mass.),
93, 827-839. doi: 10.1016/S0092-8674(00)81443-9.
|
Tyrosine phosphorylated stat-1-DNA complex . SNAP output
|
1bg1
|
transcription-DNA |
X-ray (2.25 Å) |
Becker S, Groner B, Muller CW |
(1998) "Three-dimensional
structure of the Stat3beta homodimer bound to DNA."
Nature, 394, 145-151. doi:
10.1038/28101.
|
Transcription factor stat3b-DNA complex . SNAP output
|
1bgb
|
hydrolase-DNA |
X-ray (2.0 Å) |
Horton NC, Perona JJ |
(1998) "Recognition
of flanking DNA sequences by EcoRV endonuclease
involves alternative patterns of water-mediated
contacts." J.Biol.Chem.,
273, 21721-21729. doi: 10.1074/jbc.273.34.21721.
|
Ecorv endonuclease complex with 5'-cgggatatccc DNA .
SNAP output
|
1bhm
|
hydrolase-DNA |
X-ray (2.2 Å) |
Newman M, Strzelecka T, Dorner LF, Schildkraut I,
Aggarwal AK |
(1995) "Structure
of Bam HI endonuclease bound to DNA: partial folding
and unfolding on DNA binding." Science,
269, 656-663.
|
Restriction endonuclease bamhi complex with DNA .
SNAP output
|
1bj6
|
viral protein-DNA |
NMR |
Morellet N, Demene H, Teilleux V, Huynh-Dinh T, de
Rocquigny H, Fournie-Zaluski MC, Roques BP |
(1998) "Structure
of the complex between the HIV-1 nucleocapsid protein
NCp7 and the single-stranded pentanucleotide
d(ACGCC)." J.Mol.Biol.,
283, 419-434. doi: 10.1006/jmbi.1998.2098.
|
1h NMR of (12-53) ncp7-d(acgcc) complex, 10 structures
. SNAP output
|
1bl0
|
transcription-DNA |
X-ray (2.3 Å) |
Rhee S, Martin RG, Rosner JL, Davies DR |
(1998) "A novel
DNA-binding motif in MarA: the first structure for an
AraC family transcriptional activator."
Proc.Natl.Acad.Sci.USA, 95,
10413-10418. doi: 10.1073/pnas.95.18.10413.
|
Multiple antibiotic resistance protein (mara)-DNA
complex . SNAP
output
|
1bnk
|
hydrolase-DNA |
X-ray (2.7 Å) |
Lau AY, Scharer OD, Samson L, Verdine GL, Ellenberger
T |
(1998) "Crystal
structure of a human alkylbase-DNA repair enzyme
complexed to DNA: mechanisms for nucleotide flipping
and base excision." Cell(Cambridge,Mass.),
95, 249-258. doi: 10.1016/S0092-8674(00)81755-9.
|
Human 3-methyladenine DNA glycosylase complexed to DNA
. SNAP output
|
1bnz
|
DNA binding protein-DNA |
X-ray (2.0 Å) |
Gao YG, Su SY, Robinson H, Padmanabhan S, Lim L,
McCrary BS, Edmondson SP, Shriver JW, Wang AH |
(1998) "The
crystal structure of the hyperthermophile chromosomal
protein Sso7d bound to DNA."
Nat.Struct.Biol., 5, 782-786.
doi: 10.1038/1822.
|
Sso7d hyperthermophile protein-DNA complex . SNAP output
|
1bp7
|
transcription-DNA |
X-ray (3.0 Å) |
Jurica MS, Monnat Jr RJ, Stoddard BL |
(1998) "DNA
recognition and cleavage by the LAGLIDADG homing
endonuclease I-CreI." Mol.Cell,
2, 469-476. doi: 10.1016/S1097-2765(00)80146-X.
|
Group i mobile intron endonuclease i-crei complexed
with homing site DNA . SNAP output
|
1bpx
|
transferase-DNA |
X-ray (2.4 Å) |
Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier
H |
(1997) "Crystal
structures of human DNA polymerase beta complexed with
gapped and nicked DNA: evidence for an induced fit
mechanism." Biochemistry,
36, 11205-11215. doi: 10.1021/bi9703812.
|
DNA polymerase beta-DNA complex . SNAP output
|
1bpy
|
transferase-DNA |
X-ray (2.2 Å) |
Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier
H |
(1997) "Crystal
structures of human DNA polymerase beta complexed with
gapped and nicked DNA: evidence for an induced fit
mechanism." Biochemistry,
36, 11205-11215. doi: 10.1021/bi9703812.
|
Human DNA polymerase beta complexed with gapped DNA and
ddctp . SNAP output
|
1bpz
|
transferase-DNA |
X-ray (2.6 Å) |
Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier
H |
(1997) "Crystal
structures of human DNA polymerase beta complexed with
gapped and nicked DNA: evidence for an induced fit
mechanism." Biochemistry,
36, 11205-11215. doi: 10.1021/bi9703812.
|
Human DNA polymerase beta complexed with nicked DNA .
SNAP output
|
1brn
|
hydrolase-DNA |
X-ray (1.76 Å) |
Buckle AM, Fersht AR |
(1994) "Subsite
binding in an RNase: structure of a
barnase-tetranucleotide complex at 1.76-A
resolution." Biochemistry,
33, 1644-1653. doi: 10.1021/bi00173a005.
|
Subsite binding in an rnase: structure of a
barnase-tetranucleotide complex at 1.76 angstroms
resolution . SNAP
output
|
1bss
|
hydrolase-DNA |
X-ray (2.15 Å) |
Horton NC, Newberry KJ, Perona JJ |
(1998) "Metal
ion-mediated substrate-assisted catalysis in type II
restriction endonucleases."
Proc.Natl.Acad.Sci.USA, 95,
13489-13494. doi: 10.1073/pnas.95.23.13489.
|
Ecorv-t93a-DNA-ca2+ . SNAP output
|
1bsu
|
hydrolase-DNA |
X-ray (2.0 Å) |
Martin AM, Sam MD, Reich NO, Perona JJ |
(1999) "Structural
and energetic origins of indirect readout in
site-specific DNA cleavage by a restriction
endonuclease." Nat.Struct.Biol.,
6, 269-277. doi: 10.1038/6707.
|
Structural and energetic origins of indirect readout in
site-specific DNA cleavage by a restriction
endonuclease . SNAP
output
|
1bua
|
hydrolase-DNA |
X-ray (2.15 Å) |
Martin AM, Sam MD, Reich NO, Perona JJ |
(1999) "Structural
and energetic origins of indirect readout in
site-specific DNA cleavage by a restriction
endonuclease." Nat.Struct.Biol.,
6, 269-276. doi: 10.1038/6707.
|
Structural and energetic origins of indirect readout in
site-specific DNA cleavage by a restriction
endonuclease . SNAP
output
|
1bvo
|
complex (transcription factor-DNA) |
X-ray (2.7 Å) |
Cramer P, Varrot A, Barillas-Mury C, Kafatos FC,
Muller CW |
(1999) "Structure
of the specificity domain of the Dorsal homologue
Gambif1 bound to DNA." Structure
Fold.Des., 7, 841-852. doi:
10.1016/S0969-2126(99)80107-5.
|
Dorsal homologue gambif1 bound to DNA . SNAP output
|
1by4
|
gene regulation-DNA |
X-ray (2.1 Å) |
Zhao Q, Chasse SA, Devarakonda S, Sierk ML, Ahvazi B,
Rastinejad F |
(2000) "Structural
basis of RXR-DNA interactions."
J.Mol.Biol., 296, 509-520.
doi: 10.1006/jmbi.1999.3457.
|
Structure and mechanism of the homodimeric assembly of
the rxr on DNA . SNAP
output
|
1c0w
|
gene regulation-DNA |
X-ray (3.2 Å) |
Pohl E, Holmes RK, Hol WG |
(1999) "Crystal
structure of a cobalt-activated diphtheria toxin
repressor-DNA complex reveals a metal-binding SH3-like
domain." J.Mol.Biol.,
292, 653-667. doi: 10.1006/jmbi.1999.3073.
|
Crystal structure of the cobalt-activated diphtheria
toxin repressor-DNA complex reveals a metal binding
sh-like domain . SNAP
output
|
1c7u
|
transcription-DNA |
NMR |
Huang K, Louis JM, Donaldson L, Lim FL, Sharrocks AD,
Clore GM |
(2000) "Solution
structure of the MEF2A-DNA complex: structural basis
for the modulation of DNA bending and specificity by
MADS-box transcription factors." Embo J.,
19, 2615-2628. doi: 10.1093/emboj/19.11.2615.
|
Complex of the DNA binding core domain of the
transcription factor mef2a with a 20mer oligonucleotide
. SNAP output
|
1c7y
|
recombination-DNA |
X-ray (3.1 Å) |
Ariyoshi M, Nishino T, Iwasaki H, Shinagawa H,
Morikawa K |
(2000) "Crystal
structure of the holliday junction DNA in complex with
a single RuvA tetramer."
Proc.Natl.Acad.Sci.USA, 97,
8257-8262. doi: 10.1073/pnas.140212997.
|
E.coli ruva-holliday junction complex . SNAP output
|
1c8c
|
DNA binding protein-DNA |
X-ray (1.45 Å) |
Su S, Gao YG, Robinson H, Liaw YC, Edmondson SP,
Shriver JW, Wang AH |
(2000) "Crystal
structures of the chromosomal proteins Sso7d/Sac7d
bound to DNA containing T-G mismatched base-pairs."
J.Mol.Biol., 303, 395-403.
doi: 10.1006/jmbi.2000.4112.
|
Crystal structures of the chromosomal proteins
sso7d-sac7d bound to DNA containing t-g mismatched base
pairs . SNAP output
|
1c9b
|
transcription-DNA |
X-ray (2.65 Å) |
Tsai FT, Sigler PB |
(2000) "Structural
basis of preinitiation complex assembly on human pol II
promoters." EMBO J., 19,
25-36. doi: 10.1093/emboj/19.1.25.
|
Crystal structure of a human tbp core domain-human
tfiib core domain complex bound to an extended,
modified adenoviral major late promoter (admlp) .
SNAP output
|
1ca5
|
structural protein-DNA |
X-ray (2.2 Å) |
Su S, Gao Y-G, Robinson H, Liaw YC, Edmondson SP,
Shriver JW, Wang AH-J |
(2000) "Crystal
structures of the chromosomal proteins Sso7d/Sac7d
bound to DNA containing T-G mismatched base-pairs."
J.Mol.Biol., 303, 395-403.
doi: 10.1006/jmbi.2000.4112.
|
Intercalation site of hyperthermophile chromosomal
protein sso7d-sac7d bound to DNA . SNAP output
|
1ca6
|
structural protein-DNA |
X-ray (2.2 Å) |
Su S, Gao Y-G, Robinson H, Liaw YC, Edmondson SP,
Shriver JW, Wang AH-J |
(2000) "Crystal
structures of the chromosomal proteins Sso7d/Sac7d
bound to DNA containing T-G mismatched base-pairs."
J.Mol.Biol., 303, 395-403.
doi: 10.1006/jmbi.2000.4112.
|
Intercalation site of hyperthermophile chromosomal
protein sso7d-sac7d bound to DNA . SNAP output
|
1cbv
|
immune system-DNA |
X-ray (2.66 Å) |
Herron JN, He XM, Ballard DW, Blier PR, Pace PE,
Bothwell AL, Voss Jr EW, Edmundson AB |
(1991) "An
autoantibody to single-stranded DNA: comparison of the
three-dimensional structures of the unliganded Fab and
a deoxynucleotide-Fab complex." Proteins,
11, 159-175. doi: 10.1002/prot.340110302.
|
An autoantibody to single-stranded DNA: comparison of
the three-dimensional structures of the unliganded fab
and a deoxynucleotide-fab complex . SNAP output
|
1cdw
|
transcription-DNA |
X-ray (1.9 Å) |
Nikolov DB, Chen H, Halay ED, Hoffman A, Roeder RG,
Burley SK |
(1996) "Crystal
structure of a human TATA box-binding protein/TATA
element complex." Proc.Natl.Acad.Sci.USA,
93, 4862-4867. doi: 10.1073/pnas.93.10.4862.
|
Human tbp core domain complexed with DNA . SNAP output
|
1cez
|
transferase-DNA |
X-ray (2.4 Å) |
Cheetham GM, Jeruzalmi D, Steitz TA |
(1999) "Structural
basis for initiation of transcription from an RNA
polymerase-promoter complex." Nature,
399, 80-83. doi: 10.1038/19999.
|
Crystal structure of a t7 RNA polymerase-t7 promoter
complex . SNAP
output
|
1cf7
|
transcription-DNA |
X-ray (2.6 Å) |
Zheng N, Fraenkel E, Pabo CO, Pavletich NP |
(1999) "Structural
basis of DNA recognition by the heterodimeric cell
cycle transcription factor E2F-DP." Genes
Dev., 13, 666-674.
|
Structural basis of DNA recognition by the
heterodimeric cell cycle transcription factor e2f-dp .
SNAP output
|
1cgp
|
transcription-DNA |
X-ray (3.0 Å) |
Schultz SC, Shields GC, Steitz TA |
(1991) "Crystal
structure of a CAP-DNA complex: the DNA is bent by 90
degrees." Science, 253,
1001-1007.
|
Catabolite gene activator protein (cap)-DNA complex +
adenosine-3',5'-cyclic-monophosphate . SNAP output
|
1cit
|
transcription-DNA |
X-ray (2.7 Å) |
Meinke G, Sigler PB |
(1999) "DNA-binding
mechanism of the monomeric orphan nuclear receptor
NGFI-B." Nat.Struct.Biol.,
6, 471-477. doi: 10.1038/8276.
|
DNA-binding mechanism of the monomeric orphan nuclear
receptor ngfi-b . SNAP
output
|
1cjg
|
transcription-DNA |
NMR |
Spronk CA, Bonvin AM, Radha PK, Melacini G, Boelens
R, Kaptein R |
(1999) "The
solution structure of Lac repressor headpiece 62
complexed to a symmetrical lac operator."
Structure Fold.Des., 7,
1483-1492. doi: 10.1016/S0969-2126(00)88339-2.
|
NMR structure of lac repressor hp62-DNA complex .
SNAP output
|
1ckq
|
protein-DNA |
X-ray (1.85 Å) |
Horvath M, Choi J, Kim Y, Wilkosz PA, Chandrasekhar
K, Rosenberg JM |
"The Integration of Recognition and Cleavage: X-Ray
Structures of Pre- Transition State and Post-Reactive
DNA-Eco Ri Endonuclease Complexes." |
Pre-transition state eco ri endonuclease-cognate DNA
(tcgcgaattcgcg) complex . SNAP output
|
1ckt
|
gene regulation-DNA |
X-ray (2.5 Å) |
Ohndorf UM, Rould MA, He Q, Pabo CO, Lippard SJ |
(1999) "Basis
for recognition of cisplatin-modified DNA by
high-mobility-group proteins." Nature,
399, 708-712. doi: 10.1038/21460.
|
Crystal structure of hmg1 domain a bound to a
cisplatin-modified DNA duplex . SNAP output
|
1cl8
|
protein-DNA |
X-ray (1.8 Å) |
Horvath M, Rosenberg JM |
"Iap (Inner-Adenine to Purine): A Cognate EcoRI-DNA
Base Analog Complex." |
A pre-transition state eco ri endonuclease-cognate DNA
(tcgcgapttcgcg) complex with DNA base analog purine (p)
. SNAP output
|
1clq
|
transferase-DNA |
X-ray (2.7 Å) |
Shamoo Y, Steitz TA |
(1999) "Building
a replisome from interacting pieces: sliding clamp
complexed to a peptide from DNA polymerase and a
polymerase editing complex."
Cell(Cambridge,Mass.), 99,
155-166. doi: 10.1016/S0092-8674(00)81647-5.
|
Crystal structure of a replication fork DNA polymerase
editing complex at 2.7 Å resolution . SNAP output
|
1cma
|
transcription-DNA |
X-ray (2.8 Å) |
Somers WS, Phillips SE |
(1992) "Crystal
structure of the met repressor-operator complex at 2.8
A resolution reveals DNA recognition by
beta-strands." Nature,
359, 387-393. doi: 10.1038/359387a0.
|
Met repressor-DNA complex + s-adenosyl-methionine .
SNAP output
|
1co0
|
transcription |
NMR |
Brocchieri L, Zhou GP, Jardetzky O |
(2002) "Allostery and Induced Fit, NMR and Molecular
Modeling Study of the trp-repressor - mtr DNA complex."
Structures and Mechanisms, ACS Symposium Series,
827, 340-366. |
NMR study of trp repressor-mtr operator DNA complex .
SNAP output
|
1cqt
|
gene regulation-DNA |
X-ray (3.2 Å) |
Chasman D, Cepek K, Sharp PA, Pabo CO |
(1999) "Crystal
structure of an OCA-B peptide bound to an Oct-1 POU
domain/octamer DNA complex: specific recognition of a
protein-DNA interface." Genes Dev.,
13, 2650-2657. doi: 10.1101/gad.13.20.2650.
|
Crystal structure of a ternary complex containing an
oca-b peptide, the oct-1 pou domain, and an octamer
element . SNAP
output
|
1crx
|
replication-DNA |
X-ray (2.4 Å) |
Guo F, Gopaul DN, van Duyne GD |
(1997) "Structure
of Cre recombinase complexed with DNA in a
site-specific recombination synapse."
Nature, 389, 40-46. doi:
10.1038/37925.
|
Cre recombinase-DNA complex reaction intermediate i .
SNAP output
|
1cw0
|
hydrolase-DNA |
X-ray (2.3 Å) |
Tsutakawa SE, Jingami H, Morikawa K |
(1999) "Recognition
of a TG mismatch: the crystal structure of very short
patch repair endonuclease in complex with a DNA
duplex." Cell(Cambridge,Mass.),
99, 615-623. doi: 10.1016/S0092-8674(00)81550-0.
|
Crystal structure analysis of very short patch repair
(vsr) endonuclease in complex with a duplex DNA .
SNAP output
|
1cyq
|
hydrolase-DNA |
X-ray (1.93 Å) |
Galburt EA, Chevalier B, Tang W, Jurica MS, Flick KE,
Monnat Jr RJ, Stoddard BL |
(1999) "A novel
endonuclease mechanism directly visualized for
I-PpoI." Nat.Struct.Biol.,
6, 1096-1099. doi: 10.1038/70027.
|
Intron encoded homing endonuclease i-ppoi (h98a)-DNA
homing site complex . SNAP output
|
1cz0
|
hydrolase-DNA |
X-ray (2.1 Å) |
Galburt EA, Chevalier B, Tang W, Jurica MS, Flick KE,
Monnat Jr RJ, Stoddard BL |
(1999) "A novel
endonuclease mechanism directly visualized for
I-PpoI." Nat.Struct.Biol.,
6, 1096-1099. doi: 10.1038/70027.
|
Intron encoded homing endonuclease i-ppoi-DNA complex
lacking catalytic metal ion . SNAP output
|
1d02
|
hydrolase-DNA |
X-ray (1.7 Å) |
Deibert M, Grazulis S, Janulaitis A, Siksnys V, Huber
R |
(1999) "Crystal
structure of MunI restriction endonuclease in complex
with cognate DNA at 1.7 A resolution." EMBO
J., 18, 5805-5816. doi: 10.1093/emboj/18.21.5805.
|
Crystal structure of muni restriction endonuclease in
complex with cognate DNA . SNAP output
|
1d0e
|
transferase-DNA |
X-ray (3.0 Å) |
Najmudin S, Cote ML, Sun D, Yohannan S, Montano SP,
Gu J, Georgiadis MM |
(2000) "Crystal
structures of an N-terminal fragment from Moloney
murine leukemia virus reverse transcriptase complexed
with nucleic acid: functional implications for
template-primer binding to the fingers domain."
J.Mol.Biol., 296, 613-632.
doi: 10.1006/jmbi.1999.3477.
|
Crystal structures of the n-terminal fragment from
moloney murine leukemia virus reverse transcriptase
complexed with nucleic acid: functional implications
for template-primer binding to the fingers domain .
SNAP output
|
1d1u
|
hydrolase-DNA |
X-ray (2.3 Å) |
Cote ML, Yohannan SJ, Georgiadis MM |
(2000) "Use of
an N-terminal fragment from moloney murine leukemia
virus reverse transcriptase to facilitate
crystallization and analysis of a pseudo-16-mer DNA
molecule containing G-A mispairs." Acta
Crystallogr.,Sect.D, 56,
1120-1131. doi: 10.1107/S0907444900008246.
|
Use of an n-terminal fragment from moloney murine
leukemia virus reverse transcriptase to facilitate
crystallization and analysis of a pseudo-16-mer DNA
molecule containing g-a mispairs . SNAP output
|
1d2i
|
hydrolase-DNA |
X-ray (1.7 Å) |
Lukacs CM, Kucera R, Schildkraut I, Aggarwal AK |
(2000) "Understanding
the immutability of restriction enzymes: crystal
structure of BglII and its DNA substrate at 1.5 A
resolution." Nat.Struct.Biol.,
7, 134-140. doi: 10.1038/72405.
|
Crystal structure of restriction endonuclease bglii
complexed with DNA 16-mer . SNAP output
|
1d3u
|
gene regulation-DNA |
X-ray (2.4 Å) |
Littlefield O, Korkhin Y, Sigler PB |
(1999) "The
structural basis for the oriented assembly of a
TBP/TFB/promoter complex."
Proc.Natl.Acad.Sci.USA, 96,
13668-13673. doi: 10.1073/pnas.96.24.13668.
|
Tata-binding protein-transcription factor
(ii)b-bre+tata-box complex from pyrococcus woesei .
SNAP output
|
1d5y
|
transcription-DNA |
X-ray (2.7 Å) |
Kwon HJ, Bennik MH, Demple B, Ellenberger T |
(2000) "Crystal
structure of the Escherichia coli Rob transcription
factor in complex with DNA."
Nat.Struct.Biol., 7, 424-430.
doi: 10.1038/75213.
|
Crystal structure of the e. coli rob transcription
factor in complex with DNA . SNAP output
|
1d66
|
transcription-DNA |
X-ray (2.7 Å) |
Marmorstein R, Carey M, Ptashne M, Harrison SC |
(1992) "DNA
recognition by GAL4: structure of a protein-DNA
complex." Nature, 356,
408-414. doi: 10.1038/356408a0.
|
DNA recognition by gal4: structure of a protein-DNA
complex . SNAP
output
|
1d8y
|
transferase-DNA |
X-ray (2.08 Å) |
Teplova M, Wallace ST, Tereshko V, Minasov G, Symons
AM, Cook PD, Manoharan M, Egli M |
(1999) "Structural
origins of the exonuclease resistance of a zwitterionic
RNA." Proc.Natl.Acad.Sci.USA,
96, 14240-14245. doi: 10.1073/pnas.96.25.14240.
|
Crystal structure of the complex of DNA polymerase i
klenow fragment with DNA . SNAP output
|
1dc1
|
hydrolase-DNA |
X-ray (1.7 Å) |
van der Woerd MJ, Pelletier JJ, Xu S, Friedman
AM |
(2001) "Restriction
enzyme BsoBI-DNA complex: a tunnel for recognition of
degenerate DNA sequences and potential histidine
catalysis." Structure, 9,
133-144. doi: 10.1016/S0969-2126(01)00564-0.
|
Restriction enzyme bsobi-DNA complex structure:
encirclement of the DNA and histidine-catalyzed
hydrolysis within a canonical restriction enzyme fold .
SNAP output
|
1dct
|
transferase-DNA |
X-ray (2.8 Å) |
Reinisch KM, Chen L, Verdine GL, Lipscomb WN |
(1995) "The
crystal structure of HaeIII methyltransferase
convalently complexed to DNA: an extrahelical cytosine
and rearranged base pairing."
Cell(Cambridge,Mass.), 82,
143-153. doi: 10.1016/0092-8674(95)90060-8.
|
DNA (cytosine-5) methylase from haeiii covalently bound
to DNA . SNAP output
|
1ddn
|
gene regulation-DNA |
X-ray (3.0 Å) |
White A, Ding X, vanderSpek JC, Murphy JR, Ringe
D |
(1998) "Structure
of the metal-ion-activated diphtheria toxin
repressor/tox operator complex." Nature,
394, 502-506. doi: 10.1038/28893.
|
Diphtheria tox repressor (c102d mutant)-tox DNA
operator complex . SNAP
output
|
1de8
|
lyase-DNA |
X-ray (2.95 Å) |
Mol CD, Izumi T, Mitra S, Tainer JA |
(2000) "DNA-bound
structures and mutants reveal abasic DNA binding by
APE1 and DNA repair coordination [corrected."
Nature, 403, 451-456. doi:
10.1038/35000249.
|
Human apurinic-apyrimidinic endonuclease-1 (ape1) bound
to abasic DNA . SNAP
output
|
1de9
|
lyase-DNA |
X-ray (3.0 Å) |
Mol CD, Izumi T, Mitra S, Tainer JA |
(2000) "DNA-bound
structures and mutants reveal abasic DNA binding by
APE1 and DNA repair coordination." Nature,
403, 451-456. doi: 10.1038/35000249.
|
Human ape1 endonuclease with bound abasic DNA and mn2+
ion . SNAP output
|
1dew
|
lyase-DNA |
X-ray (2.65 Å) |
Mol CD, Izumi T, Mitra S, Tainer JA |
(2000) "DNA-bound
structures and mutants reveal abasic DNA binding by
APE1 and DNA repair coordination." Nature,
403, 451-456. doi: 10.1038/35000249.
|
Crystal structure of human ape1 bound to abasic DNA .
SNAP output
|
1dfm
|
hydrolase-DNA |
X-ray (1.5 Å) |
Lukacs CM, Kucera R, Schildkraut I, Aggarwal AK |
(2000) "Understanding
the immutability of restriction enzymes: crystal
structure of BglII and its DNA substrate at 1.5 A
resolution." Nat.Struct.Biol.,
7, 134-140. doi: 10.1038/72405.
|
Crystal structure of restriction endonuclease bglii
complexed with DNA 16-mer . SNAP output
|
1dgc
|
transcription-DNA |
X-ray (3.0 Å) |
Konig P, Richmond TJ |
(1993) "The X-ray
structure of the GCN4-bZIP bound to ATF/CREB site DNA
shows the complex depends on DNA flexibility."
J.Mol.Biol., 233, 139-154.
doi: 10.1006/jmbi.1993.1490.
|
The x-ray structure of the gcn4-bzip bound to atf-creb
site DNA shows the complex depends on DNA flexibility .
SNAP output
|
1dh3
|
transcription-DNA |
X-ray (3.0 Å) |
Schumacher MA, Goodman RH, Brennan RG |
(2000) "The
structure of a CREB bZIP.somatostatin CRE complex
reveals the basis for selective dimerization and
divalent cation-enhanced DNA binding."
J.Biol.Chem., 275,
35242-35247. doi: 10.1074/jbc.M007293200.
|
Crystal structure of a creb bzip-cre complex reveals
the basis for creb faimly selective dimerization and
DNA binding . SNAP
output
|
1diz
|
hydrolase-DNA |
X-ray (2.5 Å) |
Hollis T, Ichikawa Y, Ellenberger T |
(2000) "DNA
bending and a flip-out mechanism for base excision by
the helix-hairpin-helix DNA glycosylase, Escherichia
coli AlkA." EMBO J., 19,
758-766. doi: 10.1093/emboj/19.4.758.
|
Crystal structure of e. coli 3-methyladenine DNA
glycosylase (alka) complexed with DNA . SNAP output
|
1dmu
|
hydrolase-DNA |
X-ray (2.2 Å) |
Newman M, Lunnen K, Wilson G, Greci J, Schildkraut I,
Phillips SE |
(1998) "Crystal
structure of restriction endonuclease BglI bound to its
interrupted DNA recognition sequence." EMBO
J., 17, 5466-5476. doi: 10.1093/emboj/17.18.5466.
|
Crystal structure of the restriction endonuclease bgli
(e.c.3.1.21.4) bound to its DNA recognition sequence .
SNAP output
|
1dnk
|
hydrolase-DNA |
X-ray (2.3 Å) |
Weston SA, Lahm A, Suck D |
(1992) "X-ray
structure of the DNase I-d(GGTATACC)2 complex at 2.3 A
resolution." J.Mol.Biol.,
226, 1237-1256. doi: 10.1016/0022-2836(92)91064-V.
|
The x-ray structure of the dnase i-d(ggtatacc)2 complex
at 2.3 angstroms resolution . SNAP output
|
1dp7
|
transcription-DNA |
X-ray (1.5 Å) |
Gajiwala KS, Chen H, Cornille F, Roques BP, Reith W,
Mach B, Burley SK |
(2000) "Structure
of the winged-helix protein hRFX1 reveals a new mode of
DNA binding." Nature,
403, 916-921. doi: 10.1038/35002634.
|
Cocrystal structure of rfx-dbd in complex with its
cognate x-box binding site . SNAP output
|
1drg
|
hydrolase, ligase-DNA |
X-ray (2.55 Å) |
Woods KC, Martin SS, Chu VC, Baldwin EP |
(2001) "Quasi-equivalence
in site-specific recombinase structure and function:
crystal structure and activity of trimeric Cre
recombinase bound to a three-way Lox DNA junction."
J.Mol.Biol., 313, 49-69. doi:
10.1006/jmbi.2001.5012.
|
Crystal structure of trimeric cre recombinase-lox
complex . SNAP
output
|
1dsc
|
DNA-antibiotic |
NMR |
Lian C, Robinson H, Wang AH-J |
(1996) "Structure of Actinomycin D Bound with
(Gaagcttc)2 and (Gatgcttc)2 and its Binding to the
(Cag)N:(Ctg)N Triplet Sequence by NMR Analysis."
J.Am.Chem.Soc., 118, 8791.
doi: 10.1021/JA961631P.
|
NMR study of DNA (5'-d(*gp*ap*ap*gp*cp*tp*tp*c)-3')
self-complementary duplex complexed with actinomycin d,
minimized average structure . SNAP output
|
1dsd
|
DNA-antibiotic |
NMR |
Lian C, Robinson H, Wang AH-J |
(1996) "Structure of Actinomycin D Bound with
(Gaagcttc)2 and (Gatgcttc)2 and its Binding to the
(Cag)N:(Ctg)N Triplet Sequence by NMR Analysis."
J.Am.Chem.Soc., 118, 8791.
doi: 10.1021/JA961631P.
|
NMR study of DNA (5'-d(*gp*ap*tp*gp*cp*tp*tp*c)-3') t:t
mismatched duplex complexed with actinomycin d,
minimized average structure . SNAP output
|
1dsz
|
transcription-DNA |
X-ray (1.7 Å) |
Rastinejad F, Wagner T, Zhao Q, Khorasanizadeh S |
(2000) "Structure
of the RXR-RAR DNA-binding complex on the retinoic acid
response element DR1." EMBO J.,
19, 1045-1054. doi: 10.1093/emboj/19.5.1045.
|
Structure of the rxr-rar DNA-binding domain heterodimer
in complex with the retinoic acid response element dr1
. SNAP output
|
1du0
|
transcription-DNA |
X-ray (2.0 Å) |
Grant RA, Rould MA, Klemm JD, Pabo CO |
(2000) "Exploring
the role of glutamine 50 in the homeodomain-DNA
interface: crystal structure of engrailed (Gln50 -->
ala) complex at 2.0 A." Biochemistry,
39, 8187-8192. doi: 10.1021/bi000071a.
|
Engrailed homeodomain q50a variant DNA complex .
SNAP output
|
1dux
|
transcription-DNA |
X-ray (2.1 Å) |
Mo Y, Vaessen B, Johnston K, Marmorstein R |
(2000) "Structure
of the elk-1-DNA complex reveals how DNA-distal
residues affect ETS domain recognition of DNA."
Nat.Struct.Biol., 7, 292-297.
doi: 10.1038/74055.
|
Elk-1-DNA structure reveals how residues distal from
DNA-binding surface affect DNA-recognition . SNAP output
|
1e3m
|
DNA binding |
X-ray (2.2 Å) |
Lamers MH, Perrakis A, Enzlin JH, Winterwerp HHK, De
Wind N, Sixma TK |
(2000) "The
Crystal Structure of DNA Mismatch Repair Protein Muts
Binding to a G X T Mismatch." Nature,
407, 711. doi: 10.1038/35037523.
|
The crystal structure of e. coli muts binding to DNA
with a g:t mismatch . SNAP output
|
1e3o
|
transcription |
X-ray (1.9 Å) |
Remenyi A, Tomilin A, Pohl E, Lins K, Philippsen A,
Reinbold R, Scholer HR, Wilmanns M |
(2001) "Differential
Dimer Activities of the Transcription Factor Oct-1 by
DNA-Induced Interface Swapping." Mol.Cell,
8, 569. doi: 10.1016/S1097-2765(01)00336-7.
|
Crystal structure of oct-1 pou dimer bound to more .
SNAP output
|
1ea4
|
gene regulation-DNA |
X-ray (2.95 Å) |
Costa M, Sola M, Del G, Eritja R, Hernaindez-Arriaga
AM, Espinosa M, Gomis-Rueth FX, Coll M |
(2001) "Plasmid
Transcriptional Repressor Copg Oligomerises to Render
Helical Superstructures Unbound and in Complexes with
Oligonucleotides." J.Mol.Biol.,
310, 403. doi: 10.1006/JMBI.2001.4760.
|
Transcriptional repressor copg-22bp dsDNA complex .
SNAP output
|
1ebm
|
lyase-DNA |
X-ray (2.1 Å) |
Bruner SD, Norman DP, Verdine GL |
(2000) "Structural
basis for recognition and repair of the endogenous
mutagen 8-oxoguanine in DNA." Nature,
403, 859-866. doi: 10.1038/35002510.
|
Crystal structure of the human 8-oxoguanine glycosylase
(hogg1) bound to a substrate oligonucleotide . SNAP output
|
1ecr
|
replication-DNA |
X-ray (2.7 Å) |
Kamada K, Horiuchi T, Ohsumi K, Shimamoto N, Morikawa
K |
(1996) "Structure
of a replication-terminator protein complexed with
DNA." Nature, 383,
598-603. doi: 10.1038/383598a0.
|
Escherichia coli replication terminator protein (tus)
complexed with DNA . SNAP output
|
1efa
|
transcription-DNA |
X-ray (2.6 Å) |
Bell CE, Lewis M |
(2000) "A closer
view of the conformation of the Lac repressor bound to
operator." Nat.Struct.Biol.,
7, 209-214. doi: 10.1038/78907.
|
Crystal structure of the lac repressor dimer bound to
operator and the anti-inducer onpf . SNAP output
|
1egw
|
transcription-DNA |
X-ray (1.5 Å) |
Santelli E, Richmond TJ |
(2000) "Crystal
structure of MEF2A core bound to DNA at 1.5 A
resolution." J.Mol.Biol.,
297, 437-449. doi: 10.1006/jmbi.2000.3568.
|
Crystal structure of mef2a core bound to DNA . SNAP output
|
1ehl
|
immune system |
X-ray (2.4 Å) |
Yokoyama H, Mizutani R, Satow Y, Komatsu Y, Ohtsuka
E, Nikaido O |
(2000) "Crystal
structure of the 64M-2 antibody Fab fragment in complex
with a DNA dT(6-4)T photoproduct formed by ultraviolet
radiation." J.Mol.Biol.,
299, 711-723. doi: 10.1006/jmbi.2000.3772.
|
64m-2 antibody fab complexed with d(5ht)(6-4)t .
SNAP output
|
1ej9
|
isomerase-DNA |
X-ray (2.6 Å) |
Redinbo MR, Champoux JJ, Hol WG |
(2000) "Novel
insights into catalytic mechanism from a crystal
structure of human topoisomerase I in complex with
DNA." Biochemistry, 39,
6832-6840. doi: 10.1021/bi992690t.
|
Crystal structure of human topoisomerase i DNA complex
. SNAP output
|
1emh
|
hydrolase-DNA |
X-ray (1.8 Å) |
Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan
HE, Blackburn GM, Tainer JA |
(2000) "Uracil-DNA
glycosylase-DNA substrate and product structures:
conformational strain promotes catalytic efficiency by
coupled stereoelectronic effects."
Proc.Natl.Acad.Sci.USA, 97,
5083-5088. doi: 10.1073/pnas.97.10.5083.
|
Crystal structure of human uracil-DNA glycosylase bound
to uncleaved substrate-containing DNA . SNAP output
|
1emj
|
hydrolase-DNA |
X-ray (2.0 Å) |
Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan
HE, Blackburn GM, Tainer JA |
(2000) "Uracil-DNA
glycosylase-DNA substrate and product structures:
conformational strain promotes catalytic efficiency by
coupled stereoelectronic effects."
Proc.Natl.Acad.Sci.USA, 97,
5083-5088. doi: 10.1073/pnas.97.10.5083.
|
Uracil-DNA glycosylase bound to DNA containing a
4'-thio-2'deoxyuridine analog product . SNAP output
|
1eo3
|
hydrolase-DNA |
X-ray (2.0 Å) |
Horton NC, Connolly BA, Perona JJ |
(2000) "Inhibition of EcoRV Endonuclease by
Deoxyribo-3'-S-phosphorothiolates: A High-Resolution
X-ray Crystallographic Study." J.Am.Chem.Soc.,
122, 3314-3324. doi: 10.1021/ja993719j.
|
Inhibition of ecorv endonuclease by
deoxyribo-3'-s-phosphorothiolates: a high resolution
x-ray crystallographic study . SNAP output
|
1eo4
|
hydrolase-DNA |
X-ray (1.9 Å) |
Horton NC, Connolly BA, Perona JJ |
(2000) "Inhibition of EcoRV Endonuclease by
Deoxyribo-3'-S-phosphorothiolates: A High-Resolution
X-ray Crystallographic Study." J.Am.Chem.Soc.,
122, 3314-3324. doi: 10.1021/ja993719j.
|
Ecorv bound to mn2+ and cognate DNA containing a 3's
substition at the cleavage site . SNAP output
|
1eon
|
hydrolase-DNA |
X-ray (1.6 Å) |
Horton NC, Connolly BA, Perona JJ |
(2000) "Inhibition of EcoRV Endonuclease by
Deoxyribo-3'-S-phosphorothiolates: A High-Resolution
X-ray Crystallographic Study." J.Am.Chem.Soc.,
122, 3314-3324. doi: 10.1021/ja993719j.
|
Ecorv bound to 3'-s-phosphorothiolate DNA and ca2+ .
SNAP output
|
1eoo
|
hydrolase-DNA |
X-ray (2.16 Å) |
Horton NC, Perona JJ |
(2000) "Crystallographic
snapshots along a protein-induced DNA-bending
pathway." Proc.Natl.Acad.Sci.USA,
97, 5729-5734. doi: 10.1073/pnas.090370797.
|
Ecorv bound to cognate DNA . SNAP output
|
1eop
|
hydrolase-DNA |
X-ray (2.6 Å) |
Horton NC, Perona JJ |
(2000) "Crystallographic
snapshots along a protein-induced DNA-bending
pathway." Proc.Natl.Acad.Sci.USA,
97, 5729-5734. doi: 10.1073/pnas.090370797.
|
Ecorv bound to cognate DNA . SNAP output
|
1eqz
|
structural protein-DNA |
X-ray (2.5 Å) |
Harp JM, Hanson BL, Timm DE, Bunick GJ |
(2000) "Asymmetries
in the nucleosome core particle at 2.5 A
resolution." Acta Crystallogr.,Sect.D,
56, 1513-1534. doi: 10.1107/S0907444900011847.
|
X-ray structure of the nucleosome core particle at 2.5
Å resolution . SNAP
output
|
1eri
|
hydrolase-DNA |
X-ray (2.5 Å) |
Kim YC, Grable JC, Love R, Greene PJ, Rosenberg
JM |
(1990) "Refinement
of Eco RI endonuclease crystal structure: a revised
protein chain tracing." Science,
249, 1307-1309.
|
X-ray structure of the DNA-eco ri endonuclease-DNA
recognition complex: the recognition network and the
integration of recognition and cleavage . SNAP output
|
1esg
|
hydrolase-DNA |
X-ray (1.9 Å) |
Viadiu H, Aggarwal AK |
(2000) "Structure
of BamHI bound to nonspecific DNA: a model for DNA
sliding." Mol.Cell, 5,
889-895. doi: 10.1016/S1097-2765(00)80329-9.
|
Restriction endonuclease bamhi bound to a non-specific
DNA. . SNAP output
|
1evw
|
hydrolase-DNA |
X-ray (3.1 Å) |
Galburt EA, Chadsey MS, Jurica MS, Chevalier BS, Erho
D, Tang W, Monnat Jr RJ, Stoddard BL |
(2000) "Conformational
changes and cleavage by the homing endonuclease I-PpoI:
a critical role for a leucine residue in the active
site." J.Mol.Biol., 300,
877-887. doi: 10.1006/jmbi.2000.3874.
|
L116a mutant of the homing endonuclease i-ppoi
complexed to homing site DNA. . SNAP output
|
1ewn
|
hydrolase-DNA |
X-ray (2.1 Å) |
Lau AY, Wyatt MD, Glassner BJ, Samson LD, Ellenberger
T |
(2000) "Molecular
basis for discriminating between normal and damaged
bases by the human alkyladenine glycosylase, AAG."
Proc.Natl.Acad.Sci.USA, 97,
13573-13578. doi: 10.1073/pnas.97.25.13573.
|
Crystal structure of the human aag DNA repair
glycosylase complexed with 1,n6-ethenoadenine-DNA .
SNAP output
|
1ewq
|
replication-DNA |
X-ray (2.2 Å) |
Obmolova G, Ban C, Hsieh P, Yang W |
(2000) "Crystal
structures of mismatch repair protein MutS and its
complex with a substrate DNA." Nature,
407, 703-710. doi: 10.1038/35037509.
|
Crystal structure taq muts complexed with a
heteroduplex DNA at 2.2 Å resolution . SNAP output
|
1exi
|
transcription-DNA |
X-ray (3.12 Å) |
Heldwein EE, Brennan RG |
(2001) "Crystal
structure of the transcription activator BmrR bound to
DNA and a drug." Nature,
409, 378-382. doi: 10.1038/35053138.
|
Crystal structure of transcription activator bmrr, from
b. subtilis, bound to 21 base pair bmr operator and
tpsb . SNAP output
|
1exj
|
transcription-DNA |
X-ray (3.0 Å) |
Heldwein EE, Brennan RG |
(2001) "Crystal
structure of the transcription activator BmrR bound to
DNA and a drug." Nature,
409, 378-382. doi: 10.1038/35053138.
|
Crystal structure of transcription activator bmrr, from
b. subtilis, bound to 21 base pair bmr operator and tpp
. SNAP output
|
1eyg
|
replication-DNA |
X-ray (2.8 Å) |
Raghunathan S, Kozlov AG, Lohman TM, Waksman G |
(2000) "Structure
of the DNA binding domain of E. coli SSB bound to
ssDNA." Nat.Struct.Biol.,
7, 648-652. doi: 10.1038/77943.
|
Crystal structure of chymotryptic fragment of e. coli
ssb bound to two 35-mer single strand dnas . SNAP output
|
1eyu
|
hydrolase-DNA |
X-ray (1.78 Å) |
Horton JR, Cheng X |
(2000) "PvuII
endonuclease contains two calcium ions in active
sites." J.Mol.Biol., 300,
1049-1056. doi: 10.1006/jmbi.2000.3938.
|
High resolution structure of the pvuii
endonculease-cognate DNA complex at ph 4.6 . SNAP output
|
1f0o
|
hydrolase-DNA |
X-ray (2.5 Å) |
Horton JR, Cheng X |
(2000) "PvuII
endonuclease contains two calcium ions in active
sites." J.Mol.Biol., 300,
1049-1056. doi: 10.1006/jmbi.2000.3938.
|
Pvuii endonuclease-cognate DNA complex
(glutaraldehyde-crosslinked crystal) at ph 7.5 with two
calcium ions at each active site . SNAP output
|
1f0v
|
hydrolase-DNA |
X-ray (1.7 Å) |
Liu YS, Gotte G, Libonati M, Eisenberg DS |
(2001) "A
domain-swapped RNase A dimer with implications for
amyloid formation." Nat.Struct.Biol.,
8, 211-214. doi: 10.1038/84941.
|
Crystal structure of an rnase a dimer displaying a new
type of 3d domain swapping . SNAP output
|
1f2i
|
transcription-DNA |
X-ray (2.35 Å) |
Wang BS, Grant RA, Pabo CO |
(2001) "Selected
peptide extension contacts hydrophobic patch on
neighboring zinc finger and mediates dimerization on
DNA." Nat.Struct.Biol.,
8, 589-593. doi: 10.1038/89617.
|
Cocrystal structure of selected zinc finger dimer bound
to DNA . SNAP output
|
1f44
|
hydrolase, ligase-DNA |
X-ray (2.05 Å) |
Woods KC, Martin SS, Chu VC, Baldwin EP |
(2001) "Quasi-equivalence
in site-specific recombinase structure and function:
crystal structure and activity of trimeric Cre
recombinase bound to a three-way Lox DNA junction."
J.Mol.Biol., 313, 49-69. doi:
10.1006/jmbi.2001.5012.
|
Crystal structure of trimeric cre recombinase-lox
complex . SNAP
output
|
1f4k
|
replication-DNA |
X-ray (2.5 Å) |
Wilce JA, Vivian JP, Hastings AF, Otting G, Folmer
RH, Duggin IG, Wake RG, Wilce MC |
(2001) "Structure
of the RTP-DNA complex and the mechanism of polar
replication fork arrest."
Nat.Struct.Biol., 8, 206-210.
doi: 10.1038/84934.
|
Crystal structure of the replication terminator
protein-b-site DNA complex . SNAP output
|
1f4r
|
hydrolase-DNA |
X-ray (2.4 Å) |
Lau AY, Wyatt MD, Glassner BJ, Samson LD, Ellenberger
T |
(2000) "Molecular
basis for discriminating between normal and damaged
bases by the human alkyladenine glycosylase, AAG."
Proc.Natl.Acad.Sci.USA, 97,
13573-13578. doi: 10.1073/pnas.97.25.13573.
|
Crystal structure of the human aag DNA repair
glycosylase complexed with 1,n6-ethenoadenine-DNA .
SNAP output
|
1f4s
|
transcription-DNA |
NMR |
Cahuzac B, Cerdan R, Felenbok B, Guittet E |
(2001) "The
solution structure of an AlcR-DNA complex sheds light
onto the unique tight and monomeric DNA binding of a
Zn(2)Cys(6) protein." Structure,
9, 827-836. doi: 10.1016/S0969-2126(01)00640-2.
|
Structure of transcriptional factor alcr in complex
with a target DNA . SNAP
output
|
1f5e
|
transcription-DNA |
NMR |
Cahuzac B, Cerdan R, Felenbok B, Guittet E |
(2001) "The
solution structure of an AlcR-DNA complex sheds light
onto the unique tight and monomeric DNA binding of a
Zn(2)Cys(6) protein." Structure,
9, 827-836. doi: 10.1016/S0969-2126(01)00640-2.
|
Structure of transcriptional factor alcr in complex
with a target DNA . SNAP
output
|
1f5t
|
transcription-DNA |
X-ray (3.0 Å) |
Chen CS, White A, Love J, Murphy JR, Ringe D |
(2000) "Methyl
groups of thymine bases are important for nucleic acid
recognition by DtxR." Biochemistry,
39, 10397-10407. doi: 10.1021/bi0009284.
|
Diphtheria tox repressor (c102d mutant) complexed with
nickel and dtxr consensus binding sequence . SNAP output
|
1f66
|
structural protein-DNA |
X-ray (2.6 Å) |
Suto RK, Clarkson MJ, Tremethick DJ, Luger K |
(2000) "Crystal
structure of a nucleosome core particle containing the
variant histone H2A.Z." Nat.Struct.Biol.,
7, 1121-1124. doi: 10.1038/81971.
|
2.6 a crystal structure of a nucleosome core particle
containing the variant histone h2a.z . SNAP output
|
1f6o
|
hydrolase-DNA |
X-ray (2.4 Å) |
Lau AY, Wyatt MD, Glassner BJ, Samson LD, Ellenberger
T |
(2000) "Molecular
basis for discriminating between normal and damaged
bases by the human alkyladenine glycosylase, AAG."
Proc.Natl.Acad.Sci.USA, 97,
13573-13578. doi: 10.1073/pnas.97.25.13573.
|
Crystal structure of the human aag DNA repair
glycosylase complexed with DNA . SNAP output
|
1fiu
|
hydrolase-DNA |
X-ray (1.6 Å) |
Deibert M, Grazulis S, Sasnauskas G, Siksnys V, Huber
R |
(2000) "Structure
of the tetrameric restriction endonuclease NgoMIV in
complex with cleaved DNA."
Nat.Struct.Biol., 7, 792-799.
doi: 10.1038/79032.
|
Tetrameric restriction endonuclease ngomiv in complex
with cleaved DNA . SNAP
output
|
1fja
|
DNA-antibiotic |
NMR |
Chen H, Liu X, Patel DJ |
(1996) "DNA
Bending and Unwinding Associated with Actinomycin D
Antibiotics Bound to Partially Overlapping Sites on
DNA." J.Mol.Biol., 258,
457. doi: 10.1006/JMBI.1996.0262.
|
NMR study of deoxyribonucleic acid complexed with
actinomycin d . SNAP
output
|
1fjl
|
transcription-DNA |
X-ray (2.0 Å) |
Wilson DS, Guenther B, Desplan C, Kuriyan J |
(1995) "High
resolution crystal structure of a paired (Pax) class
cooperative homeodomain dimer on DNA."
Cell(Cambridge,Mass.), 82,
709-719. doi: 10.1016/0092-8674(95)90468-9.
|
Homeodomain from the drosophila paired protein bound to
a DNA oligonucleotide . SNAP output
|
1fjx
|
transferase-DNA |
X-ray (2.26 Å) |
Vilkaitis G, Dong A, Weinhold E, Cheng X,
Klimasauskas S |
(2000) "Functional
roles of the conserved threonine 250 in the target
recognition domain of HhaI DNA methyltransferase."
J.Biol.Chem., 275,
38722-38730.
|
Structure of ternary complex of hhai methyltransferase
mutant (t250g) in complex with DNA and adohcy .
SNAP output
|
1flo
|
ligase, lyase-DNA |
X-ray (2.65 Å) |
Chen Y, Narendra U, Iype LE, Cox MM, Rice PA |
(2000) "Crystal
structure of a Flp recombinase-Holliday junction
complex: assembly of an active oligomer by helix
swapping." Mol.Cell, 6,
885-897. doi: 10.1016/S1097-2765(00)00086-1.
|
Flp recombinase-holliday junction complex i . SNAP output
|
1fn7
|
hydrolase-DNA |
X-ray (2.6 Å) |
Norman DP, Bruner SD, Verdine GL |
(2001) "Coupling
of substrate recognition and catalysis by a human
base-excision DNA repair protein."
J.Am.Chem.Soc., 123, 359-360.
doi: 10.1021/ja003144m.
|
Coupling of damage recognition and catalysis by a human
base-excision DNA repair protein . SNAP output
|
1fok
|
hydrolase-DNA |
X-ray (2.8 Å) |
Wah DA, Hirsch JA, Dorner LF, Schildkraut I, Aggarwal
AK |
(1997) "Structure
of the multimodular endonuclease FokI bound to
DNA." Nature, 388,
97-100. doi: 10.1038/40446.
|
Structure of restriction endonuclease foki bound to DNA
. SNAP output
|
1fos
|
transcription-DNA |
X-ray (3.05 Å) |
Glover JN, Harrison SC |
(1995) "Crystal
structure of the heterodimeric bZIP transcription
factor c-Fos-c-Jun bound to DNA." Nature,
373, 257-261. doi: 10.1038/373257a0.
|
Two human c-fos:c-jun:DNA complexes . SNAP output
|
1fw6
|
replication-DNA |
X-ray (2.7 Å) |
Junop MS, Obmolova G, Rausch K, Hsieh P, Yang W |
(2001) "Composite
active site of an ABC ATPase: MutS uses ATP to verify
mismatch recognition and authorize DNA repair."
Mol.Cell, 7, 1-12. doi:
10.1016/S1097-2765(01)00149-6.
|
Crystal structure of a taq muts-DNA-adp ternary complex
. SNAP output
|
1fyl
|
transcription-DNA |
X-ray (2.1 Å) |
Littlefield O, Nelson HC |
(2001) "Crystal
packing interaction that blocks crystallization of a
site-specific DNA binding protein-DNA complex."
Proteins, 45, 219-228. doi:
10.1002/prot.1142.
|
Serendipitous crystal structure containing the heat
shock transcription factor's DNA binding domain and
cognate DNA in a head-to-head orientation . SNAP output
|
1fym
|
transcription-DNA |
X-ray (2.2 Å) |
Littlefield O, Nelson HC |
(2001) "Crystal
packing interaction that blocks crystallization of a
site-specific DNA binding protein-DNA complex."
Proteins, 45, 219-228. doi:
10.1002/prot.1142.
|
Serendipitous crystal structure containing the heat
shock transcription factor's DNA binding domain and
cognate DNA in a tail-to-tail orientation . SNAP output
|
1g2d
|
transcription-DNA |
X-ray (2.2 Å) |
Wolfe SA, Grant RA, Elrod-Erickson M, Pabo CO |
(2001) "Beyond
the "recognition code": structures of two Cys2His2 zinc
finger/TATA box complexes." Structure,
9, 717-723. doi: 10.1016/S0969-2126(01)00632-3.
|
Structure of a cys2his2 zinc finger-tata box complex
(clone #2) . SNAP
output
|
1g2f
|
transcription-DNA |
X-ray (2.0 Å) |
Wolfe SA, Grant RA, Elrod-Erickson M, Pabo CO |
(2001) "Beyond
the "recognition code": structures of two Cys2His2 zinc
finger/TATA box complexes." Structure,
9, 717-723. doi: 10.1016/S0969-2126(01)00632-3.
|
Structure of a cys2his2 zinc finger-tata box complex
(tatazf;clone #6) . SNAP
output
|
1g38
|
transferase-DNA |
X-ray (2.0 Å) |
Goedecke K, Pignot M, Goody RS, Scheidig AJ, Weinhold
E |
(2001) "Structure
of the N6-adenine DNA methyltransferase M.TaqI in
complex with DNA and a cofactor analog."
Nat.Struct.Biol., 8, 121-125.
doi: 10.1038/84104.
|
Adenine-specific methyltransferase m. taq i-DNA complex
. SNAP output
|
1g3x
|
DNA |
X-ray (2.7 Å) |
Malinina L, Soler-Lopez M, Aymami J, Subirana JA |
(2002) "Intercalation
of an acridine-peptide drug in an AA/TT base step in
the crystal structure of [d(CGCGAATTCGCG)](2) with six
duplexes and seven Mg(2+) ions in the asymmetric
unit." Biochemistry, 41,
9341-9348. doi: 10.1021/bi020135c.
|
Intercalation of an 9acridine-peptide drug in a DNA
dodecamer . SNAP
output
|
1g4d
|
viral protein-DNA |
NMR |
Wojciak JM, Iwahara J, Clubb RT |
(2001) "The Mu
repressor-DNA complex contains an immobilized 'wing'
within the minor groove."
Nat.Struct.Biol., 8, 84-90.
doi: 10.1038/89582.
|
NMR structure of the mu bacteriophage repressor
DNA-binding domain-DNA complex . SNAP output
|
1g9y
|
hydrolase-DNA |
X-ray (2.05 Å) |
Chevalier BS, Monnat Jr RJ, Stoddard BL |
(2001) "The
homing endonuclease I-CreI uses three metals, one of
which is shared between the two active sites."
Nat.Struct.Biol., 8, 312-316.
doi: 10.1038/86181.
|
Homing endonuclease i-crei - DNA substrate complex with
calcium . SNAP
output
|
1g9z
|
hydrolase-DNA |
X-ray (1.8 Å) |
Chevalier BS, Monnat Jr RJ, Stoddard BL |
(2001) "The
homing endonuclease I-CreI uses three metals, one of
which is shared between the two active sites."
Nat.Struct.Biol., 8, 312-316.
doi: 10.1038/86181.
|
Laglidadg homing endonuclease i-crei - DNA product
complex with magnesium . SNAP output
|
1ga5
|
transcription-DNA |
X-ray (2.4 Å) |
Sierk ML, Zhao Q, Rastinejad F |
(2001) "DNA
Deformability as a Recognition Feature in the RevErb
Response Element." Biochemistry,
40, 12833-12843. doi: 10.1021/bi011086r.
|
Crystal structure of the orphan nuclear receptor
rev-erb(alpha) DNA-binding domain bound to its cognate
response element . SNAP
output
|
1gat
|
transcription-DNA |
NMR |
Omichinski JG, Clore GM, Schaad O, Felsenfeld G,
Trainor C, Appella E, Stahl SJ, Gronenborn AM |
(1993) "NMR
structure of a specific DNA complex of Zn-containing
DNA binding domain of GATA-1." Science,
261, 438-446. doi: 10.1021/bi00131a004.
|
Solution structure of the specific DNA complex of the
zinc containing DNA binding domain of the erythroid
transcription factor gata-1 by multidimensional NMR .
SNAP output
|
1gau
|
transcription-DNA |
NMR |
Omichinski JG, Clore GM, Schaad O, Felsenfeld G,
Trainor C, Appella E, Stahl SJ, Gronenborn AM |
(1993) "NMR
structure of a specific DNA complex of Zn-containing
DNA binding domain of GATA-1." Science,
261, 438-446. doi: 10.1021/bi00131a004.
|
Solution structure of the specific DNA complex of the
zinc containing DNA binding domain of the erythroid
transcription factor gata-1 by multidimensional NMR .
SNAP output
|
1gcc
|
transcription-DNA |
NMR |
Allen MD, Yamasaki K, Ohme-Takagi M, Tateno M, Suzuki
M |
(1998) "A novel
mode of DNA recognition by a beta-sheet revealed by the
solution structure of the GCC-box binding domain in
complex with DNA." EMBO J.,
17, 5484-5496. doi: 10.1093/emboj/17.18.5484.
|
Solution NMR structure of the complex of gcc-box
binding domain of aterf1 and gcc-box DNA, minimized
average structure . SNAP
output
|
1gd2
|
transcription-DNA |
X-ray (2.0 Å) |
Fujii Y, Shimizu T, Toda T, Yanagida M, Hakoshima
T |
(2000) "Structural
basis for the diversity of DNA recognition by bZIP
transcription factors." Nat.Struct.Biol.,
7, 889-893. doi: 10.1038/82822.
|
Crystal structure of bzip transcription factor pap1
bound to DNA . SNAP
output
|
1gdt
|
DNA binding protein-DNA |
X-ray (3.0 Å) |
Yang W, Steitz TA |
(1995) "Crystal
structure of the site-specific recombinase gamma delta
resolvase complexed with a 34 bp cleavage site."
Cell(Cambridge,Mass.), 82,
193-207. doi: 10.1016/0092-8674(95)90307-0.
|
Crystal structure of a site-specific recombinase,
gamma-delta resolvase complexed with a 34 bp cleavage
site . SNAP output
|
1gji
|
transcription-DNA |
X-ray (2.85 Å) |
Huang DB, Chen YQ, Ruetsche M, Phelps CB, Ghosh
G |
(2001) "X-ray
crystal structure of proto-oncogene product c-Rel bound
to the CD28 response element of IL-2."
Structure, 9, 669-678. doi:
10.1016/S0969-2126(01)00635-9.
|
Crystal structure of c-rel bound to DNA . SNAP output
|
1glu
|
transcription-DNA |
X-ray (2.9 Å) |
Luisi BF, Xu WX, Otwinowski Z, Freedman LP, Yamamoto
KR, Sigler PB |
(1991) "Crystallographic
analysis of the interaction of the glucocorticoid
receptor with DNA." Nature,
352, 497-505. doi: 10.1038/352497a0.
|
Crystallographic analysis of the interaction of the
glucocorticoid receptor with DNA . SNAP output
|
1gm5
|
helicase |
X-ray (3.24 Å) |
Singleton MR, Scaife S, Wigley DB |
(2001) "Structural
Analysis of DNA Replication Fork Reversal by Recg."
Cell(Cambridge,Mass.), 107,
79. doi: 10.1016/S0092-8674(01)00501-3.
|
Structure of recg bound to three-way DNA junction .
SNAP output
|
1gt0
|
transcription |
X-ray (2.6 Å) |
Remenyi A, Lins K, Nissen LJ, Reinbold R, Scholer HR,
Wilmanns M |
(2003) "Crystal
Structure of a POU/Hmg/DNA Ternary Complex Suggests
Differential Assembly of Oct4 and Sox2 on Two
Enhancers." Genes Dev.,
17, 2048. doi: 10.1101/GAD.269303.
|
Crystal structure of a pou-hmg-DNA ternary complex .
SNAP output
|
1gtw
|
transcription-DNA |
X-ray (1.85 Å) |
Tahirov TH, Inoue-Bungo T, Sato K, Sasaki M, Ogata
K |
"Structural Basis for Flexible Base Recognition by
C/Ebpbeta." |
Crystal structure of c-ebpbeta bzip homodimer bound to
a DNA fragment from the tom-1a promoter . SNAP output
|
1gu4
|
transcription-DNA |
X-ray (1.8 Å) |
Tahirov TH, Inoue-Bungo T, Sato K, Sasaki M, Ogata
K |
"Structural Basis for Flexible Base Recognition by
C/Ebpbeta." |
Crystal structure of c-ebpbeta bzip homodimer bound to
a high affinity DNA fragment . SNAP output
|
1gu5
|
transcription-DNA |
X-ray (2.1 Å) |
Tahirov TH, Inoue-Bungo T, Sato K, Sasaki M, Ogata
K |
"Structural Basis for Flexible Base Recognition by
C/Ebpbeta." |
Crystal structure of c-ebpbeta bzip homodimer bound to
a DNA fragment from the mim-1 promoter . SNAP output
|
1gxp
|
transcriptional activator |
X-ray (2.5 Å) |
Blanco AG, Sola M, Gomis-Ruth FX, Coll M |
(2002) "Tandem
DNA Recognition by Two-Component Signal Transduction
Transcriptional Activator Phob."
Structure, 10, 701. doi:
10.1016/S0969-2126(02)00761-X.
|
Phob effector domain in complex with pho box DNA. .
SNAP output
|
1h0m
|
transcription-DNA |
X-ray (3.0 Å) |
Vannini A, Volpari C, Gargioli C, Muraglia E, Cortese
R, De Francesco R, Neddermann P, Di Marco S |
(2002) "The
Crystal Structure of the Quorum Sensing Protein Trar
Bound to its Autoinducer and Target DNA." Embo
J., 21, 4393. doi: 10.1093/EMBOJ/CDF459.
|
Three-dimensional structure of the quorum sensing
protein trar bound to its autoinducer and to its target
DNA . SNAP output
|
1h38
|
transferase |
X-ray (2.9 Å) |
Tahirov TH, Temiakov D, Anikin M, Patlan V,
Mcallister WT, Vassylyev DG, Yokoyama S |
(2002) "Structure
of a T7 RNA Polymerase Elongation Complex at 2.9 A
Resolution." Nature, 420,
43. doi: 10.1038/NATURE01129.
|
Structure of a t7 RNA polymerase elongation complex at
2.9a resolution . SNAP
output
|
1h6f
|
transcription factor |
X-ray (1.7 Å) |
Coll M, Seidman JG, Muller CW |
(2002) "Structure
of the DNA-Bound T-Box Domain of Human Tbx3, a
Transcription Factor Responsible for Ulnar- Mammary
Syndrome." Structure, 10,
343. doi: 10.1016/S0969-2126(02)00722-0.
|
Human tbx3, a transcription factor responsible for
ulnar-mammary syndrome, bound to a palindromic DNA site
. SNAP output
|
1h88
|
transcription-DNA |
X-ray (2.8 Å) |
Tahirov TH, Sato K, Ichikawa-Iwata E, Sasaki M,
Inoue-Bungo T, Shiina M, Kimura K, Takata S, Fujikawa A,
Morii H, Kumasaka T, Yamamoto M, Ishii S, Ogata K |
(2002) "Mechanism
of C-Myb-C/Ebpbeta Cooperation from Separated Sites on
a Promoter." Cell(Cambridge,Mass.),
108, 57. doi: 10.1016/S0092-8674(01)00636-5.
|
Crystal structure of ternary protein-DNA complex1 .
SNAP output
|
1h89
|
transcription-DNA |
X-ray (2.45 Å) |
Tahirov TH, Sato K, Ichikawa-Iwata E, Sasaki M,
Inoue-Bungo T, Shiina M, Kimura K, Takata S, Fujikawa A,
Morii H, Kumasaka T, Yamamoto M, Ishii S, Ogata K |
(2002) "Mechanism
of C-Myb-C/Ebpbeta Cooperation from Separated Sites on
a Promoter." Cell(Cambridge,Mass.),
108, 57. doi: 10.1016/S0092-8674(01)00636-5.
|
Crystal structure of ternary protein-DNA complex2 .
SNAP output
|
1h8a
|
transcription-DNA |
X-ray (2.23 Å) |
Tahirov TH, Sato K, Ichikawa-Iwata E, Sasaki M,
Inoue-Bungo T, Shiina M, Kimura K, Takata S, Fujikawa A,
Morii H, Kumasaka T, Yamamoto M, Ishii S, Ogata K |
(2002) "Mechanism
of C-Myb-C/Ebpbeta Cooperation from Separated Sites on
a Promoter." Cell(Cambridge,Mass.),
108, 57. doi: 10.1016/S0092-8674(01)00636-5.
|
Crystal structure of ternary protein-DNA complex3 .
SNAP output
|
1h9d
|
transcription factor |
X-ray (2.6 Å) |
Bravo J, Li Z, Speck NA, Warren AJ |
(2001) "The
Leukemia-Associated Aml1 (Runx1)-Cbfbeta Complex
Functions as a DNA-Induced Molecular Clamp."
Nat.Struct.Biol., 8, 371.
doi: 10.1038/86264.
|
Aml1-cbf-beta-DNA complex . SNAP output
|
1h9t
|
transcriptional regulation |
X-ray (3.25 Å) |
Van Aalten DMF, Dirusso CC, Knudsen J |
(2001) "The
Structural Basis of Acyl Coenzyme A-Dependent
Regulation of the Transcription Factor Fadr."
Embo J., 20, 2041. doi:
10.1093/EMBOJ/20.8.2041.
|
Fadr, fatty acid responsive transcription factor from
e. coli in complex with fadb operator . SNAP output
|
1hao
|
hydrolase-hydrolase inhibitor-DNA |
X-ray (2.8 Å) |
Padmanabhan K, Tulinsky A |
(1996) "An
ambiguous structure of a DNA 15-mer thrombin
complex." Acta Crystallogr.,Sect.D,
52, 272-282. doi: 10.1107/S0907444995013977.
|
Complex of human alpha-thrombin with a 15mer
oligonucleotide ggttggtgtggttgg (based on NMR model of
DNA) . SNAP output
|
1hap
|
hydrolase-hydrolase inhibitor-DNA |
X-ray (2.8 Å) |
Padmanabhan K, Tulinsky A |
(1996) "An
ambiguous structure of a DNA 15-mer thrombin
complex." Acta Crystallogr.,Sect.D,
52, 272-282. doi: 10.1107/S0907444995013977.
|
Complex of human alpha-thrombin with a 15mer
oligonucleotide ggttggtgtggttgg (based on x-ray model
of DNA) . SNAP
output
|
1hbx
|
gene regulation |
X-ray (3.15 Å) |
Hassler M, Richmond TJ |
(2001) "The
B-Box Dominates Sap-1/Srf Interactions in the Structure
of the Ternary Complex." Embo J.,
20, 3018. doi: 10.1093/EMBOJ/20.12.3018.
|
Ternary complex of sap-1 and srf with specific sre DNA
. SNAP output
|
1hcq
|
transcription-DNA |
X-ray (2.4 Å) |
Schwabe JW, Chapman L, Finch JT, Rhodes D |
(1993) "The
crystal structure of the estrogen receptor DNA-binding
domain bound to DNA: how receptors discriminate between
their response elements."
Cell(Cambridge,Mass.), 75,
567-578. doi: 10.1016/0092-8674(93)90390-C.
|
The crystal structure of the estrogen receptor
DNA-binding domain bound to DNA: how receptors
discriminate between their response elements . SNAP output
|
1hcr
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Feng JA, Johnson RC, Dickerson RE |
(1994) "Hin
recombinase bound to DNA: the origin of specificity in
major and minor groove interactions."
Science, 263, 348-355.
|
Hin recombinase bound to DNA: the origin of specificity
in major and minor groove interactions . SNAP output
|
1hdd
|
transcription-DNA |
X-ray (2.8 Å) |
Kissinger CR, Liu BS, Martin-Blanco E, Kornberg TB,
Pabo CO |
(1990) "Crystal
structure of an engrailed homeodomain-DNA complex at
2.8 A resolution: a framework for understanding
homeodomain-DNA interactions."
Cell(Cambridge,Mass.), 63,
579-590. doi: 10.1016/0092-8674(90)90453-L.
|
Crystal structure of an engrailed homeodomain-DNA
complex at 2.8 angstroms resolution: a framework for
understanding homeodomain-DNA interactions . SNAP output
|
1hf0
|
transcription |
X-ray (2.7 Å) |
Remenyi A, Tomilin A, Pohl E, Lins K, Philippsen A,
Reinbold R, Scholer HR, Wilmanns M |
(2001) "Differential
Dimer Activities of the Transcription Factor Oct-1 by
DNA-Induced Interface Swapping." Mol.Cell,
8, 569. doi: 10.1016/S1097-2765(01)00336-7.
|
Crystal structure of the DNA-binding domain of oct-1
bound to DNA as a dimer . SNAP output
|
1hht
|
RNA polymerase |
X-ray (2.9 Å) |
Butcher SJ, Grimes JM, Makeyev EV, Bamford DH, Stuart
DI |
(2001) "A
Mechanism for Initiating RNA-Dependent RNA
Polymerization." Nature,
410, 235. doi: 10.1038/35065653.
|
RNA dependent RNA polymerase from dsrna bacteriophage
phi6 plus template . SNAP output
|
1hi0
|
RNA polymerase |
X-ray (3.0 Å) |
Butcher SJ, Grimes JM, Makeyev EV, Bamford DH, Stuart
DI |
(2001) "A
Mechanism for Initiating RNA-Dependent RNA
Polymerization." Nature,
410, 235. doi: 10.1038/35065653.
|
RNA dependent RNA polymerase from dsrna bacteriophage
phi6 plus initiation complex . SNAP output
|
1hjb
|
transcription-DNA |
X-ray (3.0 Å) |
Tahirov TH, Inoue-Bungo T, Morii H, Fujikawa A,
Sasaki M, Kimura K, Shiina M, Sato K, Kumasaka T,
Yamamoto M, Ishii S, Ogata K |
(2001) "Structural
Analyses of DNA Recognition by the Aml1/Runx-1 Runt
Domain and its Allosteric Control by Cbfbeta."
Cell(Cambridge,Mass.), 104,
755. doi: 10.1016/S0092-8674(01)00271-9.
|
Crystal structure of runx-1-aml1-cbfalpha runt domain
and c-ebpbeta bzip homodimer bound to a DNA fragment
from the csf-1r promoter . SNAP output
|
1hjc
|
transcription-DNA |
X-ray (2.65 Å) |
Tahirov TH, Inoue-Bungo T, Morii H, Fujikawa A,
Sasaki M, Kimura K, Shiina M, Sato K, Kumasaka T,
Yamamoto M, Ishii S, Ogata K |
(2001) "Structural
Analyses of DNA Recognition by the Aml1/Runx-1 Runt
Domain and its Allosteric Control by Cbfbeta."
Cell(Cambridge,Mass.), 104,
755. doi: 10.1016/S0092-8674(01)00271-9.
|
Crystal structure of runx-1-aml1-cbfalpha runt domain
bound to a DNA fragment from the csf-1r promoter .
SNAP output
|
1hlo
|
transcription-DNA |
X-ray (2.8 Å) |
Brownlie P, Ceska T, Lamers M, Romier C, Stier G, Teo
H, Suck D |
(1997) "The
crystal structure of an intact human Max-DNA complex:
new insights into mechanisms of transcriptional
control." Structure, 5,
509-520. doi: 10.1016/S0969-2126(97)00207-4.
|
The crystal structure of an intact human max-DNA
complex: new insights into mechanisms of
transcriptional control . SNAP output
|
1hlv
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Tanaka Y, Nureki O, Kurumizaka H, Fukai S, Kawaguchi
S, Ikuta M, Iwahara J, Okazaki T, Yokoyama S |
(2001) "Crystal
structure of the CENP-B protein-DNA complex: the
DNA-binding domains of CENP-B induce kinks in the
CENP-B box DNA." EMBO J.,
20, 6612-6618. doi: 10.1093/emboj/20.23.6612.
|
Crystal structure of cenp-b(1-129) complexed with the
cenp-b box DNA . SNAP
output
|
1hlz
|
transcription-DNA |
X-ray (2.8 Å) |
Sierk ML, Zhao Q, Rastinejad F |
(2001) "DNA
Deformability as a Recognition Feature in the RevErb
Response Element." Biochemistry,
40, 12833-12843. doi: 10.1021/bi011086r.
|
Crystal structure of the orphan nuclear receptor
rev-erb(alpha) DNA-binding domain bound to its cognate
response element . SNAP
output
|
1hry
|
DNA binding protein-DNA |
NMR |
Werner MH, Huth JR, Gronenborn AM, Clore GM |
(1995) "Molecular
basis of human 46X,Y sex reversal revealed from the
three-dimensional solution structure of the human
SRY-DNA complex." Cell(Cambridge,Mass.),
81, 704-705. doi: 10.1016/0092-8674(95)90532-4.
|
The 3d structure of the human sry-DNA complex solved by
multid-dimensional heteronuclear-edited and-filtered
NMR . SNAP output
|
1hrz
|
DNA binding protein-DNA |
NMR |
Werner MH, Huth JR, Gronenborn AM, Clore GM |
(1995) "Molecular
basis of human 46X,Y sex reversal revealed from the
three-dimensional solution structure of the human
SRY-DNA complex." Cell(Cambridge,Mass.),
81, 704-705. doi: 10.1016/0092-8674(95)90532-4.
|
The 3d structure of the human sry-DNA complex solved by
multi-dimensional heteronuclear-edited and-filtered NMR
. SNAP output
|
1hu0
|
hydrolase-DNA |
X-ray (2.35 Å) |
Fromme JC, Bruner SD, Yang W, Karplus M, Verdine
GL |
(2003) "Product-Assisted
Catalysis in base-excision DNA Repair."
Nat.Struct.Biol., 10,
204-211. doi: 10.1038/nsb902.
|
Crystal structure of an hogg1-DNA borohydride trapped
intermediate complex . SNAP output
|
1huo
|
transferase-DNA |
X-ray (2.6 Å) |
Arndt JW, Gong W, Zhong X, Showalter AK, Liu J,
Dunlap CA, Lin Z, Paxson C, Tsai MD, Chan MK |
(2001) "Insight
into the catalytic mechanism of DNA polymerase beta:
structures of intermediate complexes."
Biochemistry, 40, 5368-5375.
doi: 10.1021/bi002176j.
|
Crystal structure of DNA polymerase beta complexed with
DNA and cr-tmppcp . SNAP
output
|
1hut
|
hydrolase-hydrolase inhibitor-DNA |
X-ray (2.9 Å) |
Padmanabhan K, Padmanabhan KP, Ferrara JD, Sadler JE,
Tulinsky A |
(1993) "The
structure of alpha-thrombin inhibited by a 15-mer
single-stranded DNA aptamer."
J.Biol.Chem., 268,
17651-17654.
|
The structure of alpha-thrombin inhibited by a 15-mer
single-stranded DNA aptamer . SNAP output
|
1huz
|
transferase-DNA |
X-ray (2.6 Å) |
Arndt JW, Gong W, Zhong X, Showalter AK, Liu J,
Dunlap CA, Lin Z, Paxson C, Tsai MD, Chan MK |
(2001) "Insight
into the catalytic mechanism of DNA polymerase beta:
structures of intermediate complexes."
Biochemistry, 40, 5368-5375.
doi: 10.1021/bi002176j.
|
Crystal structure of DNA polymerase complexed with DNA
and cr-pcp . SNAP
output
|
1hvn
|
viral protein-DNA |
NMR |
South TL, Summers MF |
(1993) "Zinc- and
sequence-dependent binding to nucleic acids by the
N-terminal zinc finger of the HIV-1 nucleocapsid
protein: NMR structure of the complex with the Psi-site
analog, dACGCC." Protein Sci.,
2, 3.
|
Zinc-and sequence-dependent binding to nucleic acids by
the n-terminal zinc finger domain of the hiv-1
nucleocapsid protein: NMR structure of the complex with
the psi-site analog, d-acgcc . SNAP output
|
1hvo
|
viral protein-DNA |
NMR |
South TL, Summers MF |
(1993) "Zinc- and
sequence-dependent binding to nucleic acids by the
N-terminal zinc finger of the HIV-1 nucleocapsid
protein: NMR structure of the complex with the Psi-site
analog, dACGCC." Protein Sci.,
2, 3.
|
Zinc-and sequence-dependent binding to nucleic acids by
the n-terminal zinc finger domain of the hiv-1
nucleocapsid protein: NMR structure of the complex with
the psi-site analog, d-acgcc . SNAP output
|
1hw2
|
transcription-DNA |
X-ray (3.25 Å) |
Xu Y, Heath RJ, Li Z, Rock CO, White SW |
(2001) "The
FadR.DNA complex. Transcriptional control of fatty acid
metabolism in Escherichia coli."
J.Biol.Chem., 276,
17373-17379. doi: 10.1074/jbc.M100195200.
|
Fadr-DNA complex: transcriptional control of fatty acid
metabolism in echerichia coli . SNAP output
|
1hwt
|
gene regulation-DNA |
X-ray (2.5 Å) |
King DA, Zhang L, Guarente L, Marmorstein R |
(1999) "Structure
of a HAP1-DNA complex reveals dramatically asymmetric
DNA binding by a homodimeric protein."
Nat.Struct.Biol., 6, 64-71.
doi: 10.1038/4940.
|
Structure of a hap1-DNA complex reveals dramatically
asymmetric DNA binding by a homodimeric protein .
SNAP output
|
1hys
|
transferase-DNA-RNA hybrid |
X-ray (3.0 Å) |
Sarafianos SG, Das K, Tantillo C, Clark Jr AD, Ding
J, Whitcomb JM, Boyer PL, Hughes SH, Arnold E |
(2001) "Crystal
structure of HIV-1 reverse transcriptase in complex
with a polypurine tract RNA:DNA." EMBO J.,
20, 1449-1461. doi: 10.1093/emboj/20.6.1449.
|
Crystal structure of hiv-1 reverse transcriptase in
complex with a polypurine tract RNA:DNA . SNAP output
|
1i3j
|
hydrolase-DNA |
X-ray (2.2 Å) |
Van Roey P, Waddling CA, Fox KM, Belfort M,
Derbyshire V |
(2001) "Intertwined
structure of the DNA-binding domain of intron
endonuclease I-TevI with its substrate." EMBO
J., 20, 3631-3637. doi: 10.1093/emboj/20.14.3631.
|
Crystal structure of the DNA-binding domain of intron
endonuclease i-tevi with its substrate . SNAP output
|
1i3w
|
DNA-antibiotic |
X-ray (1.7 Å) |
Robinson H, Gao YG, Yang X, Sanishvili R, Joachimiak
A, Wang AH |
(2001) "Crystallographic
Analysis of a Novel Complex of Actinomycin D Bound to
the DNA Decamer Cgatcgatcg." Biochemistry,
40, 5587. doi: 10.1021/BI002859Z.
|
Actinomycin d binding to cgatcgatcg . SNAP output
|
1i6h
|
transcription-DNA-RNA hybrid |
X-ray (3.3 Å) |
Gnatt AL, Cramer P, Fu J, Bushnell DA, Kornberg
RD |
(2001) "Structural
basis of transcription: an RNA polymerase II elongation
complex at 3.3 A resolution." Science,
292, 1876-1882. doi: 10.1126/science.1059495.
|
RNA polymerase ii elongation complex . SNAP output
|
1i6j
|
transferase-DNA |
X-ray (2.0 Å) |
Cote ML, Georgiadis MM |
(2001) "Structure
of a pseudo-16-mer DNA with stacked guanines and two
G-A mispairs complexed with the N-terminal fragment of
Moloney murine leukemia virus reverse
transcriptase." Acta Crystallogr.,Sect.D,
57, 1238-1250. doi: 10.1107/S090744490100943X.
|
Crystal structure of a pseudo-16-mer DNA with stacked
guanines and two g-a mispairs complexed with the
n-terminal fragment of moloney murine leukemia virus
reverse transcriptase . SNAP output
|
1i7d
|
isomerase-DNA |
X-ray (2.05 Å) |
Changela A, DiGate RJ, Mondragon A |
(2001) "Crystal
structure of a complex of a type IA DNA topoisomerase
with a single-stranded DNA molecule."
Nature, 411, 1077-1081. doi:
10.1038/35082615.
|
Noncovalent complex of e.coli DNA topoisomerase iii
with an 8-base single-stranded DNA oligonucleotide .
SNAP output
|
1i8m
|
immune system-DNA |
X-ray (2.1 Å) |
Tanner JJ, Komissarov AA, Deutscher SL |
(2001) "Crystal
Structure of an Antigen-Binding Fragment Bound to
Single-Stranded DNA." J.Mol.Biol.,
314, 807-822. doi: 10.1006/jmbi.2001.5178.
|
Crystal structure of a recombinant anti-single-stranded
DNA antibody fragment complexed with dt5 . SNAP output
|
1iaw
|
hydrolase-DNA |
X-ray (2.4 Å) |
Huai Q, Colandene JD, Topal MD, Ke H |
(2001) "Structure
of NaeI-DNA complex reveals dual-mode DNA recognition
and complete dimer rearrangement."
Nat.Struct.Biol., 8, 665-669.
doi: 10.1038/90366.
|
Crystal structure of naei complexed with 17mer DNA .
SNAP output
|
1ic8
|
transcription-DNA |
X-ray (2.6 Å) |
Chi Y-I, Frantz JD, Oh B-C, Hansen L, Dhe-Paganon S,
Shoelson SE |
(2002) "Diabetes
mutations delineate an atypical POU domains in
HNF1-Alpha." Mol.Cell,
10, 1129-1137. doi: 10.1016/S1097-2765(02)00704-9.
|
Hepatocyte nuclear factor 1a bound to DNA : mody3 gene
product . SNAP
output
|
1id3
|
structural protein-DNA |
X-ray (3.1 Å) |
White CL, Suto RK, Luger K |
(2001) "Structure
of the yeast nucleosome core particle reveals
fundamental changes in internucleosome
interactions." EMBO J.,
20, 5207-5218. doi: 10.1093/emboj/20.18.5207.
|
Crystal structure of the yeast nucleosome core particle
reveals fundamental differences in inter-nucleosome
interactions . SNAP
output
|
1if1
|
transcription-DNA |
X-ray (3.0 Å) |
Escalante CR, Yie J, Thanos D, Aggarwal AK |
(1998) "Structure
of IRF-1 with bound DNA reveals determinants of
interferon regulation." Nature,
391, 103-106. doi: 10.1038/34224.
|
Interferon regulatory factor 1 (irf-1) complex with DNA
. SNAP output
|
1ig4
|
transcription-DNA |
NMR |
Ohki I, Shimotake N, Fujita N, Jee J, Ikegami T,
Nakao M, Shirakawa M |
(2001) "Solution
structure of the methyl-CpG binding domain of human
MBD1 in complex with methylated DNA."
Cell(Cambridge,Mass.), 105,
487-497. doi: 10.1016/S0092-8674(01)00324-5.
|
Solution structure of the methyl-cpg-binding domain of
human mbd1 in complex with methylated DNA . SNAP output
|
1ig7
|
transcription-DNA |
X-ray (2.2 Å) |
Hovde S, Abate-Shen C, Geiger JH |
(2001) "Crystal
structure of the Msx-1 homeodomain/DNA complex."
Biochemistry, 40,
12013-12021. doi: 10.1021/bi0108148.
|
Msx-1 homeodomain-DNA complex structure . SNAP output
|
1ig9
|
transferase-DNA |
X-ray (2.6 Å) |
Franklin MC, Wang J, Steitz TA |
(2001) "Structure
of the Replicating Complex of a Pol Alpha Family DNA
Polymerase." Cell(Cambridge,Mass.),
105, 657-667. doi: 10.1016/S0092-8674(01)00367-1.
|
Structure of the replicating complex of a pol alpha
family DNA polymerase . SNAP output
|
1ign
|
DNA binding protein-DNA |
X-ray (2.25 Å) |
Konig P, Giraldo R, Chapman L, Rhodes D |
(1996) "The
crystal structure of the DNA-binding domain of yeast
RAP1 in complex with telomeric DNA."
Cell(Cambridge,Mass.), 85,
125-136. doi: 10.1016/S0092-8674(00)81088-0.
|
DNA-binding domain of rap1 in complex with telomeric
DNA site . SNAP
output
|
1ihf
|
transcription-DNA |
X-ray (2.5 Å) |
Rice PA, Yang S, Mizuuchi K, Nash HA |
(1996) "Crystal
structure of an IHF-DNA complex: a protein-induced DNA
U-turn." Cell(Cambridge,Mass.),
87, 1295-1306. doi: 10.1016/S0092-8674(00)81824-3.
|
Integration host factor-DNA complex . SNAP output
|
1ijs
|
virus-DNA |
X-ray (3.25 Å) |
Llamas-Saiz AL, Agbandje-McKenna M, Parker JS, Wahid
AT, Parrish CR, Rossmann MG |
(1996) "Structural
analysis of a mutation in canine parvovirus which
controls antigenicity and host range."
Virology, 225, 65-71. doi:
10.1006/viro.1996.0575.
|
Cpv (strain d) mutant a300d, complex (viral coat-DNA),
vp2, ph=7.5, t=4 degrees c . SNAP output
|
1ijw
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Chiu TK, Sohn C, Dickerson RE, Johnson RC |
(2002) "Testing
water-mediated DNA recognition by the Hin
recombinase." EMBO J.,
21, 801-814. doi: 10.1093/emboj/21.4.801.
|
Testing the water-mediated hin recombinase DNA
recognition by systematic mutations. . SNAP output
|
1imh
|
transcription-DNA |
X-ray (2.86 Å) |
Stroud JC, Lopez-Rodriguez C, Rao A, Chen L |
(2002) "Structure
of a TonEBP-DNA complex reveals DNA encircled by a
transcription factor." Nat.Struct.Biol.,
9, 90-94. doi: 10.1038/nsb749.
|
Tonebp-DNA complex . SNAP output
|
1io4
|
transcription-DNA |
X-ray (3.0 Å) |
Tahirov TH, Inoue-Bungo T, Morii H, Fujikawa A,
Sasaki M, Kimura K, Shiina M, Sato K, Kumasaka T,
Yamamoto M, Ishii S, Ogata K |
(2001) "Structural
analyses of DNA recognition by the AML1/Runx-1 Runt
domain and its allosteric control by CBFbeta."
Cell(Cambridge,Mass.), 104,
755-767. doi: 10.1016/S0092-8674(01)00271-9.
|
Crystal structure of runx-1-aml1-cbfalpha runt
domain-cbfbeta core domain heterodimer and c-ebpbeta
bzip homodimer bound to a DNA fragment from the csf-1r
promoter . SNAP
output
|
1ipp
|
transcription-DNA |
X-ray (2.2 Å) |
Flick KE, Jurica MS, Monnat Jr RJ, Stoddard BL |
(1998) "DNA
binding and cleavage by the nuclear intron-encoded
homing endonuclease I-PpoI." Nature,
394, 96-101. doi: 10.1038/27952.
|
Homing endonuclease-DNA complex . SNAP output
|
1iu3
|
replication inhibitor-DNA |
X-ray (3.0 Å) |
Fujikawa N, Kurumizaka H, Nureki O, Tanaka Y, Yamazoe
M, Hiraga S, Yokoyama S |
(2004) "Structural
and biochemical analyses of hemimethylated DNA binding
by the SeqA protein." Nucleic Acids Res.,
32, 82-92. doi: 10.1093/nar/gkh173.
|
Crystal structure of the e.coli seqa protein complexed
with hemimethylated DNA . SNAP output
|
1iv6
|
DNA binding protein-DNA |
NMR |
Nishikawa T, Okamura H, Nagadoi A, Konig P, Rhodes D,
Nishimura Y |
(2001) "Solution
structure of a telomeric DNA complex of human
TRF1." Structure, 9,
1237-1251. doi: 10.1016/S0969-2126(01)00688-8.
|
Solution structure of the DNA complex of human trf1 .
SNAP output
|
1ixy
|
transferase-DNA |
X-ray (2.5 Å) |
Lariviere L, Morera S |
(2002) "A
Base-flipping Mechanism for the T4 Phage
beta-Glucosyltransferase and Identification of a
Transition-state Analog." J.Mol.Biol.,
324, 483-490. doi: 10.1016/S0022-2836(02)01091-4.
|
Ternary complex of t4 phage bgt with udp and a 13 mer
DNA duplex . SNAP
output
|
1j1v
|
replication-DNA |
X-ray (2.1 Å) |
Fujikawa N, Kurumizaka H, Nureki O, Terada T,
Shirouzu M, Katayama T, Yokoyama S |
(2003) "Structural
basis of replication origin recognition by the DnaA
protein." NUCLEIC ACIDS RES.,
31, 2077-2086. doi: 10.1093/nar/gkg309.
|
Crystal structure of dnaa domainiv complexed with
dnaabox DNA . SNAP
output
|
1j3e
|
replication-DNA |
X-ray (2.5 Å) |
Fujikawa N, Kurumizaka H, Nureki O, Tanaka Y, Yamazoe
M, Hiraga S, Yokoyama S |
(2004) "Structural
and biochemical analyses of hemimethylated DNA binding
by the SeqA protein." Nucleic Acids Res.,
32, 82-92. doi: 10.1093/nar/gkh173.
|
Crystal structure of the e.coli seqa protein complexed
with n6-methyladenine- guanine mismatch DNA . SNAP output
|
1j46
|
transcription-DNA |
NMR |
Murphy EC, Zhurkin VB, Louis JM, Cornilescu G, Clore
GM |
(2001) "Structural
basis for SRY-dependent 46-X,Y sex reversal: modulation
of DNA bending by a naturally occurring point
mutation." J.Mol.Biol.,
312, 481-499. doi: 10.1006/jmbi.2001.4977.
|
3d solution NMR structure of the wild type hmg-box
domain of the human male sex determining factor sry
complexed to DNA . SNAP
output
|
1j47
|
transcription-DNA |
NMR |
Murphy EC, Zhurkin VB, Louis JM, Cornilescu G, Clore
GM |
(2001) "Structural
basis for SRY-dependent 46-X,Y sex reversal: modulation
of DNA bending by a naturally occurring point
mutation." J.Mol.Biol.,
312, 481-499. doi: 10.1006/jmbi.2001.4977.
|
3d solution NMR structure of the m9i mutant of the
hmg-box domain of the human male sex determining factor
sry complexed to DNA . SNAP output
|
1j4w
|
transcription-DNA |
NMR |
Braddock DT, Louis JM, Baber JL, Levens D, Clore
GM |
(2002) "Structure
and dynamics of KH domains from FBP bound to
single-stranded DNA." Nature,
415, 1051-1056. doi: 10.1038/4151051a.
|
Complex of the kh3 and kh4 domains of fbp with a
single_stranded 29mer DNA oligonucleotide from the fuse
element of the c-myc oncogene . SNAP output
|
1j59
|
gene regulation-DNA |
X-ray (2.5 Å) |
Parkinson G, Wilson C, Gunasekera A, Ebright YW,
Ebright RE, Berman HM |
(1996) "Structure
of the CAP-DNA complex at 2.5 angstroms resolution: a
complete picture of the protein-DNA interface."
J.Mol.Biol., 260, 395-408.
doi: 10.1006/jmbi.1996.0409.
|
Catabolite gene activator protein (cap)-DNA complex +
adenosine-3',5'-cyclic-monophosphate . SNAP output
|
1j5k
|
transcription-DNA |
NMR |
Braddock DT, Baber JL, Levens D, Clore GM |
(2002) "Molecular
basis of sequence-specific single-stranded DNA
recognition by KH domains: solution structure of a
complex between hnRNP K KH3 and single-stranded
DNA." EMBO J., 21,
3476-3485. doi: 10.1093/emboj/cdf352.
|
Complex of the kh3 domain of hnrnp k with a
single_stranded 10mer DNA oligonucleotide . SNAP output
|
1j5n
|
DNA binding protein-DNA |
NMR |
Masse JE, Wong B, Yen Y-M, Allain FH-T, Johnson RC,
Feigon J |
(2002) "The S.
cerevisiae architectural HMGB protein NHP6A complexed
with DNA: DNA and protein conformational changes upon
binding." J.Mol.Biol.,
323, 263-284. doi: 10.1016/S0022-2836(02)00938-5.
|
Solution structure of the non-sequence-specific hmgb
protein nhp6a in complex with sry DNA . SNAP output
|
1j5o
|
transferase-immune system-DNA |
X-ray (3.5 Å) |
Sarafianos SG, Das K, Clark Jr AD, Ding J, Boyer PL,
Hughes SH, Arnold E |
(1999) "Lamivudine
(3TC) resistance in HIV-1 reverse transcriptase
involves steric hindrance with beta-branched amino
acids." Proc.Natl.Acad.Sci.USA,
96, 10027-10032. doi: 10.1073/pnas.96.18.10027.
|
Crystal structure of met184ile mutant of hiv-1 reverse
transcriptase in complex with double stranded DNA
template-primer . SNAP
output
|
1j75
|
immune system-DNA |
X-ray (1.85 Å) |
Schwartz T, Behlke J, Lowenhaupt K, Heinemann U, Rich
A |
(2001) "Structure
of the DLM-1-Z-DNA complex reveals a conserved family
of Z-DNA-binding proteins."
Nat.Struct.Biol., 8, 761-765.
doi: 10.1038/nsb0901-761.
|
Crystal structure of the DNA-binding domain zalpha of
dlm-1 bound to z-DNA . SNAP output
|
1j9n
|
DNA binding protein-DNA |
NMR |
Gomez-Pinto I, Marchan V, Gago F, Grandas A, Gonzalez
C |
(2003) "Solution
structure and stability of tryptophan-containing
nucleopeptide duplexes." Chembiochem,
4, 40-49. doi: 10.1002/cbic.200390012.
|
Solution structure of the nucleopeptide
[ac-lys-trp-lys-hse(p3*dgcatcg)-ala]-[p5*dcgtagc] .
SNAP output
|
1jb7
|
DNA-binding protein-DNA |
X-ray (1.86 Å) |
Horvath MP, Schultz SC |
(2001) "DNA
G-quartets in a 1.86 A resolution structure of an
Oxytricha nova telomeric protein-DNA complex."
J.Mol.Biol., 310, 367-377.
doi: 10.1006/jmbi.2001.4766.
|
DNA g-quartets in a 1.86 Å resolution structure of an
oxytricha nova telomeric protein-DNA complex . SNAP output
|
1je8
|
transcription-DNA |
X-ray (2.12 Å) |
Maris AE, Sawaya MR, Kaczor-Grzeskowiak M, Jarvis MR,
Bearson SM, Kopka ML, Schroder I, Gunsalus RP, Dickerson
RE |
(2002) "Dimerization
allows DNA target site recognition by the NarL response
regulator." Nat.Struct.Biol.,
9, 771-778. doi: 10.1038/nsb845.
|
Two-component response regulator narl-DNA complex: DNA
bending found in a high affinity site . SNAP output
|
1jey
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Walker JR, Corpina RA, Goldberg J |
(2001) "Structure
of the Ku heterodimer bound to DNA and its implications
for double-strand break repair." Nature,
412, 607-614. doi: 10.1038/35088000.
|
Crystal structure of the ku heterodimer bound to DNA .
SNAP output
|
1jfi
|
transcription-DNA |
X-ray (2.62 Å) |
Kamada K, Shu F, Chen H, Malik S, Stelzer G, Roeder
RG, Meisterernst M, Burley SK |
(2001) "Crystal
structure of negative cofactor 2 recognizing the
TBP-DNA transcription complex."
Cell(Cambridge,Mass.), 106,
71-81. doi: 10.1016/S0092-8674(01)00417-2.
|
Crystal structure of the nc2-tbp-DNA ternary complex .
SNAP output
|
1jfs
|
transcription-DNA |
X-ray (2.9 Å) |
Huffman JL, Lu F, Zalkin H, Brennan RG |
(2002) "Role of
residue 147 in the gene regulatory function of the
Escherichia coli purine repressor."
Biochemistry, 41, 511-520.
doi: 10.1021/bi0156660.
|
Purine repressor mutant-hypoxanthine-purf operator
complex . SNAP
output
|
1jft
|
transcription-DNA |
X-ray (2.5 Å) |
Huffman JL, Lu F, Zalkin H, Brennan RG |
(2002) "Role of
residue 147 in the gene regulatory function of the
Escherichia coli purine repressor."
Biochemistry, 41, 511-520.
doi: 10.1021/bi0156660.
|
Purine repressor mutant-hypoxanthine-purf operator
complex . SNAP
output
|
1jgg
|
transcription-DNA |
X-ray (2.0 Å) |
Hirsch JA, Aggarwal AK |
(1995) "Structure
of the even-skipped homeodomain complexed to AT-rich
DNA: new perspectives on homeodomain specificity."
EMBO J., 14, 6280-6291.
|
Even-skipped homeodomain complexed to at-rich DNA .
SNAP output
|
1jh9
|
transcription-DNA |
X-ray (2.55 Å) |
Huffman JL, Lu F, Zalkin H, Brennan RG |
(2002) "Role of
residue 147 in the gene regulatory function of the
Escherichia coli purine repressor."
Biochemistry, 41, 511-520.
doi: 10.1021/bi0156660.
|
Purine repressor mutant-hypoxanthine-purf operator
complex . SNAP
output
|
1jj4
|
transcription-DNA |
X-ray (2.4 Å) |
Kim SS, Tam JK, Wang AF, Hegde RS |
(2000) "The
structural basis of DNA target discrimination by
papillomavirus E2 proteins." J.Biol.Chem.,
275, 31245-31254. doi: 10.1074/jbc.M004541200.
|
Human papillomavirus type 18 e2 DNA-binding domain
bound to its DNA target . SNAP output
|
1jj6
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Chiu TK, Sohn C, Dickerson RE, Johnson RC |
(2002) "Testing
water-mediated DNA recognition by the Hin
recombinase." EMBO J.,
21, 801-814. doi: 10.1093/emboj/21.4.801.
|
Testing the water-mediated hin recombinase DNA
recognition by systematic mutations. . SNAP output
|
1jj8
|
DNA binding protein-DNA |
X-ray (2.75 Å) |
Chiu TK, Sohn C, Dickerson RE, Johnson RC |
(2002) "Testing
water-mediated DNA recognition by the Hin
recombinase." EMBO J.,
21, 801-814. doi: 10.1093/emboj/21.4.801.
|
Testing the water-mediated hin recombinase DNA
recognition by systematic mutations . SNAP output
|
1jk1
|
transcription-DNA |
X-ray (1.9 Å) |
Miller JC, Pabo CO |
(2001) "Rearrangement
of side-chains in a Zif268 mutant highlights the
complexities of zinc finger-DNA recognition."
J.Mol.Biol., 313, 309-315.
doi: 10.1006/jmbi.2001.4975.
|
Zif268 d20a mutant bound to wt DNA site . SNAP output
|
1jk2
|
transcription-DNA |
X-ray (1.65 Å) |
Miller JC, Pabo CO |
(2001) "Rearrangement
of side-chains in a Zif268 mutant highlights the
complexities of zinc finger-DNA recognition."
J.Mol.Biol., 313, 309-315.
doi: 10.1006/jmbi.2001.4975.
|
Zif268 d20a mutant bound to the gct DNA site . SNAP output
|
1jko
|
DNA binding protein-DNA |
X-ray (2.24 Å) |
Chiu TK, Sohn C, Dickerson RE, Johnson RC |
(2002) "Testing
water-mediated DNA recognition by the Hin
recombinase." EMBO J.,
21, 801-814. doi: 10.1093/emboj/21.4.801.
|
Testing the water-mediated hin recombinase DNA
recognition by systematic mutations . SNAP output
|
1jkp
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Chiu TK, Sohn C, Dickerson RE, Johnson RC |
(2002) "Testing
water-mediated DNA recognition by the Hin
recombinase." EMBO J.,
21, 801-814. doi: 10.1093/emboj/21.4.801.
|
Testing the water-mediated hin recombinase DNA
recognition by systematic mutations . SNAP output
|
1jkq
|
DNA binding protein-DNA |
X-ray (2.86 Å) |
Chiu TK, Sohn C, Dickerson RE, Johnson RC |
(2002) "Testing
water-mediated DNA recognition by the Hin
recombinase." EMBO J.,
21, 801-814. doi: 10.1093/emboj/21.4.801.
|
Testing the water-mediated hin recombinase DNA
recognition by systematic mutations . SNAP output
|
1jkr
|
DNA binding protein-DNA |
X-ray (2.28 Å) |
Chiu TK, Sohn C, Dickerson RE, Johnson RC |
(2002) "Testing
water-mediated DNA recognition by the Hin
recombinase." EMBO J.,
21, 801-814. doi: 10.1093/emboj/21.4.801.
|
Testing the water-mediated hin recombinase DNA
recognition by systematic mutations . SNAP output
|
1jmc
|
replication-DNA |
X-ray (2.4 Å) |
Bochkarev A, Pfuetzner RA, Edwards AM, Frappier
L |
(1997) "Structure
of the single-stranded-DNA-binding domain of
replication protein A bound to DNA."
Nature, 385, 176-181. doi:
10.1038/385176a0.
|
Single stranded DNA-binding domain of human replication
protein a bound to single stranded DNA, rpa70 subunit,
residues 183-420 . SNAP
output
|
1jnm
|
transcription-DNA |
X-ray (2.2 Å) |
Kim Y, Podust LM |
"Crystal Structure of the Jun bZIP homodimer
complexed with CRE." |
Crystal structure of the jun-cre complex . SNAP output
|
1jt0
|
transcription-DNA |
X-ray (2.9 Å) |
Schumacher MA, Miller MC, Grkovic S, Brown MH,
Skurray RA, Brennan RG |
(2002) "Structural
basis for cooperative DNA binding by two dimers of the
multidrug-binding protein QacR." EMBO J.,
21, 1210-1218. doi: 10.1093/emboj/21.5.1210.
|
Crystal structure of a cooperative qacr-DNA complex .
SNAP output
|
1jwl
|
transcription-DNA |
X-ray (4.0 Å) |
Bell CE, Lewis M |
(2001) "Crystallographic
analysis of Lac repressor bound to natural operator
O1." J.Mol.Biol., 312,
921-926. doi: 10.1006/jmbi.2001.5024.
|
Structure of the dimeric lac repressor-operator o1-onpf
complex . SNAP
output
|
1jx4
|
transferase-DNA |
X-ray (1.7 Å) |
Ling H, Boudsocq F, Woodgate R, Yang W |
(2001) "Crystal
structure of a Y-family DNA polymerase in action: a
mechanism for error-prone and lesion-bypass
replication." Cell(Cambridge,Mass.),
107, 91-102. doi: 10.1016/S0092-8674(01)00515-3.
|
Crystal structure of a y-family DNA polymerase in a
ternary complex with DNA substrates and an incoming
nucleotide . SNAP
output
|
1jxl
|
transferase-DNA |
X-ray (2.1 Å) |
Ling H, Boudsocq F, Woodgate R, Yang W |
(2001) "Crystal
structure of a Y-family DNA polymerase in action: a
mechanism for error-prone and lesion-bypass
replication." Cell(Cambridge,Mass.),
107, 91-102. doi: 10.1016/S0092-8674(01)00515-3.
|
Crystal structure of a y-family DNA polymerase in a
ternary complex with DNA substrates and an incoming
nucleotide . SNAP
output
|
1k3w
|
hydrolase-DNA |
X-ray (1.42 Å) |
Zharkov DO, Golan G, Gilboa R, Fernandes AS, Gerchman
SE, Kycia JH, Rieger RA, Grollman AP, Shoham G |
(2002) "Structural
analysis of an Escherichia coli endonuclease VIII
covalent reaction intermediate." EMBO J.,
21, 789-800. doi: 10.1093/emboj/21.4.789.
|
Crystal structure of a trapped reaction intermediate of
the DNA repair enzyme endonuclease viii with DNA .
SNAP output
|
1k3x
|
hydrolase-DNA |
X-ray (1.25 Å) |
Zharkov DO, Golan G, Gilboa R, Fernandes AS, Gerchman
SE, Kycia JH, Rieger RA, Grollman AP, Shoham G |
(2002) "Structural
analysis of an Escherichia coli endonuclease VIII
covalent reaction intermediate." EMBO J.,
21, 789-800. doi: 10.1093/emboj/21.4.789.
|
Crystal structure of a trapped reaction intermediate of
the DNA repair enzyme endonuclease viii with
brominated-DNA . SNAP
output
|
1k4s
|
isomerase-DNA |
X-ray (3.2 Å) |
Staker BL, Hjerrild K, Feese MD, Behnke CA, Burgin Jr
AB, Stewart LJ |
(2002) "The
mechanism of topoisomerase I poisoning by a
camptothecin analog."
Proc.Natl.Acad.Sci.USA, 99,
15387-15392. doi: 10.1073/pnas.242259599.
|
Human DNA topoisomerase i in covalent complex with a 22
base pair DNA duplex . SNAP output
|
1k4t
|
isomerase-DNA |
X-ray (2.1 Å) |
Staker BL, Hjerrild K, Feese MD, Behnke CA, Burgin Jr
AB, Stewart LJ |
(2002) "The
mechanism of topoisomerase I poisoning by a
camptothecin analog."
Proc.Natl.Acad.Sci.USA, 99,
15387-15392. doi: 10.1073/pnas.242259599.
|
Human DNA topoisomerase i (70 kda) in complex with the
poison topotecan and covalent complex with a 22 base
pair DNA duplex . SNAP
output
|
1k61
|
transcription-DNA |
X-ray (2.1 Å) |
Aishima J, Gitti RK, Noah JE, Gan HH, Schlick T,
Wolberger C |
(2002) "A
Hoogsteen base pair embedded in undistorted B-DNA."
NUCLEIC ACIDS RES., 30,
5244-5252. doi: 10.1093/nar/gkf661.
|
Matalpha2 homeodomain bound to DNA . SNAP output
|
1k6o
|
transcription-DNA |
X-ray (3.19 Å) |
Mo Y, Ho W, Johnston K, Marmorstein R |
(2001) "Crystal
structure of a ternary SAP-1/SRF/c-fos SRE DNA
complex." J.Mol.Biol.,
314, 495-506. doi: 10.1006/jmbi.2001.5138.
|
Crystal structure of a ternary sap-1-srf-c-fos sre DNA
complex . SNAP
output
|
1k78
|
transcription-DNA |
X-ray (2.25 Å) |
Garvie CW, Hagman J, Wolberger C |
(2001) "Structural
studies of Ets-1/Pax5 complex formation on DNA."
Mol.Cell, 8, 1267-1276. doi:
10.1016/S1097-2765(01)00410-5.
|
Pax5(1-149)+ets-1(331-440)+DNA . SNAP output
|
1k79
|
transcription-DNA |
X-ray (2.4 Å) |
Garvie CW, Hagman J, Wolberger C |
(2001) "Structural
studies of Ets-1/Pax5 complex formation on DNA."
Mol.Cell, 8, 1267-1276. doi:
10.1016/S1097-2765(01)00410-5.
|
Ets-1(331-440)+ggaa duplex . SNAP output
|
1k7a
|
transcription-DNA |
X-ray (2.8 Å) |
Garvie CW, Hagman J, Wolberger C |
(2001) "Structural
studies of Ets-1/Pax5 complex formation on DNA."
Mol.Cell, 8, 1267-1276. doi:
10.1016/S1097-2765(01)00410-5.
|
Ets-1(331-440)+ggag duplex . SNAP output
|
1k82
|
hydrolase-DNA |
X-ray (2.1 Å) |
Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman
SE, Matz E, Kycia JH, Grollman AP, Shoham G |
(2002) "Structure
of formamidopyrimidine-DNA glycosylase covalently
complexed to DNA." J.Biol.Chem.,
277, 19811-19816. doi: 10.1074/jbc.M202058200.
|
Crystal structure of e.coli formamidopyrimidine-DNA
glycosylase (fpg) covalently trapped with DNA .
SNAP output
|
1k8g
|
DNA binding protein-DNA |
X-ray (2.6 Å) |
Classen S, Ruggles JA, Schultz SC |
(2001) "Crystal
structure of the N-terminal domain of Oxytricha nova
telomere end-binding protein alpha subunit both
uncomplexed and complexed with telomeric ssDNA."
J.Mol.Biol., 314, 1113-1125.
doi: 10.1006/jmbi.2000.5191.
|
Crystal structure of the n-terminal domain of oxytricha
nova telomere end binding protein alpha subunit both
uncomplexed and complexed with telomeric ssDNA .
SNAP output
|
1kb2
|
transcription-DNA |
X-ray (2.7 Å) |
Shaffer PL, Gewirth DT |
(2002) "Structural
basis of VDR-DNA interactions on direct repeat response
elements." EMBO J., 21,
2242-2252. doi: 10.1093/emboj/21.9.2242.
|
Crystal structure of vdr DNA-binding domain bound to
mouse osteopontin (spp) response element . SNAP output
|
1kb4
|
transcription-DNA |
X-ray (2.8 Å) |
Shaffer PL, Gewirth DT |
(2002) "Structural
basis of VDR-DNA interactions on direct repeat response
elements." EMBO J., 21,
2242-2252. doi: 10.1093/emboj/21.9.2242.
|
Crystal structure of vdr DNA-binding domain bound to a
canonical direct repeat with three base pair spacer
(dr3) response element . SNAP output
|
1kb6
|
transcription-DNA |
X-ray (2.7 Å) |
Shaffer PL, Gewirth DT |
(2002) "Structural
basis of VDR-DNA interactions on direct repeat response
elements." EMBO J., 21,
2242-2252. doi: 10.1093/emboj/21.9.2242.
|
Crystal structure of vdr DNA-binding domain bound to
rat osteocalcin (oc) response element . SNAP output
|
1kbu
|
hydrolase, ligase-DNA |
X-ray (2.2 Å) |
Martin SS, Pulido E, Chu VC, Lechner TS, Baldwin
EP |
(2002) "The
Order of Strand Exchanges in Cre-LoxP Recombination and
its Basis Suggested by the Crystal Structure of a
Cre-LoxP Holliday Junction Complex."
J.Mol.Biol., 319, 107-127.
doi: 10.1016/S0022-2836(02)00246-2.
|
Cre recombinase bound to a loxp holliday junction .
SNAP output
|
1kc6
|
hydrolase-DNA |
X-ray (2.6 Å) |
Horton NC, Dorner LF, Perona JJ |
(2002) "Sequence
selectivity and degeneracy of a restriction
endonuclease mediated by DNA intercalation."
Nat.Struct.Biol., 9, 42-47.
doi: 10.1038/nsb741.
|
Hincii bound to cognate DNA . SNAP output
|
1kc8
|
ribosome |
X-ray (3.01 Å) |
Hansen J, Moore PB, Steitz TA |
(2003) "Structures
of Five Antibiotics Bound at the Peptidyl Transferase
Center of the Large Ribosomal Subunit."
J.Mol.Biol., 330, 1061-1075.
doi: 10.1016/S0022-2836(03)00668-5.
|
Co-crystal structure of blasticidin s bound to the 50s
ribosomal subunit . SNAP
output
|
1kdh
|
transferase-DNA |
X-ray (3.0 Å) |
Delarue M, Boule JB, Lescar J, Expert-Bezancon N,
Jourdan N, Sukumar N, Rougeon F, Papanicolaou C |
(2002) "Crystal
structures of a template-independent DNA polymerase:
murine terminal deoxynucleotidyltransferase."
EMBO J., 21, 427-439. doi:
10.1093/emboj/21.3.427.
|
Binary complex of murine terminal deoxynucleotidyl
transferase with a primer single stranded DNA .
SNAP output
|
1keg
|
immune system-DNA |
X-ray (2.4 Å) |
Yokoyama H, Mizutani R, Satow Y, Sato K, Komatsu Y,
Ohtsuka E, Nikaido O |
(2012) "Structure
of the DNA (6-4) photoproduct dTT(6-4)TT in complex
with the 64M-2 antibody Fab fragment implies increased
antibody-binding affinity by the flanking
nucleotides." Acta Crystallogr.,Sect.D,
68, 232-238. doi: 10.1107/S0907444912000327.
|
Antibody 64m-2 fab complexed with dtt(6-4)tt . SNAP output
|
1kfs
|
transferase-DNA |
X-ray (2.1 Å) |
Brautigam CA, Steitz TA |
(1998) "Structural
principles for the inhibition of the 3'-5' exonuclease
activity of Escherichia coli DNA polymerase I by
phosphorothioates." J.Mol.Biol.,
277, 363-377. doi: 10.1006/jmbi.1997.1586.
|
DNA polymerase i klenow fragment (e.c.2.7.7.7)
mutant-DNA complex . SNAP output
|
1kfv
|
hydrolase-DNA |
X-ray (2.55 Å) |
Serre L, Pereira de Jesus K, Boiteux S, Zelwer C,
Castaing B |
(2002) "Crystal
structure of the Lactococcus lactis
formamidopyrimidine-DNA glycosylase bound to an abasic
site analogue-containing DNA." EMBO J.,
21, 2854-2865. doi: 10.1093/emboj/cdf304.
|
Crystal structure of lactococcus lactis
formamido-pyrimidine DNA glycosylase (alias fpg or
mutm) non covalently bound to an ap site containing
DNA. . SNAP output
|
1kix
|
DNA binding protein-DNA |
X-ray (2.7 Å) |
Peersen OB, Ruggles JA, Schultz SC |
(2002) "Dimeric
structure of the Oxytricha nova telomere end-binding
protein alpha-subunit bound to ssDNA."
Nat.Struct.Biol., 9, 182-187.
|
Dimeric structure of the o. nova telomere end binding
protein alpha subunit with bound ssDNA . SNAP output
|
1kln
|
transferase-DNA |
X-ray (3.2 Å) |
Beese LS, Derbyshire V, Steitz TA |
(1993) "Structure
of DNA polymerase I Klenow fragment bound to duplex
DNA." Science, 260,
352-355.
|
DNA polymerase i klenow fragment (e.c.2.7.7.7)
mutant-DNA complex . SNAP output
|
1kqq
|
transcription-DNA |
NMR |
Iwahara J, Iwahara M, Daughdrill GW, Ford J, Clubb
RT |
(2002) "The
structure of the Dead ringer-DNA complex reveals how
AT-rich interaction domains (ARIDs) recognize DNA."
EMBO J., 21, 1197-1209. doi:
10.1093/emboj/21.5.1197.
|
Solution structure of the dead ringer arid-DNA complex
. SNAP output
|
1krp
|
transferase-DNA |
X-ray (2.2 Å) |
Brautigam CA, Steitz TA |
(1998) "Structural
principles for the inhibition of the 3'-5' exonuclease
activity of Escherichia coli DNA polymerase I by
phosphorothioates." J.Mol.Biol.,
277, 363-377. doi: 10.1006/jmbi.1997.1586.
|
DNA polymerase i klenow fragment (e.c.2.7.7.7)
mutant-DNA complex . SNAP output
|
1ksp
|
transferase-DNA |
X-ray (2.3 Å) |
Brautigam CA, Steitz TA |
(1998) "Structural
principles for the inhibition of the 3'-5' exonuclease
activity of Escherichia coli DNA polymerase I by
phosphorothioates." J.Mol.Biol.,
277, 363-377. doi: 10.1006/jmbi.1997.1586.
|
DNA polymerase i klenow fragment (e.c.2.7.7.7)
mutant-DNA complex . SNAP output
|
1ksx
|
replication-DNA |
X-ray (3.2 Å) |
Enemark EJ, Stenlund A, Joshua-Tor L |
(2002) "Crystal
structures of two intermediates in the assembly of the
papillomavirus replication initiation complex."
EMBO J., 21, 1487-1496. doi:
10.1093/emboj/21.6.1487.
|
Crystal structures of two intermediates in the assembly
of the papillomavirus replication initiation complex .
SNAP output
|
1ksy
|
replication-DNA |
X-ray (3.05 Å) |
Enemark EJ, Stenlund A, Joshua-Tor L |
(2002) "Crystal
structures of two intermediates in the assembly of the
papillomavirus replication initiation complex."
EMBO J., 21, 1487-1496. doi:
10.1093/emboj/21.6.1487.
|
Crystal structures of two intermediates in the assembly
of the papillomavirus replication initiation complex .
SNAP output
|
1ku7
|
transcription-DNA |
X-ray (2.4 Å) |
Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA,
Weinman O, Trester-Zedlitz ML, Darst SA |
(2002) "Structure
of the bacterial RNA polymerase promoter specificity
sigma subunit." Mol.Cell,
9, 527-539. doi: 10.1016/S1097-2765(02)00470-7.
|
Crystal structure of thermus aquatics RNA polymerase
sigmaa subunit region 4 bound to-35 element DNA .
SNAP output
|
1kx3
|
structural protein-DNA |
X-ray (2.0 Å) |
Davey CA, Sargent DF, Luger K, Maeder AW, Richmond
TJ |
(2002) "Solvent
Mediated Interactions in the Structure of the
Nucleosome Core Particle at 1.9 A Resolution."
J.Mol.Biol., 319, 1097-1113.
doi: 10.1016/S0022-2836(02)00386-8.
|
X-ray structure of the nucleosome core particle,
ncp146, at 2.0 Å resolution . SNAP output
|
1kx4
|
structural protein-DNA |
X-ray (2.6 Å) |
Davey CA, Sargent DF, Luger K, Maeder AW, Richmond
TJ |
(2002) "Solvent
Mediated Interactions in the Structure of the
Nucleosome Core Particle at 1.9 A Resolution."
J.Mol.Biol., 319, 1097-1113.
doi: 10.1016/S0022-2836(02)00386-8.
|
X-ray structure of the nucleosome core particle,
ncp146b, at 2.6 Å resolution . SNAP output
|
1kx5
|
structural protein-DNA |
X-ray (1.94 Å) |
Davey CA, Sargent DF, Luger K, Maeder AW, Richmond
TJ |
(2002) "Solvent
Mediated Interactions in the Structure of the
Nucleosome Core Particle at 1.9 A Resolution."
J.Mol.Biol., 319, 1097-1113.
doi: 10.1016/S0022-2836(02)00386-8.
|
X-ray structure of the nucleosome core particle,
ncp147, at 1.9 Å resolution . SNAP output
|
1l1m
|
transcription regulator-DNA |
NMR |
Kalodimos CG, Bonvin AM, Salinas RK, Wechselberger R,
Boelens R, Kaptein R |
(2002) "Plasticity
in protein-DNA recognition: lac repressor interacts
with its natural operator 01 through alternative
conformations of its DNA-binding domain." EMBO
J., 21, 2866-2876. doi: 10.1093/emboj/cdf318.
|
Solution structure of a dimer of lac repressor
DNA-binding domain complexed to its natural operator o1
. SNAP output
|
1l1t
|
hydrolase-DNA |
X-ray (1.8 Å) |
Fromme JC, Verdine GL |
(2002) "Structural
insights into lesion recognition and repair by the
bacterial 8-oxoguanine DNA glycosylase MutM."
Nat.Struct.Biol., 9, 544-552.
|
Mutm (fpg) bound to abasic-site containing DNA .
SNAP output
|
1l1v
|
DNA-antibiotic |
NMR |
Chou SH, Chin KH, Chen FM |
(2002) "Looped
Out and Perpendicular: Deformation of Watson-Crick Base
Pair Associated with Actinomycin D Binding."
Proc.Natl.Acad.Sci.USA, 99,
6625. doi: 10.1073/PNAS.102580399.
|
Unusual actd-dna_ta complex structure . SNAP output
|
1l1z
|
hydrolase-DNA |
X-ray (1.7 Å) |
Fromme JC, Verdine GL |
(2002) "Structural
insights into lesion recognition and repair by the
bacterial 8-oxoguanine DNA glycosylase MutM."
Nat.Struct.Biol., 9, 544-552.
|
Mutm (fpg) covalent-DNA intermediate . SNAP output
|
1l2b
|
hydrolase-DNA |
X-ray (2.4 Å) |
Fromme JC, Verdine GL |
(2002) "Structural
insights into lesion recognition and repair by the
bacterial 8-oxoguanine DNA glycosylase MutM."
Nat.Struct.Biol., 9, 544-552.
|
Mutm (fpg) DNA end-product structure . SNAP output
|
1l2c
|
hydrolase-DNA |
X-ray (2.2 Å) |
Fromme JC, Verdine GL |
(2002) "Structural
insights into lesion recognition and repair by the
bacterial 8-oxoguanine DNA glycosylase MutM."
Nat.Struct.Biol., 9, 544-552.
|
Mutm (fpg)-DNA estranged thymine mismatch recognition
complex . SNAP
output
|
1l2d
|
hydrolase-DNA |
X-ray (2.0 Å) |
Fromme JC, Verdine GL |
(2002) "Structural
insights into lesion recognition and repair by the
bacterial 8-oxoguanine DNA glycosylase MutM."
Nat.Struct.Biol., 9, 544-552.
|
Mutm (fpg)-DNA estranged guanine mismatch recognition
complex . SNAP
output
|
1l3l
|
transcription-DNA |
X-ray (1.66 Å) |
Zhang RG, Pappas T, Brace JL, Miller PC, Oulmassov T,
Molyneaux JM, Anderson JC, Bashkin JK, Winans SC,
Joachimiak A |
(2002) "Structure
of a bacterial quorum-sensing transcription factor
complexed with pheromone and DNA." Nature,
417, 971-974. doi: 10.1038/nature00833.
|
Crystal structure of a bacterial quorum-sensing
transcription factor complexed with pheromone and DNA .
SNAP output
|
1l3s
|
transferase-DNA |
X-ray (1.7 Å) |
Johnson SJ, Taylor JS, Beese LS |
(2003) "Processive
DNA synthesis observed in a polymerase crystal suggests
a mechanism for the prevention of frameshift
mutations." Proc.Natl.Acad.Sci.USA,
100, 3895-3900. doi: 10.1073/pnas.0630532100.
|
Crystal structure of bacillus DNA polymerase i fragment
complexed to 9 base pairs of duplex DNA. . SNAP output
|
1l3t
|
transferase-DNA |
X-ray (1.7 Å) |
Johnson SJ, Taylor JS, Beese LS |
(2003) "Processive
DNA synthesis observed in a polymerase crystal suggests
a mechanism for the prevention of frameshift
mutations." Proc.Natl.Acad.Sci.USA,
100, 3895-3900. doi: 10.1073/pnas.0630532100.
|
Crystal structure of bacillus DNA polymerase i fragment
product complex with 10 base pairs of duplex DNA
following addition of a single dttp residue . SNAP output
|
1l3u
|
transferase-DNA |
X-ray (1.8 Å) |
Johnson SJ, Taylor JS, Beese LS |
(2003) "Processive
DNA synthesis observed in a polymerase crystal suggests
a mechanism for the prevention of frameshift
mutations." Proc.Natl.Acad.Sci.USA,
100, 3895-3900. doi: 10.1073/pnas.0630532100.
|
Crystal structure of bacillus DNA polymerase i fragment
product complex with 11 base pairs of duplex DNA
following addition of a dttp and a datp residue. .
SNAP output
|
1l3v
|
transferase-DNA |
X-ray (1.71 Å) |
Johnson SJ, Taylor JS, Beese LS |
(2003) "Processive
DNA synthesis observed in a polymerase crystal suggests
a mechanism for the prevention of frameshift
mutations." Proc.Natl.Acad.Sci.USA,
100, 3895-3900. doi: 10.1073/pnas.0630532100.
|
Crystal structure of bacillus DNA polymerase i fragment
product complex with 15 base pairs of duplex DNA
following addition of dttp, datp, dctp, and dgtp
residues. . SNAP
output
|
1l5u
|
transferase-DNA |
X-ray (1.95 Å) |
Johnson SJ, Taylor JS, Beese LS |
(2003) "Processive
DNA synthesis observed in a polymerase crystal suggests
a mechanism for the prevention of frameshift
mutations." Proc.Natl.Acad.Sci.USA,
100, 3895-3900. doi: 10.1073/pnas.0630532100.
|
Crystal structure of bacillus DNA polymerase i fragment
product complex with 12 base pairs of duplex DNA
following addition of a dttp, a datp, and a dctp
residue. . SNAP
output
|
1lat
|
transcription-DNA |
X-ray (1.9 Å) |
Gewirth DT, Sigler PB |
(1995) "The basis
for half-site specificity explored through a
non-cognate steroid receptor-DNA complex."
Nat.Struct.Biol., 2, 386-394.
doi: 10.1038/nsb0595-386.
|
Glucocorticoid receptor mutant-DNA complex . SNAP output
|
1lau
|
hydrolase-DNA |
X-ray (1.8 Å) |
Savva R, McAuley-Hecht K, Brown T, Pearl L |
(1995) "The
structural basis of specific base-excision repair by
uracil-DNA glycosylase." Nature,
373, 487-493. doi: 10.1038/373487a0.
|
Uracil-DNA glycosylase . SNAP output
|
1lb2
|
gene regulation-DNA |
X-ray (3.1 Å) |
Benoff B, Yang H, Lawson CL, Parkinson G, Liu J,
Blatter E, Ebright YW, Berman HM, Ebright RH |
(2002) "Structural
basis of transcription activation: the CAP-alpha
CTD-DNA complex." Science,
297, 1562-1566. doi: 10.1126/science.1076376.
|
Structure of the e. coli alpha c-terminal domain of RNA
polymerase in complex with cap and DNA . SNAP output
|
1lcc
|
gene regulation-DNA |
NMR |
Chuprina VP, Rullmann JA, Lamerichs RM, van Boom JH,
Boelens R, Kaptein R |
(1993) "Structure
of the complex of lac repressor headpiece and an 11
base-pair half-operator determined by nuclear magnetic
resonance spectroscopy and restrained molecular
dynamics." J.Mol.Biol.,
234, 446-462. doi: 10.1006/jmbi.1993.1598.
|
Structure of the complex of lac repressor headpiece and
an 11 base-pair half-operator determined by nuclear
magnetic resonance spectroscopy and restrained
molecular dynamics . SNAP output
|
1lcd
|
gene regulation-DNA |
NMR |
Chuprina VP, Rullmann JA, Lamerichs RM, van Boom JH,
Boelens R, Kaptein R |
(1993) "Structure
of the complex of lac repressor headpiece and an 11
base-pair half-operator determined by nuclear magnetic
resonance spectroscopy and restrained molecular
dynamics." J.Mol.Biol.,
234, 446-462. doi: 10.1006/jmbi.1993.1598.
|
Structure of the complex of lac repressor headpiece and
an 11 base-pair half-operator determined by nuclear
magnetic resonance spectroscopy and restrained
molecular dynamics . SNAP output
|
1le5
|
transcription-DNA |
X-ray (2.75 Å) |
Berkowitz B, Huang DB, Chen-Park FE, Sigler PB, Ghosh
G |
(2002) "The
X-ray crystal structure of the NF-kB p50/p65
heterodimer bound to the Interferon beta-kB site."
J.Biol.Chem., 277,
24694-24700. doi: 10.1074/jbc.M200006200.
|
Crystal structure of a nf-kb heterodimer bound to an
ifnb-kb . SNAP
output
|
1le8
|
transcription-DNA |
X-ray (2.3 Å) |
Ke A, Mathias JR, Vershon AK, Wolberger C |
(2002) "Structural
and Thermodynamic Characterization of the DNA Binding
Properties of a Triple Alanine Mutant of
MATalpha2." Structure,
10, 961-971. doi: 10.1016/S0969-2126(02)00790-6.
|
Crystal structure of the mata1-matalpha2-3a heterodimer
bound to DNA complex . SNAP output
|
1le9
|
transcription-DNA |
X-ray (3.0 Å) |
Berkowitz B, Huang DB, Chen-Park FE, Sigler PB, Ghosh
G |
(2002) "The
x-ray crystal structure of the NF-kappa B p50.p65
heterodimer bound to the interferon beta -kappa B
site." J.Biol.Chem., 277,
24694-24700. doi: 10.1074/jbc.M200006200.
|
Crystal structure of a nf-kb heterodimer bound to the
ig-hiv-kb siti . SNAP
output
|
1lei
|
transcription-DNA |
X-ray (2.7 Å) |
Chen-Park FE, Huang DB, Noro B, Thanos D, Ghosh
G |
(2002) "The kB
DNA sequence from the HIV Long Terminal Repeat
functions as an allosteric regulator of HIV
transcription." J.Biol.Chem.,
277, 24701-24708. doi: 10.1074/jbc.M200007200.
|
The kb DNA sequence from the hlv-ltr functions as an
allosteric regulator of hiv transcription . SNAP output
|
1lfu
|
transcription |
NMR |
Sprules T, Green N, Featherstone M, Gehring K |
(2003) "Lock and
Key Binding of the HOX YPWM Peptide to the PBX
Homeodomain." J.Biol.Chem.,
278, 1053-1058. doi: 10.1074/jbc.M207504200.
|
NMR solution structure of the extended pbx homeodomain
bound to DNA . SNAP
output
|
1lli
|
transcription-DNA |
X-ray (2.1 Å) |
Lim WA, Hodel A, Sauer RT, Richards FM |
(1994) "The
crystal structure of a mutant protein with altered but
improved hydrophobic core packing."
Proc.Natl.Acad.Sci.USA, 91,
423-427. doi: 10.1073/pnas.91.1.423.
|
The crystal structure of a mutant protein with altered
but improved hydrophobic core packing . SNAP output
|
1llm
|
transcription-DNA |
X-ray (1.5 Å) |
Wolfe SA, Grant RA, Pabo CO |
(2003) "Structure
of a designed dimeric zinc finger protein bound to
DNA." Biochemistry, 42,
13401-13409. doi: 10.1021/bi034830b.
|
Crystal structure of a zif23-gcn4 chimera bound to DNA
. SNAP output
|
1lmb
|
transcription-DNA |
X-ray (1.8 Å) |
Beamer LJ, Pabo CO |
(1992) "Refined
1.8 A crystal structure of the lambda
repressor-operator complex." J.Mol.Biol.,
227, 177-196. doi: 10.1016/0022-2836(92)90690-L.
|
Refined 1.8 angstrom crystal structure of the lambda
repressor-operator complex . SNAP output
|
1lo1
|
hormone-growth factor receptor-DNA |
NMR |
Gearhart MD, Holmbeck SMA, Evans RM, Dyson HJ, Wright
PE |
(2003) "Monomeric
Complex of Human Orphan Estrogen Related Receptor-2
with DNA: A Pseudo-dimer Interface Mediates Extended
Half-site Recognition." J.Mol.Biol.,
327, 819-832. doi: 10.1016/S0022-2836(03)00183-9.
|
Estrogen related receptor 2 DNA binding domain in
complex with DNA . SNAP
output
|
1lpq
|
isomerase-DNA |
X-ray (3.14 Å) |
Lesher DT, Pommier Y, Stewart L, Redinbo MR |
(2002) "8-Oxoguanine
rearranges the active site of human topoisomerase
I." Proc.Natl.Acad.Sci.USA,
99, 12102-12107. doi: 10.1073/pnas.192282699.
|
Human DNA topoisomerase i (70 kda) in non-covalent
complex with a 22 base pair DNA duplex containing an
8-oxog lesion . SNAP
output
|
1lq1
|
transcription-DNA |
X-ray (2.3 Å) |
Zhao H, Msadek T, Zapf J, Madhusudan, Hoch JA,
Varughese KI |
(2002) "DNA
complexed structure of the key transcription factor
initiating development in sporulating bacteria."
Structure, 10, 1041-1050.
doi: 10.1016/S0969-2126(02)00803-1.
|
DNA complexed structure of the key transcription factor
initiating development in sporulation bacteria .
SNAP output
|
1lrr
|
replication inhibitor-DNA |
X-ray (2.65 Å) |
Guarne A, Zhao Q, Guirlando R, Yang W |
(2002) "Insights
into negative modulation of E. coli replication
initiation from the structure of SeqA-hemimethylated
DNA complex." NAT.STRUCT.BIOL.,
9, 839-843.
|
Crystal structure of e. coli seqa complexed with
hemimethylated DNA . SNAP output
|
1lv5
|
transferase-DNA |
X-ray (1.95 Å) |
Johnson SJ, Taylor JS, Beese LS |
(2003) "Processive
DNA synthesis observed in a polymerase crystal suggests
a mechanism for the prevention of frameshift
mutations." Proc.Natl.Acad.Sci.USA,
100, 3895-3900. doi: 10.1073/pnas.0630532100.
|
Crystal structure of the closed conformation of
bacillus DNA polymerase i fragment bound to DNA and
dctp . SNAP output
|
1lws
|
hydrolase-DNA |
X-ray (3.5 Å) |
Moure CM, Gimble FS, Quiocho FA |
(2002) "Crystal
structure of the intein homing endonuclease PI-SceI
bound to its recognition sequence."
Nat.Struct.Biol., 9, 764-770.
doi: 10.1038/nsb840.
|
Crystal structure of the intein homing endonuclease
pi-scei bound to its recognition sequence . SNAP output
|
1lwt
|
hydrolase-DNA |
X-ray (3.2 Å) |
Moure CM, Gimble FS, Quiocho FA |
(2002) "Crystal
structure of the intein homing endonuclease PI-SceI
bound to its recognition sequence."
Nat.Struct.Biol., 9, 764-770.
doi: 10.1038/nsb840.
|
Crystal structure of the intein homing endonuclease
pi-scei bound to its substrate DNA (ca2+ free) .
SNAP output
|
1lwv
|
hydrolase-DNA |
X-ray (2.3 Å) |
Fromme JC, Bruner SD, Yang W, Karplus M, Verdine
GL |
(2003) "Product-Assisted
Catalysis in Base Excision DNA Repair."
Nat.Struct.Biol., 10,
204-211. doi: 10.1038/nsb902.
|
Borohydride-trapped hogg1 intermediate structure
co-crystallized with 8-aminoguanine . SNAP output
|
1lww
|
hydrolase-DNA |
X-ray (2.1 Å) |
Fromme JC, Bruner SD, Yang W, Karplus M, Verdine
GL |
(2003) "Product-Assisted
Catalysis in Base Excision DNA Repair."
Nat.Struct.Biol., 10,
204-211. doi: 10.1038/nsb902.
|
Borohydride-trapped hogg1 intermediate structure
co-crystallized with 8-bromoguanine . SNAP output
|
1lwy
|
hydrolase-DNA |
X-ray (2.01 Å) |
Fromme JC, Bruner SD, Yang W, Karplus M, Verdine
GL |
(2003) "Product-Assisted
Catalysis in Base Excision DNA Repair."
Nat.Struct.Biol., 10,
204-211. doi: 10.1038/nsb902.
|
Hogg1 borohydride-trapped intermediate without
8-oxoguanine . SNAP
output
|
1m07
|
hydrolase-DNA |
X-ray (1.8 Å) |
Leu Y-J, Chern S-S, Wang S-C, Hsiao Y-Y, Amiraslanov
I, Liaw Y-C, Liao Y-D |
(2003) "Residues
involved in the catalysis, base specificity, and
cytotoxicity of ribonuclease from Rana catesbeiana
based upon mutagenesis and X-ray crystallography."
J.Biol.Chem., 278, 7300-7309.
doi: 10.1074/jbc.M206701200.
|
Residues involved in the catalysis and base specificity
of cytotoxic ribonuclease from bullfrog (rana
catesbeiana) . SNAP
output
|
1m0e
|
transferase-DNA |
X-ray (2.5 Å) |
Zhou L, Cheng X, Connolly BA, Dickman MJ, Hurd PJ,
Hornby DP |
(2002) "ZEBULARINE:
A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALENT
COMPLEX WITH DNA METHYLTRANSFERASES."
J.MOL.BIOL., 321, 591-599.
doi: 10.1016/S0022-2836(02)00676-9.
|
Zebularine: a novel DNA methylation inhibitor that
forms a covalent complex with DNA methyltransferase .
SNAP output
|
1m18
|
structural protein-DNA |
X-ray (2.45 Å) |
Suto RK, Edayathumangalam RS, White CL, Melander C,
Gottesfeld JM, Dervan PB, Luger K |
(2003) "Crystal
Structures of Nucleosome Core Particles in Complex with
Minor Groove DNA-binding Ligands."
J.Mol.Biol., 326, 371-380.
doi: 10.1016/S0022-2836(02)01407-9.
|
Ligand binding alters the structure and dynamics of
nucleosomal DNA . SNAP
output
|
1m19
|
structural protein-DNA |
X-ray (2.3 Å) |
Suto RK, Edayathumangalam RS, White CL, Melander C,
Gottesfeld JM, Dervan PB, Luger K |
(2003) "Crystal
Structures of Nucleosome Core Particles in Complex with
Minor Groove DNA-binding Ligands."
J.Mol.Biol., 326, 371-380.
doi: 10.1016/S0022-2836(02)01407-9.
|
Ligand binding alters the structure and dynamics of
nucleosomal DNA . SNAP
output
|
1m1a
|
structural protein-DNA |
X-ray (2.65 Å) |
Suto RK, Edayathumangalam RS, White CL, Melander C,
Gottesfeld JM, Dervan PB, Luger K |
(2003) "Crystal
Structures of Nucleosome Core Particles in Complex with
Minor Groove DNA-binding Ligands."
J.MOL.BIOL., 326, 371-380.
doi: 10.1016/S0022-2836(02)01407-9.
|
Ligand binding alters the structure and dynamics of
nucleosomal DNA . SNAP
output
|
1m3h
|
hydrolase-DNA |
X-ray (2.05 Å) |
Chung SJ, Verdine GL |
(2004) "Structures
of End Products Resulting from Lesion Processing by a
DNA Glycosylase/Lyase." Chem.Biol.,
11, 1643-1649. doi: 10.1016/j.chembiol.2004.09.014.
|
Crystal structure of hogg1 d268e mutant with product
oligonucleotide . SNAP
output
|
1m3q
|
hydrolase-DNA |
X-ray (1.9 Å) |
Chung SJ, Verdine GL |
(2004) "Structures
of End Products Resulting from Lesion Processing by a
DNA Glycosylase/Lyase." Chem.Biol.,
11, 1643-1649. doi: 10.1016/j.chembiol.2004.09.014.
|
Crystal structure of hogg1 d268e mutant with
base-excised DNA and 8-aminoguanine . SNAP output
|
1m5r
|
transferase-DNA |
X-ray (1.8 Å) |
Lariviere L, Morera S |
(2002) "A
Base-flipping mechanism for the T4 phage
beta-glucosyltransferase and identification of a
transition state analog." J.Mol.Biol.,
324, 483-489. doi: 10.1016/S0022-2836(02)01091-4.
|
Ternary complex of t4 phage bgt with udp and a 13 mer
DNA duplex . SNAP
output
|
1m5x
|
hydrolase-DNA |
X-ray (2.25 Å) |
Chevalier B, Turmel M, Lemieux C, Monnat RJ, Stoddard
BL |
(2003) "Flexible
DNA Target Site Recognition by Divergent Homing
Endonuclease Isoschizomers I-CreI and I-MsoI."
J.Mol.Biol., 329, 253-269.
doi: 10.1016/S0022-2836(03)00447-9.
|
Crystal structure of the homing endonuclease i-msoi
bound to its DNA substrate . SNAP output
|
1m6x
|
ligase, lyase-DNA |
X-ray (2.8 Å) |
Conway AB, Chen Y, Rice PA |
(2003) "Structural
Plasticity of the Flp-Holliday Junction Complex."
J.Mol.Biol., 326, 425-434.
doi: 10.1016/S0022-2836(02)01370-0.
|
Flpe-holliday junction complex . SNAP output
|
1ma7
|
hydrolase, ligase-DNA |
X-ray (2.3 Å) |
Martin SS, Chu VC, Baldwin EP |
(2003) "Modulation
of the active complex assembly and turnover rate by
protein-DNA interactions in Cre-LoxP
recombination." Biochemistry,
42, 6814-6826. doi: 10.1021/bi0272306.
|
Crystal structure of cre site-specific recombinase
complexed with a mutant DNA substrate, loxp-a8-t27 .
SNAP output
|
1mdm
|
transcription-DNA |
X-ray (2.8 Å) |
Garvie CW, Pufall MA, Graves BJ, Wolberger C |
(2002) "STRUCTURAL
ANALYSIS OF THE AUTOINHIBITION OF ETS-1 AND ITS ROLE IN
PROTEIN PARTNERSHIPS." J.Biol.Chem.,
277, 45529-45536. doi: 10.1074/jbc.M206327200.
|
Inhibited fragment of ets-1 and paired domain of pax5
bound to DNA . SNAP
output
|
1mdy
|
transcription-DNA |
X-ray (2.8 Å) |
Ma PC, Rould MA, Weintraub H, Pabo CO |
(1994) "Crystal
structure of MyoD bHLH domain-DNA complex: perspectives
on DNA recognition and implications for transcriptional
activation." Cell(Cambridge,Mass.),
77, 451-459. doi: 10.1016/0092-8674(94)90159-7.
|
Crystal structure of myod bhlh domain bound to DNA:
perspectives on DNA recognition and implications for
transcriptional activation . SNAP output
|
1mey
|
transferase-DNA |
X-ray (2.2 Å) |
Kim CA, Berg JM |
(1996) "A 2.2 A
Resolution Crystal Structure of a Designed Zinc Finger
Protein Bound to DNA." Nat.Struct.Biol.,
3, 940-945. doi: 10.1038/nsb1196-940.
|
Crystal structure of a designed zinc finger protein
bound to DNA . SNAP
output
|
1mhd
|
complex (transcription activator-DNA) |
X-ray (2.8 Å) |
Shi Y, Wang YF, Jayaraman L, Yang H, Massague J,
Pavletich NP |
(1998) "Crystal
structure of a Smad MH1 domain bound to DNA: insights
on DNA binding in TGF-beta signaling."
Cell(Cambridge,Mass.), 94,
585-594. doi: 10.1016/S0092-8674(00)81600-1.
|
Crystal structure of a smad mh1 domain bound to DNA .
SNAP output
|
1mht
|
transferase-DNA |
X-ray (2.6 Å) |
Klimasauskas S, Kumar S, Roberts RJ, Cheng X |
(1994) "HhaI
methyltransferase flips its target base out of the DNA
helix." Cell(Cambridge,Mass.),
76, 357-369. doi: 10.1016/0092-8674(94)90342-5.
|
Covalent ternary structure of hhai methyltransferase,
DNA and s-adenosyl-l-homocysteine . SNAP output
|
1mj1
|
ribosome |
cryo-EM (13.0 Å) |
Stark H, Rodnina MV, Wieden H-J, Zemlin F,
Wintermeyer W, van Heel M |
(2002) "Ribosome
Interactions of Aminoacyl-tRNA and Elongation Factor TU
in the Codon Recognition Complex."
Nat.Struct.Biol., 9, 849-854.
|
Fitting the ternary complex of ef-tu-trna-gtp and
ribosomal proteins into a 13 a cryo-EM map of the coli
70s ribosome . SNAP
output
|
1mj2
|
transcription-DNA |
X-ray (2.4 Å) |
Garvie CW, Phillips SE |
(2000) "Direct
and indirect readout in mutant Met repressor-operator
complexes." Structure Fold.Des.,
8, 905-914. doi: 10.1016/S0969-2126(00)00182-9.
|
Methionine repressor mutant (q44k) plus corepressor
(s-adenosyl methionine) complexed to a consensus
operator sequence . SNAP
output
|
1mje
|
gene regulation-antitumor protein-DNA |
X-ray (3.5 Å) |
Yang H, Jeffrey PD, Miller J, Kinnucan E, Sun Y,
Thoma NH, Zheng N, Chen PL, Lee WH, Pavletich NP |
(2002) "BRCA2
function in DNA binding and recombination from a
BRCA2-DSS1-ssDNA structure." Science,
297, 1837-1848. doi: 10.1126/science.297.5588.1837.
|
Structure of a brca2-dss1-ssDNA complex . SNAP output
|
1mjm
|
transcription-DNA |
X-ray (2.2 Å) |
Garvie CW, Phillips SE |
(2000) "Direct
and indirect readout in mutant Met repressor-operator
complexes." Structure Fold.Des.,
8, 905-914. doi: 10.1016/S0969-2126(00)00182-9.
|
Methionine aporepressor mutant (q44k) complexed to half
of the consensus operator sequence . SNAP output
|
1mjo
|
transcription-DNA |
X-ray (2.1 Å) |
Garvie CW, Phillips SE |
(2000) "Direct
and indirect readout in mutant Met repressor-operator
complexes." Structure Fold.Des.,
8, 905-914. doi: 10.1016/S0969-2126(00)00182-9.
|
Methionine holorepressor mutant (q44k) plus corepressor
(s-adenosyl methionine) complexed to the minimal met
consensus operator with the central ta step mutated to
at . SNAP output
|
1mjp
|
transcription-DNA |
X-ray (3.4 Å) |
Garvie CW, Phillips SE |
(2000) "Direct
and indirect readout in mutant Met repressor-operator
complexes." Structure Fold.Des.,
8, 905-914. doi: 10.1016/S0969-2126(00)00182-9.
|
Methionine aporepressor mutant (q44k) complexed to the
minimal met consensus operator . SNAP output
|
1mjq
|
transcription-DNA |
X-ray (2.4 Å) |
Garvie CW, Phillips SE |
(2000) "Direct
and indirect readout in mutant Met repressor-operator
complexes." Structure Fold.Des.,
8, 905-914. doi: 10.1016/S0969-2126(00)00182-9.
|
Methionine repressor mutant (q44k) plus corepressor
(s-adenosyl methionine) complexed to an altered met
consensus operator sequence . SNAP output
|
1mm8
|
transcription-DNA |
X-ray (2.8 Å) |
Steiniger-White M, Bhasin A, Lovell S, Rayment I,
Reznikoff WS |
(2002) "Evidence
for "unseen" Transposase--DNA contacts."
J.Mol.Biol., 322, 971-982.
doi: 10.1016/S0022-2836(02)00877-X.
|
Crystal structure of tn5 transposase complexed with me
DNA . SNAP output
|
1mnm
|
transcription-DNA |
X-ray (2.25 Å) |
Tan S, Richmond TJ |
(1998) "Crystal
structure of the yeast MATalpha2/MCM1/DNA ternary
complex." Nature, 391,
660-666. doi: 10.1038/35563.
|
Yeast matalpha2-mcm1-DNA ternary transcription complex
crystal structure . SNAP
output
|
1mnn
|
transcription-DNA |
X-ray (1.4 Å) |
Lamoureux JS, Stuart D, Tsang R, Wu C, Glover JN |
(2002) "Structure
of the sporulation-specific transcription factor Ndt80
bound to DNA." Embo J.,
21, 5721-5732. doi: 10.1093/emboj/cdf572.
|
Structure of the sporulation specific transcription
factor ndt80 bound to DNA . SNAP output
|
1mnv
|
DNA-antibiotic |
X-ray (2.6 Å) |
Hou M-H, Robinson H, Gao Y-G, Wang AH-J |
(2002) "Crystal
Structure of Actinomycin D Bound to the Ctg Triplet
Repeat Sequences Linked to Neurological Diseases."
Nucleic Acids Res., 30, 4910.
doi: 10.1093/NAR/GKF619.
|
Actinomycin d binding to atgctgcat . SNAP output
|
1mow
|
hydrolase-DNA |
X-ray (2.4 Å) |
Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat
Jr RJ, Stoddard BL |
(2002) "Design,
Activity and Structure of a Highly Specific Artificial
Endonuclease." Mol.Cell,
10, 895-905. doi: 10.1016/S1097-2765(02)00690-1.
|
E-drei . SNAP output
|
1mq2
|
transferase-DNA |
X-ray (3.1 Å) |
Krahn JM, Beard WA, Miller H, Grollman AP, Wilson
SH |
(2003) "Structure
of DNA Polymerase beta with the Mutagenic DNA Lesion
8-oxodeoxyguanine Reveals Structural Insights into its
Coding Potential." Structure,
11, 121-127. doi: 10.1016/S0969-2126(02)00930-9.
|
Human DNA polymerase beta complexed with gapped DNA
containing an 8-oxo-7,8-dihydro-guanine and damp .
SNAP output
|
1mq3
|
transferase-DNA |
X-ray (2.8 Å) |
Krahn JM, Beard WA, Miller H, Grollman AP, Wilson
SH |
(2003) "Structure
of DNA Polymerase beta with the Mutagenic DNA Lesion
8-oxodeoxyguanine Reveals Structural Insights into its
Coding Potential." Structure,
11, 121-127. doi: 10.1016/S0969-2126(02)00930-9.
|
Human DNA polymerase beta complexed with gapped DNA
containing an 8-oxo-7,8-dihydro-guanine template paired
with dctp . SNAP
output
|
1mse
|
DNA binding protein-DNA |
NMR |
Ogata K, Morikawa S, Nakamura H, Sekikawa A, Inoue T,
Kanai H, Sarai A, Ishii S, Nishimura Y |
(1994) "Solution
structure of a specific DNA complex of the Myb
DNA-binding domain with cooperative recognition
helices." Cell(Cambridge,Mass.),
79, 639-648. doi: 10.1016/0092-8674(94)90549-5.
|
Solution structure of a specific DNA complex of the myb
DNA-binding domain with cooperative recognition helices
. SNAP output
|
1msf
|
DNA binding protein-DNA |
NMR |
Ogata K, Morikawa S, Nakamura H, Sekikawa A, Inoue T,
Kanai H, Sarai A, Ishii S, Nishimura Y |
(1994) "Solution
structure of a specific DNA complex of the Myb
DNA-binding domain with cooperative recognition
helices." Cell(Cambridge,Mass.),
79, 639-648. doi: 10.1016/0092-8674(94)90549-5.
|
Solution structure of a specific DNA complex of the myb
DNA-binding domain with cooperative recognition helices
. SNAP output
|
1msw
|
transcription-DNA-RNA |
X-ray (2.1 Å) |
Yin YW, Steitz TA |
(2002) "Structural
Basis for the Transition from Initiation to Elongation
Transcription in T7 RNA Polymerase."
Science, 298, 1387-1395. doi:
10.1126/science.1077464.
|
Structural basis for the transition from initiation to
elongation transcription in t7 RNA polymerase .
SNAP output
|
1mtl
|
hydrolase-DNA |
X-ray (2.8 Å) |
Barrett TE, Savva R, Barlow T, Brown T, Jiricny J,
Pearl LH |
(1998) "Structure
of a DNA base-excision product resembling a cisplatin
inter-strand adduct." Nat.Struct.Biol.,
5, 697-701. doi: 10.1038/1394.
|
Non-productive mug-DNA complex . SNAP output
|
1muh
|
transcription-DNA |
X-ray (2.3 Å) |
Davies DR, Goryshin IY, Reznikoff WS, Rayment I |
(2000) "Three-dimensional
structure of the Tn5 synaptic complex transposition
intermediate." Science,
289, 77-85. doi: 10.1126/science.289.5476.77.
|
Crystal structure of tn5 transposase complexed with
transposon end DNA . SNAP output
|
1mus
|
transcription-DNA |
X-ray (1.9 Å) |
Steiniger-White M, Rayment I, Reznikoff WS |
(2004) "Structure/function
insights into Tn5 transposition."
Curr.Opin.Struct.Biol., 14,
50-57. doi: 10.1016/j.sbi.2004.01.008.
|
Crystal structure of tn5 transposase complexed with
resolved outside end DNA . SNAP output
|
1mvm
|
virus-DNA |
X-ray (3.5 Å) |
Llamas-Saiz AL, Agbandje-McKenna M, Wikoff WR,
Bratton J, Tattersall P, Rossmann MG |
(1997) "Structure
determination of minute virus of mice." Acta
Crystallogr.,Sect.D, 53, 93-102.
doi: 10.1107/S0907444996010566.
|
Mvm(strain i), complex(viral coat-DNA), vp2, ph=7.5,
t=4 degrees c . SNAP
output
|
1mw8
|
isomerase |
X-ray (1.9 Å) |
Perry K, Mondragon A |
(2003) "Structure
of a Complex between E. coli DNA Topoisomerase I and
Single-Stranded DNA." Structure,
11, 1349-1358. doi: 10.1016/j.str.2003.09.013.
|
Crystal structure of a complex between h365r mutant of
67 kda n-terminal fragment of e. coli DNA topoisomerase
i and 5'-acttcgggatg-3' . SNAP output
|
1mwi
|
hydrolase-DNA |
X-ray (2.35 Å) |
Barrett TE, Savva R, Panayotou G, Barlow T, Brown T,
Jiricny J, Pearl LH |
(1998) "Crystal
structure of a G:T/U mismatch-specific DNA glycosylase:
mismatch recognition by complementary-strand
interactions." Cell(Cambridge,Mass.),
92, 117-129. doi: 10.1016/S0092-8674(00)80904-6.
|
Crystal structure of a mug-DNA product complex .
SNAP output
|
1mwj
|
hydrolase-DNA |
X-ray (2.85 Å) |
Barrett TE, Scharer O, Savva R, Brown T, Jiricny J,
Verdine GL, Pearl LH |
(1999) "Crystal
Structure of a thwarted mismatch glycosylase DNA repair
complex." Embo J., 18,
6599-6609. doi: 10.1093/emboj/18.23.6599.
|
Crystal structure of a mug-DNA pseudo substrate complex
. SNAP output
|
1n39
|
hydrolase, lyase-DNA |
X-ray (2.2 Å) |
Norman DP, Chung SJ, Verdine GL |
(2003) "Structural
and biochemical exploration of a critical amino acid in
human 8-oxoguanine glycosylase."
Biochemistry, 42, 1564-1572.
doi: 10.1021/bi026823d.
|
Structural and biochemical exploration of a critical
amino acid in human 8-oxoguanine glycosylase . SNAP output
|
1n3a
|
hydrolase, lyase-DNA |
X-ray (2.2 Å) |
Norman DP, Chung SJ, Verdine GL |
(2003) "Structural
and biochemical exploration of a critical amino acid in
human 8-oxoguanine glycosylase."
Biochemistry, 42, 1564-1572.
doi: 10.1021/bi026823d.
|
Structural and biochemical exploration of a critical
amino acid in human 8-oxoguanine glycosylase . SNAP output
|
1n3c
|
hydrolase, lyase-DNA |
X-ray (2.7 Å) |
Norman DP, Chung SJ, Verdine GL |
(2003) "Structural
and biochemical exploration of a critical amino acid in
human 8-oxoguanine glycosylase."
Biochemistry, 42, 1564-1572.
doi: 10.1021/bi026823d.
|
Structural and biochemical exploration of a critical
amino acid in human 8-oxoguanine glycosylase . SNAP output
|
1n3e
|
hydrolase-DNA |
X-ray (2.5 Å) |
Chevalier B, Turmel M, Lemieux C, Monnat RJ, Stoddard
BL |
(2003) "Flexible
DNA Target Site Recognition by Divergent Homing
Endonuclease Isoschizomers I-CreI and I-MsoI."
J.Mol.Biol., 329, 253-269.
doi: 10.1016/S0022-2836(03)00447-9.
|
Crystal structure of i-crei bound to a palindromic DNA
sequence i (palindrome of left side of wildtype DNA
target sequence) . SNAP
output
|
1n3f
|
hydrolase-DNA |
X-ray (2.0 Å) |
Chevalier B, Turmel M, Lemieux C, Monnat RJ, Stoddard
BL |
(2003) "Flexible
DNA Target Site Recognition by Divergent Homing
Endonuclease Isoschizomers I-CreI and I-MsoI."
J.Mol.Biol., 329, 253-269.
doi: 10.1016/S0022-2836(03)00447-9.
|
Crystal structure of i-crei bound to a palindromic DNA
sequence ii (palindrome of right side of wildtype DNA
target sequence) . SNAP
output
|
1n48
|
transferase-DNA |
X-ray (2.2 Å) |
Ling H, Boudsocq F, Woodgate R, Yang W |
"A Y-family polymerase complexed with abasic lesions:
catching DNA with a loaded nucleoside triphosphate." |
Y-family DNA polymerase dpo4 in complex with DNA
containing abasic lesion . SNAP output
|
1n56
|
transferase-DNA |
X-ray (2.4 Å) |
Ling H, Boudsocq F, Woodgate R, Yang W |
(2004) "Snapshots
of replication through an abasic lesion; structural
basis for base substitutions and frameshifts."
Mol.Cell, 13, 751-762. doi:
10.1016/s1097-2765(04)00101-7.
|
Y-family DNA polymerase dpo4 in complex with DNA
containing abasic lesion . SNAP output
|
1n5y
|
transferase-immune system-DNA |
X-ray (3.1 Å) |
Sarafianos SG, Clark Jr AD, Das K, Tuske S, Birktoft
JJ, Ilankumaran P, Ramesha AR, Sayer JM, Jerina DM, Boyer
PL, Hughes SH, Arnold E |
(2002) "Structure
of HIV-1 Reverse Transcriptase with Pre-Translocation
and Post-Translocation AZTMP-Terminated DNA."
Embo J., 21, 6614-6624. doi:
10.1093/emboj/cdf637.
|
Hiv-1 reverse transcriptase crosslinked to
post-translocation aztmp-terminated DNA (complex p) .
SNAP output
|
1n6j
|
transcription-DNA |
X-ray (2.2 Å) |
Han A, Pan F, Stroud JC, Youn HD, Liu JO, Chen L |
(2003) "Sequence-specific
recruitment of transcriptional co-repressor Cabin1 by
myocyte enhancer factor-2." Nature,
422, 730-734. doi: 10.1038/nature01555.
|
Structural basis of sequence-specific recruitment of
histone deacetylases by myocyte enhancer factor-2 .
SNAP output
|
1n6q
|
transferase-immune system-DNA |
X-ray (3.0 Å) |
Sarafianos SG, Clark Jr AD, Das K, Tuske S, Birktoft
JJ, Ilankumaran I, Ramesha AR, Sayer JM, Jerina DM, Boyer
PL, Hughes SH, Arnold E |
(2002) "Structures
of HIV-1 Reverse Transcriptase with Pre- and
Post-translocation AZTMP-terminated DNA." Embo
J., 21, 6614-6624. doi: 10.1093/emboj/cdf637.
|
Hiv-1 reverse transcriptase crosslinked to
pre-translocation aztmp-terminated DNA (complex n) .
SNAP output
|
1nfk
|
transcription-DNA |
X-ray (2.3 Å) |
Ghosh G, van Duyne G, Ghosh S, Sigler PB |
(1995) "Structure
of NF-kappa B p50 homodimer bound to a kappa B
site." Nature, 373,
303-310. doi: 10.1038/373303a0.
|
Structure of the nuclear factor kappa-b (nf-kb) p50
homodimer . SNAP
output
|
1ng9
|
DNA binding protein |
X-ray (2.6 Å) |
Lamers MH, Winterwerp HHK, Sixma TK |
(2003) "The
alternating ATPase domains of MutS control DNA mismatch
repair." Embo J., 22,
746-756. doi: 10.1093/emboj/cdg064.
|
E.coli muts r697a: an atpase-asymmetry mutant .
SNAP output
|
1ngm
|
transcription-DNA |
X-ray (2.95 Å) |
Juo ZS, Kassavetis GA, Wang J, Geiduschek EP, Sigler
PB |
(2003) "Crystal
structure of a transcription factor IIIB core interface
ternary complex." Nature,
422, 534-539. doi: 10.1038/nature01534.
|
Crystal structure of a yeast brf1-tbp-DNA ternary
complex . SNAP
output
|
1nh2
|
transcription-DNA |
X-ray (1.9 Å) |
Bleichenbacher M, Tan S, Richmond TJ |
(2003) "Novel
interactions between the components of human and yeast
TFIIA/TBP/DNA complexes." J.Mol.Biol.,
332, 783-793. doi: 10.1016/S0022-2836(03)00887-8.
|
Crystal structure of a yeast tfiia-tbp-DNA complex .
SNAP output
|
1nh3
|
isomerase-DNA |
X-ray (3.1 Å) |
Chrencik JE, Burgin AB, Pommier Y, Stewart L, Redinbo
MR |
(2003) "Structural
Impact of the Leukemia Drug
1-beta-D-Arabinofuranosylcytosine (Ara-C) on the
Covalent Human Topoisomerase I-DNA Complex."
J.Biol.Chem., 278,
12461-12466. doi: 10.1074/jbc.M212930200.
|
Human topoisomerase i ara-c complex . SNAP output
|
1njw
|
transferase-DNA |
X-ray (1.9 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Guanine-thymine mismatch at the polymerase active site
. SNAP output
|
1njx
|
transferase-DNA |
X-ray (1.65 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Thymine-guanine mismatch at the polymerase active site
. SNAP output
|
1njy
|
transferase-DNA |
X-ray (2.0 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Thymine-thymine mismatch at the polymerase active site
. SNAP output
|
1njz
|
transferase-DNA |
X-ray (2.0 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Cytosine-thymine mismatch at the polymerase active site
. SNAP output
|
1nk0
|
transferase-DNA |
X-ray (1.7 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Adenine-guanine mismatch at the polymerase active site
. SNAP output
|
1nk2
|
DNA binding protein-DNA |
NMR |
Gruschus JM, Tsao DH, Wang LH, Nirenberg M, Ferretti
JA |
(1997) "Interactions
of the vnd/NK-2 homeodomain with DNA by nuclear
magnetic resonance spectroscopy: basis of binding
specificity." Biochemistry,
36, 5372-5380. doi: 10.1021/bi9620060.
|
Vnd-nk-2 homeodomain-DNA complex, NMR, 20 structures .
SNAP output
|
1nk3
|
DNA binding protein-DNA |
NMR |
Gruschus JM, Tsao DH, Wang LH, Nirenberg M, Ferretti
JA |
(1997) "Interactions
of the vnd/NK-2 homeodomain with DNA by nuclear
magnetic resonance spectroscopy: basis of binding
specificity." Biochemistry,
36, 5372-5380. doi: 10.1021/bi9620060.
|
Vnd-nk-2 homeodomain-DNA complex, NMR, minimized
average structure . SNAP
output
|
1nk4
|
transferase-DNA |
X-ray (1.6 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Guanine-guanine mismatch at the polymerase active site
. SNAP output
|
1nk5
|
transferase-DNA |
X-ray (2.1 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Adenine-adenine mismatch at the polymerase active site
. SNAP output
|
1nk6
|
transferase-DNA |
X-ray (2.1 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Cytosine-cytosine mismatch at the polymerase active
site . SNAP output
|
1nk7
|
transferase-DNA |
X-ray (1.9 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Guanine-adenine mismatch at the polymerase active site
. SNAP output
|
1nk8
|
transferase-DNA |
X-ray (1.9 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
A bacillus DNA polymerase i product complex bound to a
guanine-thymine mismatch after a single round of primer
extension, following incorporation of dctp. . SNAP output
|
1nk9
|
transferase-DNA |
X-ray (1.9 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
A bacillus DNA polymerase i product complex bound to a
guanine-thymine mismatch after two rounds of primer
extension, following incorporation of dctp and dgtp. .
SNAP output
|
1nkb
|
transferase-DNA |
X-ray (2.0 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
A bacillus DNA polymerase i product complex bound to a
guanine-thymine mismatch after three rounds of primer
extension, following incorporation of dctp, dgtp, and
dttp. . SNAP output
|
1nkc
|
transferase-DNA |
X-ray (1.8 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
A bacillus DNA polymerase i product complex bound to a
guanine-thymine mismatch after five rounds of primer
extension, following incorporation of dctp, dgtp, dttp,
and datp. . SNAP
output
|
1nke
|
transferase-DNA |
X-ray (1.8 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
A bacillus DNA polymerase i product complex bound to a
cytosine-thymine mismatch after a single round of
primer extension, following incorporation of dctp. .
SNAP output
|
1nkp
|
transcription-DNA |
X-ray (1.8 Å) |
Nair SK, Burley SK |
(2003) "X-ray
structures of Myc-Max and Mad-Max recognizing DNA:
Molecular bases of regulation by proto-oncogenic
transcription factors."
Cell(Cambridge,Mass.), 112,
193-205. doi: 10.1016/S0092-8674(02)01284-9.
|
Crystal structure of myc-max recognizing DNA . SNAP output
|
1nlw
|
transcription-DNA |
X-ray (2.0 Å) |
Nair SK, Burley SK |
(2003) "X-ray
structures of Myc-Max and Mad-Max recognizing DNA:
Molecular bases of regulation by proto-oncogenic
transcription factors."
Cell(Cambridge,Mass.), 112,
193-205. doi: 10.1016/S0092-8674(02)01284-9.
|
Crystal structure of mad-max recognizing DNA . SNAP output
|
1nne
|
DNA binding protein-DNA |
X-ray (3.11 Å) |
Alani E, Lee JY, Schofield MJ, Kijas AW, Hsieh P,
Yang W |
(2003) "Crystal
structure and biochemical analysis of the
MutS-ADP-Beryllium Fluoride complex suggests a
conserved mechanism for ATP interactions in mismatch
repair." J.Biol.Chem.,
278, 16088-16094. doi: 10.1074/jbc.M213193200.
|
Crystal structure of the muts-adpbef3-DNA complex .
SNAP output
|
1nnj
|
hydrolase |
X-ray (1.9 Å) |
Pereira de Jesus K, Serre L, Zelwer C, Castaing
B |
(2005) "Structural
insights into abasic site for Fpg specific binding and
catalysis: comparative high-resolution crystallographic
studies of Fpg bound to various models of abasic site
analogues-containing DNA." Nucleic Acids
Res., 33, 5936-5944. doi:
10.1093/nar/gki879.
|
Crystal structure complex between the lactococcus
lactis fpg and an abasic site containing DNA . SNAP output
|
1nop
|
hydrolase-DNA |
X-ray (2.3 Å) |
Davies DR, Interthal H, Champoux JJ, Hol WGJ |
(2003) "Crystal
structure of a transition state mimic for Tdp1
assembled from vanadate, DNA, and a topoisomerase
I-derived peptide." Chem.Biol.,
10, 139-147. doi: 10.1016/S1074-5521(03)00021-8.
|
Crystal structure of human tyrosyl-DNA
phosphodiesterase (tdp1) in complex with vanadate, DNA
and a human topoisomerase i-derived peptide . SNAP output
|
1noy
|
transferase-DNA |
X-ray (2.2 Å) |
Wang J, Yu P, Lin TC, Konigsberg WH, Steitz TA |
(1996) "Crystal
structures of an NH2-terminal fragment of T4 DNA
polymerase and its complexes with single-stranded DNA
and with divalent metal ions."
Biochemistry, 35, 8110-8119.
doi: 10.1021/bi960178r.
|
DNA polymerase (e.c.2.7.7.7)-DNA complex . SNAP output
|
1nvp
|
transcription-DNA |
X-ray (2.1 Å) |
Bleichenbacher M, Tan S, Richmond TJ |
(2003) "Novel
interactions between the components of human and yeast
TFIIA/TBP/DNA complexes." J.Mol.Biol.,
332, 783-793. doi: 10.1016/S0022-2836(03)00887-8.
|
Human tfiia-tbp-DNA complex . SNAP output
|
1nwq
|
transcription-DNA |
X-ray (2.8 Å) |
Miller M, Shuman JD, Sebastian T, Dauter Z, Johnson
PF |
(2003) "Structural
Basis for DNA Recognition by the Basic Region Leucine
Zipper Transcription Factor CCAAT/enhancer Binding
Protein Alpha." J.Biol.Chem.,
278, 15178-15184. doi: 10.1074/jbc.M300417200.
|
Crystal structure of c-ebpalpha-DNA complex . SNAP output
|
1nzb
|
replication-DNA |
X-ray (3.1 Å) |
Ennifar E, Meyer JEW, Buchholz F, Stewart AF, Suck
D |
(2003) "Crystal
structure of a wild-type Cre recombinase-loxP synapse
reveals a novel spacer conformation suggesting an
alternative mechanism for DNA cleavage activation."
Nucleic Acids Res., 31,
5449-5460. doi: 10.1093/nar/gkg732.
|
Crystal structure of wild type cre recombinase-loxp
synapse . SNAP
output
|
1o3q
|
gene regulation-DNA |
X-ray (3.0 Å) |
Chen S, Vojtechovsky J, Parkinson GN, Ebright RH,
Berman HM |
(2001) "Indirect
Readout of DNA Sequence at the Primary-kink Site in the
CAP-DNA Complex: DNA Binding Specificity Based on
Energetics of DNA Kinking." J.Mol.Biol.,
314, 63-74. doi: 10.1006/jmbi.2001.5089.
|
Protein-DNA recognition and DNA deformation revealed in
crystal structures of cap-DNA complexes . SNAP output
|
1o3r
|
gene regulation-DNA |
X-ray (3.0 Å) |
Chen S, Vojtechovsky J, Parkinson GN, Ebright RH,
Berman HM |
(2001) "Indirect
Readout of DNA Sequence at the Primary-kink Site in the
CAP-DNA Complex: DNA Binding Specificity Based on
Energetics of DNA Kinking." J.Mol.Biol.,
314, 63-74. doi: 10.1006/jmbi.2001.5089.
|
Protein-DNA recognition and DNA deformation revealed in
crystal structures of cap-DNA complexes . SNAP output
|
1o3s
|
gene regulation-DNA |
X-ray (3.0 Å) |
Chen S, Gunasekera A, Zhang X, Kunkel TA, Ebright RH,
Berman HM |
(2001) "Indirect
Readout of DNA Sequence at the Primary-kink Site in the
CAP-DNA Complex: Alteration of DNA Binding Specificity
Through Alteration of DNA Kinking."
J.Mol.Biol., 314, 75-82. doi:
10.1006/jmbi.2001.5090.
|
Protein-DNA recognition and DNA deformation revealed in
crystal structures of cap-DNA complexes . SNAP output
|
1o3t
|
gene regulation-DNA |
X-ray (2.8 Å) |
Chen S, Vojtechovsky J, Parkinson GN, Ebright RH,
Berman HM |
(2001) "Indirect
Readout of DNA Sequence at the Primary-kink Site in the
CAP-DNA Complex: DNA Binding Specificity Based on
Energetics of DNA Kinking." J.Mol.Biol.,
314, 63-74. doi: 10.1006/jmbi.2001.5089.
|
Protein-DNA recognition and DNA deformation revealed in
crystal structures of cap-DNA complexes . SNAP output
|
1o4x
|
transcription-DNA |
NMR |
Williams DC, Cai M, Clore GM |
(2004) "Molecular
basis for synergistic transcriptional activation by
Oct1 and Sox2 revealed from the solution structure of
the 42-kDa Oct1.Sox2.Hoxb1-DNA ternary transcription
factor complex." J.Biol.Chem.,
279, 1449-1457. doi: 10.1074/jbc.M309790200.
|
Ternary complex of the DNA binding domains of the oct1
and sox2 transcription factors with a 19mer
oligonucleotide from the hoxb1 regulatory element .
SNAP output
|
1oct
|
transcription-DNA |
X-ray (3.0 Å) |
Klemm JD, Rould MA, Aurora R, Herr W, Pabo CO |
(1994) "Crystal
structure of the Oct-1 POU domain bound to an octamer
site: DNA recognition with tethered DNA-binding
modules." Cell(Cambridge,Mass.),
77, 21-32. doi: 10.1016/0092-8674(94)90231-3.
|
Crystal structure of the oct-1 pou domain bound to an
octamer site: DNA recognition with tethered DNA-binding
modules . SNAP
output
|
1odg
|
hydrolase |
X-ray (2.8 Å) |
Bunting KA, Roe SM, Headley A, Brown T, Savva R,
Pearl LH |
(2003) "Crystal
Structure of the Escherichia Coli Dcm Very-Short-Patch
DNA Repair Endonuclease Bound to its Reaction
Product-Site in a DNA Superhelix." Nucleic
Acids Res., 31, 1633. doi:
10.1093/NAR/GKG273.
|
Very-short-patch DNA repair endonuclease bound to its
reaction product site . SNAP output
|
1odh
|
transcription factor-DNA |
X-ray (2.85 Å) |
Cohen SX, Moulin M, Hashemolhosseini S, Kilian K,
Wegner M, Muller CW |
(2003) "Crystal
Structure of the Gcm Domain-DNA Complex: A DNA-Binding
Domain with a Novel Fold and Mode of Target Site
Recognition." Embo J.,
22, 1835. doi: 10.1093/EMBOJ/CDG182.
|
Structure of the gcm domain bound to DNA . SNAP output
|
1oe4
|
hydrolase-DNA |
X-ray (2.0 Å) |
Wibley JEA, Waters TR, Haushalter K, Verdine GL,
Pearl LH |
(2003) "Structure
and Specificity of the Vertebrate Anti-Mutator
Uracil-DNA Glycosylase Smug1." Mol.Cell,
11, 1647. doi: 10.1016/S1097-2765(03)00235-1.
|
Xenopus smug1, an anti-mutator uracil-DNA glycosylase .
SNAP output
|
1oe5
|
hydrolase-DNA |
X-ray (2.3 Å) |
Wibley JEA, Waters TR, Haushalter K, Verdine GL,
Pearl LH |
(2003) "Structure
and Specificity of the Vertebrate Anti-Mutator
Uracil-DNA Glycosylase Smug1." Mol.Cell,
11, 1647. doi: 10.1016/S1097-2765(03)00235-1.
|
Xenopus smug1, an anti-mutator uracil-DNA glycosylase .
SNAP output
|
1oe6
|
hydrolase-DNA |
X-ray (2.65 Å) |
Wibley JEA, Waters TR, Haushalter K, Verdine GL,
Pearl LH |
(2003) "Structure
and Specificity of the Vertebrate Anti-Mutator
Uracil-DNA Glycosylase Smug1." Mol.Cell,
11, 1647. doi: 10.1016/S1097-2765(03)00235-1.
|
Xenopus smug1, an anti-mutator uracil-DNA glycosylase .
SNAP output
|
1oh5
|
DNA binding |
X-ray (2.9 Å) |
Natrajan G, Lamers MH, Enzlin JH, Winterwerp HHK,
Perrakis A, Sixma TK |
(2003) "Structures
of E. Coli DNA Mismatch Repair Enzyme Muts in Complex
with Different Mismatches: A Common Recognition Mode
for Diverse Substrates." Nucleic Acids
Res., 31, 4814. doi: 10.1093/NAR/GKG677.
|
The crystal structure of e. coli muts binding to DNA
with a c:a mismatch . SNAP output
|
1oh6
|
DNA binding |
X-ray (2.4 Å) |
Natrajan G, Lamers MH, Enzlin JH, Winterwerp HHK,
Perrakis A, Sixma TK |
(2003) "Structures
of E. Coli DNA Mismatch Repair Enzyme Muts in Complex
with Different Mismatches: A Common Recognition Mode
for Diverse Substrates." Nucleic Acids
Res., 31, 4814. doi: 10.1093/NAR/GKG677.
|
The crystal structure of e. coli muts binding to DNA
with an a:a mismatch . SNAP output
|
1oh7
|
DNA binding |
X-ray (2.5 Å) |
Natrajan G, Lamers MH, Enzlin JH, Winterwerp HHK,
Perrakis A, Sixma TK |
(2003) "Structures
of E. Coli DNA Mismatch Repair Enzyme Muts in Complex
with Different Mismatches: A Common Recognition Mode
for Diverse Substrates." Nucleic Acids
Res., 31, 4814. doi: 10.1093/NAR/GKG677.
|
The crystal structure of e. coli muts binding to DNA
with a g:g mismatch . SNAP output
|
1oh8
|
DNA binding |
X-ray (2.9 Å) |
Natrajan G, Lamers MH, Enzlin JH, Winterwerp HHK,
Perrakis A, Sixma TK |
(2003) "Structures
of E. Coli DNA Mismatch Repair Enzyme Muts in Complex
with Different Mismatches: A Common Recognition Mode
for Diverse Substrates." Nucleic Acids
Res., 31, 4814. doi: 10.1093/NAR/GKG677.
|
The crystal structure of e. coli muts binding to DNA
with an unpaired thymidine . SNAP output
|
1oj8
|
hydrolase |
X-ray (1.7 Å) |
Tsai C-J, Liu J-H, Liao Y-D, Chen L-Y, Cheng P-T, Sun
Y-J |
"Retro and Novel Binding Modes in Cytotoxic
Ribonucleases from Rana Catesbeiana of Two Crystal
Structures Complexed with (2',5'Cpg) and
D(Apcpgpa)." |
Novel and retro binding modes in cytotoxic
ribonucleases from rana catesbeiana of two crystal
structures complexed with d(apcpgpa) and (2',5'cpg) .
SNAP output
|
1omh
|
transferase-DNA |
X-ray (1.95 Å) |
Guasch A, Lucas M, Moncalian G, Cabezas M,
Perez-Luque R, Gomis-Ruth FX, de la Cruz F, Coll M |
(2003) "Recognition
and processing of the origin of transfer DNA by
conjugative relaxase TrwC."
Nat.Struct.Biol., 10,
1002-1010. doi: 10.1038/nsb1017.
|
Conjugative relaxase trwc in complex with orit DNA.
metal-free structure. . SNAP output
|
1orn
|
hydrolase-DNA |
X-ray (1.7 Å) |
Fromme JC, Verdine GL |
(2003) "Structure
of a Trapped Endonuclease III-DNA Covalent
Intermediate." Embo J.,
22, 3461-3471. doi: 10.1093/emboj/cdg311.
|
Structure of a trapped endonuclease iii-DNA covalent
intermediate: estranged-guanine complex . SNAP output
|
1orp
|
hydrolase-DNA |
X-ray (2.2 Å) |
Fromme JC, Verdine GL |
(2003) "Structure
of a Trapped Endonuclease III-DNA Covalent
Intermediate." Embo J.,
22, 3461-3471. doi: 10.1093/emboj/cdg311.
|
Structure of a trapped endonuclease iii-DNA covalent
intermediate: estranged-adenine complex . SNAP output
|
1osb
|
transferase-DNA |
X-ray (2.65 Å) |
Guasch A, Lucas M, Moncalian G, Cabezas M,
Perez-Luque R, Gomis-Ruth FX, de la Cruz F, Coll M |
(2003) "Recognition
and processing of the origin of transfer DNA by
conjugative relaxase TrwC."
Nat.Struct.Biol., 10,
1002-1010. doi: 10.1038/nsb1017.
|
Conjugative relaxase trwc in complex with orit DNA.
metal-free structure. . SNAP output
|
1osl
|
transcription-DNA |
NMR |
Kalodimos CG, Biris N, Bonvin AM, Levandoski MM,
Guennuegues M, Boelens R, Kaptein R |
(2004) "Structure
and flexibility adaptation in nonspecific and specific
protein-DNA complexes." Science,
305, 386-389. doi: 10.1126/science.1097064.
|
Solution structure of a dimeric lactose DNA-binding
domain complexed to a nonspecific DNA sequence .
SNAP output
|
1otc
|
protein-DNA |
X-ray (2.8 Å) |
Horvath MP, Schweiker VL, Bevilacqua JM, Ruggles JA,
Schultz SC |
(1998) "Crystal
structure of the Oxytricha nova telomere end binding
protein complexed with single strand DNA."
Cell(Cambridge,Mass.), 95,
963-974. doi: 10.1016/S0092-8674(00)81720-1.
|
The o. nova telomere end binding protein complexed with
single strand DNA . SNAP
output
|
1oup
|
hydrolase-DNA |
X-ray (2.3 Å) |
Li C-L, Hor L-I, Chang Z-F, Tsai L-C, Yang W-Z, Yuan
HS |
(2003) "DNA
binding and cleavage by the periplasmic nuclease Vvn: a
novel structure with a known active site." Embo
J., 22, 4014-4025. doi: 10.1093/emboj/cdg377.
|
Crystal structure of the periplasmic endonuclease vvn
complexed with octamer double stranded DNA . SNAP output
|
1ouq
|
replication-DNA |
X-ray (3.2 Å) |
Ennifar E, Meyer JEW, Buchholz F, Stewart AF, Suck
D |
(2003) "Crystal
structure of a wild-type Cre recombinase-loxP synapse
reveals a novel spacer conformation suggesting an
alternative mechanism for DNA cleavage activation."
Nucleic Acids Res., 31,
5449-5460. doi: 10.1093/nar/gkg732.
|
Crystal structure of wild-type cre recombinase-loxp
synapse . SNAP
output
|
1ouz
|
transcription-DNA |
X-ray (2.41 Å) |
Lynch TW, Read EK, Mattis AN, Gardner JF, Rice
PA |
(2003) "Integration
Host Factor: putting a twist on protein-DNA
recognition." J.Mol.Biol.,
330, 493-502. doi: 10.1016/S0022-2836(03)00529-1.
|
Crystal structure of a mutant ihf (betae44a) complexed
with a variant h' site (t44a) . SNAP output
|
1ovf
|
DNA-antibiotic |
NMR |
Chin K-H, Chen F-M, Chou S-H |
(2003) "Solution
Structure of the Actd-5'-Ccgtt(3)Gtgg-3' Complex: Drug
Interaction with Tandem G.T Mismatches and Hairpin Loop
Backbone." Nucleic Acids Res.,
31, 2622. doi: 10.1093/NAR/GKG353.
|
NMR structure of actd-5'-ccgttttgtgg-3' complex .
SNAP output
|
1owf
|
transcription-DNA |
X-ray (1.95 Å) |
Lynch TW, Read EK, Mattis AN, Gardner JF, Rice
PA |
(2003) "Integration
Host Factor: putting a twist on protein-DNA
recognition." J.Mol.Biol.,
330, 493-502. doi: 10.1016/S0022-2836(03)00529-1.
|
Crystal structure of a mutant ihf (betae44a) complexed
with the native h' site . SNAP output
|
1owg
|
transcription-DNA |
X-ray (2.1 Å) |
Lynch TW, Read EK, Mattis AN, Gardner JF, Rice
PA |
(2003) "Integration
Host Factor: putting a twist on protein-DNA
recognition." J.Mol.Biol.,
330, 493-502. doi: 10.1016/S0022-2836(03)00529-1.
|
Crystal structure of wt ihf complexed with an altered
h' site (t44a) . SNAP
output
|
1owr
|
transcription-DNA |
X-ray (3.0 Å) |
Stroud JC, Chen L |
(2003) "Structure
of NFAT Bound to DNA as a Monomer."
J.Mol.Biol., 334, 1009-1022.
doi: 10.1016/j.jmb.2003.09.065.
|
Crystal structure of human nfat1 bound monomerically to
DNA . SNAP output
|
1ozj
|
transcription-DNA |
X-ray (2.4 Å) |
Chai J, Wu J-W, Yan N, Massague J, Pavletich NP, Shi
Y |
(2003) "Features
of a Smad3 MH1-DNA complex. Roles of water and zinc in
DNA binding." J.Biol.Chem.,
278, 20327-20331. doi: 10.1074/jbc.C300134200.
|
Crystal structure of smad3-mh1 bound to DNA at 2.4 Å
resolution . SNAP
output
|
1p34
|
structural protein-DNA |
X-ray (2.7 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
1p3a
|
structural protein-DNA |
X-ray (3.0 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
1p3b
|
structural protein-DNA |
X-ray (3.0 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
1p3f
|
structural protein-DNA |
X-ray (2.9 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
1p3g
|
structural protein-DNA |
X-ray (2.7 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
1p3i
|
structural protein-DNA |
X-ray (2.3 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
1p3k
|
structural protein-DNA |
X-ray (2.9 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
1p3l
|
structural protein-DNA |
X-ray (2.4 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
1p3m
|
structural protein-DNA |
X-ray (2.9 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
1p3o
|
structural protein-DNA |
X-ray (2.75 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
1p3p
|
structural protein-DNA |
X-ray (2.7 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
1p47
|
transcription-DNA |
X-ray (2.2 Å) |
Peisach E, Pabo CO |
(2003) "Constraints
for Zinc Finger Linker Design as Inferred from X-ray
Crystal Structure of Tandem Zif268-DNA Complexes."
J.Mol.Biol., 330, 1-7. doi:
10.1016/S0022-2836(03)00572-2.
|
Crystal structure of tandem zif268 molecules complexed
to DNA . SNAP output
|
1p4e
|
DNA binding protein-recombination-DNA |
X-ray (2.7 Å) |
Rice PA, Chen Y |
(2003) "The role
of the conserved Trp330 in Flp-mediated recombination.
Functional and structural analysis."
J.Biol.Chem., 278,
24800-24807. doi: 10.1074/jbc.M300853200.
|
Flpe w330f mutant-DNA holliday junction complex .
SNAP output
|
1p51
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Swinger KK, Lemberg KM, Zhang Y, Rice PA |
(2003) "Flexible
DNA bending in HU-DNA cocrystal structures."
Embo J., 22, 3749-3760. doi:
10.1093/emboj/cdg351.
|
Anabaena hu-DNA cocrystal structure (ahu6) . SNAP output
|
1p59
|
hydrolase-DNA |
X-ray (2.5 Å) |
Fromme JC, Verdine GL |
(2003) "Structure
of a Trapped Endonuclease III-DNA Covalent
Intermediate." Embo J.,
22, 3461-3471. doi: 10.1093/emboj/cdg311.
|
Structure of a non-covalent endonuclease iii-DNA
complex . SNAP
output
|
1p5w
|
virus-DNA |
X-ray (3.3 Å) |
Govindasamy L, Hueffer K, Parrish CR,
Agbandje-McKenna M |
(2003) "Structures
of host range-controlling regions of the capsids of
canine and feline parvoviruses and mutants."
J.Virol., 77, 12211-12221.
doi: 10.1128/JVI.77.22.12211-12221.2003.
|
The structures of host range controlling regions of the
capsids of canine and feline parvoviruses and mutants .
SNAP output
|
1p71
|
DNA binding protein-DNA |
X-ray (1.9 Å) |
Swinger KS, Lemberg KM, Zhang Y, Rice PA |
(2003) "Flexible
DNA bending in HU-DNA cocrystal structures."
Embo J., 22, 3749-3760. doi:
10.1093/emboj/cdg351.
|
Anabaena hu-DNA corcrystal structure (tr3) . SNAP output
|
1p78
|
DNA binding protein-DNA |
X-ray (2.25 Å) |
Swinger KS, Lemberg KM, Zhang Y, Rice PA |
(2003) "Flexible
DNA bending in HU-DNA cocrystal structures."
Embo J., 22, 3749-3760. doi:
10.1093/emboj/cdg351.
|
Anabaena hu-DNA cocrystal structure (ahu2) . SNAP output
|
1p7d
|
DNA binding protein-DNA |
X-ray (2.95 Å) |
Aihara H, Kwon HJ, Nunes-Duby SE, Landy A,
Ellenberger T |
(2003) "A
Conformational Switch Controls the DNA Cleavage
Activity of Lambda Integrase." Mol.Cell,
12, 187-198. doi: 10.1016/S1097-2765(03)00268-5.
|
Crystal structure of the lambda integrase (residues
75-356) bound to DNA . SNAP output
|
1p7h
|
transcription-DNA |
X-ray (2.6 Å) |
Giffin MJ, Stroud JC, Bates DL, von Koenig KD, Hardin
J, Chen L |
(2003) "Structure
of NFAT1 bound as a dimer to the HIV-1 LTR kappa B
element." Nat.Struct.Biol.,
10, 800-806. doi: 10.1038/nsb981.
|
Structure of nfat1 bound as a dimer to the hiv-1 ltr kb
element . SNAP
output
|
1p8k
|
hydrolase-DNA |
X-ray (2.6 Å) |
Bolduc JM, Spiegel PC, Chatterjee P, Brady KL,
Downing ME, Caprara MG, Waring RB, Stoddard BL |
(2003) "Structural
and biochemical analyses of DNA and RNA binding by a
bifunctional homing endonuclease and group I intron
splicing factor." Genes Dev.,
17, 2875-2888. doi: 10.1101/gad.1109003.
|
The structure and DNA recognition of a bifunctional
homing endonuclease and group i intron splicing factor
. SNAP output
|
1pa6
|
DNA binding protein-DNA |
X-ray (2.45 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
shuffling and ssDNA recognition in Oxytricha nova
telomere end-binding protein complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttgagg . SNAP
output
|
1par
|
transcription-DNA |
X-ray (2.6 Å) |
Raumann BE, Rould MA, Pabo CO, Sauer RT |
(1994) "DNA
recognition by beta-sheets in the Arc
repressor-operator crystal structure."
Nature, 367, 754-757. doi:
10.1038/367754a0.
|
DNA recognition by beta-sheets in the arc
repressor-operator crystal structure . SNAP output
|
1pdn
|
gene regulation-DNA |
X-ray (2.5 Å) |
Xu W, Rould MA, Jun S, Desplan C, Pabo CO |
(1995) "Crystal
structure of a paired domain-DNA complex at 2.5 A
resolution reveals structural basis for Pax
developmental mutations."
Cell(Cambridge,Mass.), 80,
639-650. doi: 10.1016/0092-8674(95)90518-9.
|
Crystal structure of a paired domain-DNA complex at 2.5
angstroms resolution reveals structural basis for pax
developmental mutations . SNAP output
|
1per
|
transcription-DNA |
X-ray (2.5 Å) |
Rodgers DW, Harrison SC |
(1993) "The
complex between phage 434 repressor DNA-binding domain
and operator site OR3: structural differences between
consensus and non-consensus half-sites."
Structure, 1, 227-240. doi:
10.1016/0969-2126(93)90012-6.
|
The complex between phage 434 repression DNA-binding
domain and operator site or3: structural differences
between consensus and non-consensus half-sites .
SNAP output
|
1pfe
|
DNA-antibiotic |
X-ray (1.1 Å) |
Cuesta-Seijo JA, Sheldrick GM |
(2005) "Structures
of Complexes between Echinomycin and Duplex DNA."
Acta Crystallogr.,Sect.D, 61,
442. doi: 10.1107/S090744490500137X.
|
Echinomycin-(gcgtacgc)2 complex . SNAP output
|
1pfi
|
virus |
fiber diffraction |
Liu DJ, Day LA |
(1994) "Pf1 virus
structure: helical coat protein and DNA with paraxial
phosphates." Science,
265, 671-674.
|
Pf1 virus structure: helical coat protein and DNA with
paraxial phosphates . SNAP output
|
1pgz
|
DNA binding protein-DNA |
X-ray (2.6 Å) |
Myers JC, Moore SA, Shamoo Y |
(2003) "Structure-based
incorporation of
6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine
into the human telomeric repeat DNA as a probe for UP1
binding and destabilization of G-tetrad
structures." J.Biol.Chem.,
278, 42300-42306. doi: 10.1074/jbc.M306147200.
|
Crystal structure of up1 complexed with
d(ttagggttag(6-mi)g); a human telomeric repeat
containing
6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine
(6-mi) . SNAP output
|
1ph1
|
DNA binding protein-DNA |
X-ray (2.51 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and Ssdna Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttggggt . SNAP
output
|
1ph2
|
DNA binding protein-DNA |
X-ray (3.1 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and ssDNA Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttg . SNAP
output
|
1ph3
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and ssDNA Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttggtg . SNAP
output
|
1ph4
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and ssDNA Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttggcg . SNAP
output
|
1ph5
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and ssDNA Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttg(3dr)gg . SNAP
output
|
1ph6
|
DNA binding protein-DNA |
X-ray (2.1 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and ssDNA Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttgtgg . SNAP
output
|
1ph7
|
DNA binding protein-DNA |
X-ray (2.9 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and ssDNA Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttgigg . SNAP
output
|
1ph8
|
DNA binding protein-DNA |
X-ray (2.36 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and Ssdna Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttgcgg . SNAP
output
|
1ph9
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and ssDNA Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttgagg . SNAP
output
|
1phj
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and ssDNA Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
gg(3dr)gttttgggg . SNAP
output
|
1pji
|
hydrolase-DNA |
X-ray (1.9 Å) |
Pereira de Jesus K, Serre L, Zelwer C, Castaing
B |
(2005) "Structural
insights into abasic site for Fpg specific binding and
catalysis: comparative high-resolution crystallographic
studies of Fpg bound to various models of abasic site
analogues-containing DNA." Nucleic Acids
Res., 33, 5936-5944. doi:
10.1093/nar/gki879.
|
Crystal structure of wild type lactococcus lactis fpg
complexed to a 1,3 propanediol containing DNA .
SNAP output
|
1pjj
|
hydrolase-DNA |
X-ray (1.9 Å) |
Pereira de Jesus K, Serre L, Zelwer C, Castaing
B |
(2005) "Structural
insights into abasic site for Fpg specific binding and
catalysis: comparative high-resolution crystallographic
studies of Fpg bound to various models of abasic site
analogues-containing DNA." Nucleic Acids
Res., 33, 5936-5944. doi:
10.1093/nar/gki879.
|
Complex between the lactococcus lactis fpg and an
abasic site containing DNA. . SNAP output
|
1pm5
|
hydrolase-DNA |
X-ray (1.95 Å) |
Pereira de Jesus K, Serre L, Zelwer C, Castaing
B |
(2005) "Structural
insights into abasic site for Fpg specific binding and
catalysis: comparative high-resolution crystallographic
studies of Fpg bound to various models of abasic site
analogues-containing DNA." Nucleic Acids
Res., 33, 5936-5944. doi:
10.1093/nar/gki879.
|
Crystal structure of wild type lactococcus lactis fpg
complexed to a tetrahydrofuran containing DNA .
SNAP output
|
1pnr
|
transcription-DNA |
X-ray (2.7 Å) |
Schumacher MA, Choi KY, Zalkin H, Brennan RG |
(1994) "Crystal
structure of LacI member, PurR, bound to DNA: minor
groove binding by alpha helices." Science,
266, 763-770.
|
Purine repressor-hypoxanthine-purf-operator complex .
SNAP output
|
1po6
|
RNA binding protein-DNA |
X-ray (2.1 Å) |
Myers JC, Moore SA, Shamoo Y |
(2003) "Structure-based
incorporation of
6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine
into the human telomeric repeat DNA as a probe for UP1
binding and destabilization of G-tetrad
structures." J.BIOL.CHEM.,
278, 42300-42306. doi: 10.1074/jbc.M306147200.
|
Crystal structure of up1 complexed with
d(tagg(6mi)ttaggg): a human telomeric repeat containing
6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine
(6mi) . SNAP output
|
1pp7
|
transcription-DNA |
X-ray (2.45 Å) |
Schumacher MA, Lau AOT, Johnson PJ |
(2003) "Structural
Basis of Core Promoter Recognition in a Primitive
Eukaryote." Cell(Cambridge,Mass.),
115, 413-424. doi: 10.1016/S0092-8674(03)00887-0.
|
Crystal structure of the t. vaginalis initiator binding
protein bound to the ferredoxin inr . SNAP output
|
1pp8
|
transcription-DNA |
X-ray (3.05 Å) |
Schumacher MA, Lau AOT, Johnson PJ |
(2003) "Structural
Basis of Core Promoter Recognition in a Primitive
Eukaryote." Cell(Cambridge,Mass.),
115, 413-424. doi: 10.1016/S0092-8674(03)00887-0.
|
Crystal structure of the t. vaginalis ibp39 initiator
binding domain (ibd) bound to the alpha-scs inr element
. SNAP output
|
1pt3
|
hydrolase-DNA |
X-ray (2.5 Å) |
Hsia KC, Chak KF, Liang PH, Cheng YS, Ku WY, Yuan
HS |
(2004) "DNA
binding and degradation by the HNH protein ColE7."
STRUCTURE, 12, 205-214. doi:
10.1016/S0969-2126(04)00006-1.
|
Crystal structures of nuclease-cole7 complexed with
octamer DNA . SNAP
output
|
1pue
|
transcription-DNA |
X-ray (2.1 Å) |
Kodandapani R, Pio F, Ni CZ, Piccialli G, Klemsz M,
McKercher S, Maki RA, Ely KR |
(1996) "A new
pattern for helix-turn-helix recognition revealed by
the PU.1 ETS-domain-DNA complex." Nature,
380, 456-460. doi: 10.1038/380456a0.
|
Pu.1 ets domain-DNA complex . SNAP output
|
1puf
|
transcription-DNA |
X-ray (1.9 Å) |
LARONDE-LEBLANC NA, Wolberger C |
(2003) "STRUCTURE
OF HOXA9 AND PBX1 BOUND TO DNA: HOX HEXAPEPTIDE AND DNA
RECOGNITION ANTERIOR TO POSTERIOR." Genes
Dev., 17, 2060-2072. doi:
10.1101/gad.1103303.
|
Crystal structure of hoxa9 and pbx1 homeodomains bound
to DNA . SNAP output
|
1pv4
|
transcription-DNA |
X-ray (3.0 Å) |
Skordalakes E, Berger JM |
(2003) "Structure
of the Rho transcription terminator: mechanism of mRNA
recognition and helicase loading."
Cell(Cambridge,Mass.), 114,
135-146. doi: 10.1016/S0092-8674(03)00512-9.
|
X-ray crystal structure of the rho transcription
termination factor in complex with single stranded DNA
. SNAP output
|
1pvi
|
hydrolase-DNA |
X-ray (2.6 Å) |
Cheng X, Balendiran K, Schildkraut I, Anderson
JE |
(1994) "Structure
of PvuII endonuclease with cognate DNA." EMBO
J., 13, 3927-3935.
|
Structure of pvuii endonuclease with cognate DNA .
SNAP output
|
1pvp
|
recombination-DNA |
X-ray (2.35 Å) |
Baldwin EP, Martin SS, Abel J, Gelato KA, Kim H,
Schultz PG, Santoro SW |
(2003) "A
specificity switch in selected cre recombinase variants
is mediated by macromolecular plasticity and
water." Chem.Biol., 10,
1085-1094. doi: 10.1016/j.chembiol.2003.10.015.
|
Basis for a switch in substrate specificity: crystal
structure of selected variant of cre site-specific
recombinase, alshg bound to the engineered recognition
site loxm7 . SNAP
output
|
1pvq
|
recombination-DNA |
X-ray (2.75 Å) |
Baldwin EP, Martin SS, Abel J, Gelato KA, Kim H,
Schultz PG, Santoro SW |
(2003) "A
specificity switch in selected cre recombinase variants
is mediated by macromolecular plasticity and
water." Chem.Biol., 10,
1085-1094. doi: 10.1016/j.chembiol.2003.10.015.
|
Basis for a switch in substrate specificity: crystal
structure of selected variant of cre site-specific
recombinase, lnsgg bound to the engineered recognition
site loxm7 . SNAP
output
|
1pvr
|
recombination-DNA |
X-ray (2.65 Å) |
Baldwin EP, Martin SS, Abel J, Gelato KA, Kim H,
Schultz PG, Santoro SW |
(2003) "A
specificity switch in selected cre recombinase variants
is mediated by macromolecular plasticity and
water." Chem.Biol., 10,
1085-1094. doi: 10.1016/j.chembiol.2003.10.015.
|
Basis for a switch in substrate specificity: crystal
structure of selected variant of cre site-specific
recombinase, lnsgg bound to the loxp (wildtype)
recognition site . SNAP
output
|
1pyi
|
transcription-DNA |
X-ray (3.2 Å) |
Marmorstein R, Harrison SC |
(1994) "Crystal
structure of a PPR1-DNA complex: DNA recognition by
proteins containing a Zn2Cys6 binuclear cluster."
Genes Dev., 8, 2504-2512.
|
Crystal structure of a ppr1-DNA complex: DNA
recognition by proteins containing a zn2cys6 binuclear
cluster . SNAP
output
|
1pzu
|
transcription-DNA |
X-ray (3.1 Å) |
Jin L, Sliz P, Chen L, Macian F, Rao A, Hogan PG,
Harrison SC |
(2003) "An
asymmetric NFAT1 dimer on a pseudo-palindromic KB-like
DNA site." Nat.Struct.Biol.,
10, 807-811. doi: 10.1038/nsb975.
|
An asymmetric nfat1-rhr homodimer on a
pseudo-palindromic, kappa-b site . SNAP output
|
1q0t
|
transferase-DNA |
X-ray (3.1 Å) |
Yang Z, Horton JR, Zhou L, Zhang XJ, Dong A, Zhang X,
Schlagman SL, Kossykh V, Hattman S, Cheng X |
(2003) "Structure
of the bacteriophage T4 DNA adenine
methyltransferase." Nat.Struct.Biol.,
10, 849-855. doi: 10.1038/nsb973.
|
Ternary structure of t4dam with adohcy and DNA .
SNAP output
|
1q3f
|
hydrolase-DNA |
X-ray (1.9 Å) |
Bianchet MA, Seiple LA, Jiang YL, Ichikawa Y, Amzel
LM, Stivers JT |
(2003) "Electrostatic
guidance of glycosyl cation migration along the
reaction coordinate of uracil DNA glycosylase."
Biochemistry, 42,
12455-12460. doi: 10.1021/bi035372+.
|
Uracil DNA glycosylase bound to a cationic
1-aza-2'-deoxyribose-containing DNA . SNAP output
|
1q3u
|
replication-DNA |
X-ray (2.9 Å) |
Ennifar E, Meyer JEW, Buchholz F, Stewart AF, Suck
D |
(2003) "Crystal
structure of a wild-type Cre recombinase-loxP synapse
reveals a novel spacer conformation suggesting an
alternative mechanism for DNA cleavage activation."
Nucleic Acids Res., 31,
5449-5460. doi: 10.1093/nar/gkg732.
|
Crystal structure of a wild-type cre recombinase-loxp
synapse: pre-cleavage complex . SNAP output
|
1q3v
|
replication-DNA |
X-ray (2.91 Å) |
Ennifar E, Meyer JEW, Buchholz F, Stewart AF, Suck
D |
(2003) "Crystal
structure of a wild-type Cre recombinase-loxP synapse
reveals a novel spacer conformation suggesting an
alternative mechanism for DNA cleavage activation."
Nucleic Acids Res., 31,
5449-5460. doi: 10.1093/nar/gkg732.
|
Crystal structure of a wild-type cre recombinase-loxp
synapse: phosphotyrosine covalent intermediate .
SNAP output
|
1q9x
|
transferase,replication-DNA |
X-ray (2.69 Å) |
Freisinger E, Grollman AP, Miller H, Kisker C |
(2004) "Lesion
(in)tolerance reveals insights into DNA replication
fidelity." Embo J., 23,
1494-1505. doi: 10.1038/sj.emboj.7600158.
|
Crystal structure of enterobacteria phage rb69 gp43 DNA
polymerase complexed with tetrahydrofuran containing
DNA . SNAP output
|
1q9y
|
transferase, replication-DNA |
X-ray (2.8 Å) |
Freisinger E, Grollman AP, Miller H, Kisker C |
(2004) "Lesion
(in)tolerance reveals insights into DNA replication
fidelity." Embo J., 23,
1494-1505. doi: 10.1038/sj.emboj.7600158.
|
Crystal structure of enterobacteria phage rb69 gp43 DNA
polymerase complexed with 8-oxoguanosine containing DNA
. SNAP output
|
1qai
|
transferase-DNA |
X-ray (2.3 Å) |
Najmudin S, Cote ML, Sun D, Yohannan S, Montano SP,
Gu J, Georgiadis MM |
(2000) "Crystal
structures of an N-terminal fragment from Moloney
murine leukemia virus reverse transcriptase complexed
with nucleic acid: functional implications for
template-primer binding to the fingers domain."
J.Mol.Biol., 296, 613-622.
doi: 10.1006/jmbi.1999.3477.
|
Crystal structures of the n-terminal fragment from
moloney murine leukemia virus reverse transcriptase
complexed with nucleic acid: functional implications
for template-primer binding to the fingers domain .
SNAP output
|
1qaj
|
transferase-DNA |
X-ray (2.3 Å) |
Najmudin S, Cote ML, Sun D, Yohannan S, Montano SP,
Gu J, Georgiadis MM |
(2000) "Crystal
structures of an N-terminal fragment from Moloney
murine leukemia virus reverse transcriptase complexed
with nucleic acid: functional implications for
template-primer binding to the fingers domain."
J.Mol.Biol., 296, 613-632.
doi: 10.1006/jmbi.1999.3477.
|
Crystal structures of the n-terminal fragment from
moloney murine leukemia virus reverse transcriptase
complexed with nucleic acid: functional implications
for template-primer binding to the fingers domain .
SNAP output
|
1qbj
|
hydrolase-DNA |
X-ray (2.1 Å) |
Schwartz T, Rould MA, Lowenhaupt K, Herbert A, Rich
A |
(1999) "Crystal
structure of the Zalpha domain of the human editing
enzyme ADAR1 bound to left-handed Z-DNA."
Science, 284, 1841-1845. doi:
10.1126/science.284.5421.1841.
|
Crystal structure of the zalpha z-DNA complex .
SNAP output
|
1qln
|
nucleotidyltransferase |
X-ray (2.4 Å) |
Cheetham GMT, Steitz TA |
(1999) "Structure
of a Transcribing T7 RNA Polymerase Initiation
Complex." Science, 286,
2305. doi: 10.1126/SCIENCE.286.5448.2305.
|
Structure of a transcribing t7 RNA polymerase
initiation complex . SNAP output
|
1qn3
|
tata box-binding protein (tbp) |
X-ray (1.95 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the c(-25) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
1qn4
|
tata box-binding protein (tbp) |
X-ray (1.86 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the t(-24) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
1qn5
|
tata box-binding protein (tbp) |
X-ray (1.93 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the g(-26) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
1qn6
|
tata box-binding protein (tbp) |
X-ray (2.1 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the t(-26) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
1qn7
|
tata box-binding protein (tbp) |
X-ray (2.3 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the t(-27) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
1qn8
|
tata box-binding protein (tbp) |
X-ray (2.1 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the t(-28) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
1qn9
|
tata box-binding protein (tbp) |
X-ray (1.9 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the c(-29) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
1qna
|
tata box-binding protein (tbp) |
X-ray (1.8 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the t(-30) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
1qnb
|
tata box-binding protein (tbp) |
X-ray (2.23 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the t(-25) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
1qnc
|
tata box-binding protein (tbp) |
X-ray (2.3 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the a(-31) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
1qne
|
tata box-binding protein (tbp) |
X-ray (1.9 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the adenovirus major late promoter
tata box bound to wild-type tbp (arabidopsis thaliana
tbp isoform 2). . SNAP
output
|
1qp0
|
transcription-DNA |
X-ray (2.9 Å) |
Glasfeld A, Koehler AN, Schumacher MA, Brennan
RG |
(1999) "The role
of lysine 55 in determining the specificity of the
purine repressor for its operators through minor groove
interactions." J.Mol.Biol.,
291, 347-361. doi: 10.1006/jmbi.1999.2946.
|
Purine repressor-hypoxanthine-palindromic operator
complex . SNAP
output
|
1qp4
|
transcription-DNA |
X-ray (3.0 Å) |
Glasfeld A, Koehler AN, Schumacher MA, Brennan
RG |
(1999) "The role
of lysine 55 in determining the specificity of the
purine repressor for its operators through minor groove
interactions." J.Mol.Biol.,
291, 347-361. doi: 10.1006/jmbi.1999.2946.
|
Purine repressor-hypoxanthine-palindromic operator
complex . SNAP
output
|
1qp7
|
transcription-DNA |
X-ray (2.9 Å) |
Glasfeld A, Koehler AN, Schumacher MA, Brennan
RG |
(1999) "The role
of lysine 55 in determining the specificity of the
purine repressor for its operators through minor groove
interactions." J.Mol.Biol.,
291, 347-361. doi: 10.1006/jmbi.1999.2946.
|
Purine repressor mutant-hypoxanthine-palindromic
operator complex . SNAP
output
|
1qp9
|
transcription-DNA |
X-ray (2.8 Å) |
Lukens AK, King DA, Marmorstein R |
(2000) "Structure
of HAP1-PC7 bound to DNA: implications for DNA
recognition and allosteric effects of DNA-binding on
transcriptional activation." Nucleic Acids
Res., 28, 3853-3863. doi:
10.1093/nar/28.20.3853.
|
Structure of hap1-pc7 complexed to the uas of cyc7 .
SNAP output
|
1qpi
|
transcription-DNA |
X-ray (2.5 Å) |
Orth P, Schnappinger D, Hillen W, Saenger W, Hinrichs
W |
(2000) "Structural
basis of gene regulation by the tetracycline inducible
Tet repressor-operator system."
Nat.Struct.Biol., 7, 215-219.
doi: 10.1038/73324.
|
Crystal structure of tetracycline repressor-operator
complex . SNAP
output
|
1qps
|
hydrolase-DNA |
X-ray (2.5 Å) |
Horvath MM, Choi J, Kim Y, Wilkosz P, Rosenberg
JM |
"The Integration of Recognition and Cleavage: X-Ray
Structures of Pre- Transition State and Post-Reactive
DNA-Eco RI Endonuclease Complexes." |
The crystal structure of a post-reactive cognate
DNA-eco ri complex at 2.50 a in the presence of mn2+
ion . SNAP output
|
1qpz
|
transcription-DNA |
X-ray (2.5 Å) |
Glasfeld A, Koehler AN, Schumacher MA, Brennan
RG |
(1999) "The role
of lysine 55 in determining the specificity of the
purine repressor for its operators through minor groove
interactions." J.Mol.Biol.,
291, 347-361. doi: 10.1006/jmbi.1999.2946.
|
Purine repressor-hypoxanthine-palindromic operator
complex . SNAP
output
|
1qqa
|
gene regulation-DNA |
X-ray (3.0 Å) |
Glasfeld A, Koehler AN, Schumacher MA, Brennan
RG |
(1999) "The role
of lysine 55 in determining the specificity of the
purine repressor for its operators through minor groove
interactions." J.Mol.Biol.,
291, 347-361. doi: 10.1006/jmbi.1999.2946.
|
Purine repressor mutant-hypoxanthine-palindromic
operator complex . SNAP
output
|
1qqb
|
gene regulation-DNA |
X-ray (2.7 Å) |
Glasfeld A, Koehler AN, Schumacher MA, Brennan
RG |
(1999) "The role
of lysine 55 in determining the specificity of the
purine repressor for its operators through minor groove
interactions." J.Mol.Biol.,
291, 347-361. doi: 10.1006/jmbi.1999.2946.
|
Purine repressor mutant-hypoxanthine-palindromic
operator complex . SNAP
output
|
1qrh
|
hydrolase-DNA |
X-ray (2.5 Å) |
Choi J, Kim Y, Greene P, Hager P, Rosenberg JM |
"X-Ray Structure of the DNA-Eco RI Endonuclease
Complexes with the ED144 and RK145 Mutations." |
X-ray structure of the DNA-eco ri endonuclease
complexes with an r145k mutation at 2.7 a . SNAP output
|
1qri
|
hydrolase-DNA |
X-ray (2.6 Å) |
Choi J, Kim Y, Greene P, Hager P, Rosenberg JM |
"X-Ray Structure of the DNA-Eco RI Endonuclease
Complexes with the ED144 and RK145 Mutations." |
X-ray structure of the DNA-eco ri endonuclease
complexes with an e144d mutation at 2.7 a . SNAP output
|
1qrv
|
gene regulation-DNA |
X-ray (2.2 Å) |
Murphy IV FV, Sweet RM, Churchill ME |
(1999) "The
structure of a chromosomal high mobility group
protein-DNA complex reveals sequence-neutral mechanisms
important for non-sequence-specific DNA
recognition." EMBO J.,
18, 6610-6618. doi: 10.1093/emboj/18.23.6610.
|
Crystal structure of the complex of hmg-d and DNA .
SNAP output
|
1qsl
|
transferase-DNA |
X-ray (2.2 Å) |
Brautigam CA, Aschheim K, Steitz TA |
(1999) "Structural
elucidation of the binding and inhibitory properties of
lanthanide (III) ions at the 3'-5' exonucleolytic
active site of the Klenow fragment."
Chem.Biol., 6, 901-908. doi:
10.1016/S1074-5521(00)80009-5.
|
Klenow fragment complexed with single-stranded
substrate and europium (iii) ion . SNAP output
|
1qss
|
transferase-DNA |
X-ray (2.3 Å) |
Li Y, Mitaxov V, Waksman G |
(1999) "Structure-based
design of Taq DNA polymerases with improved properties
of dideoxynucleotide incorporation."
Proc.Natl.Acad.Sci.USA, 96,
9491-9496. doi: 10.1073/pnas.96.17.9491.
|
Ddgtp-trapped closed ternary complex of the large
fragment of DNA polymerase i from thermus aquaticus .
SNAP output
|
1qsy
|
transferase-DNA |
X-ray (2.3 Å) |
Li Y, Mitaxov V, Waksman G |
(1999) "Structure-based
design of Taq DNA polymerases with improved properties
of dideoxynucleotide incorporation."
Proc.Natl.Acad.Sci.USA, 96,
9491-9496. doi: 10.1073/pnas.96.17.9491.
|
Ddatp-trapped closed ternary complex of the large
fragment of DNA polymerase i from thermus aquaticus .
SNAP output
|
1qtm
|
transferase-DNA |
X-ray (2.3 Å) |
Li Y, Mitaxov V, Waksman G |
(1999) "Structure-based
design of Taq DNA polymerases with improved properties
of dideoxynucleotide incorporation."
Proc.Natl.Acad.Sci.USA, 96,
9491-9496. doi: 10.1073/pnas.96.17.9491.
|
Ddttp-trapped closed ternary complex of the large
fragment of DNA polymerase i from thermus aquaticus .
SNAP output
|
1qum
|
hydrolase-DNA |
X-ray (1.55 Å) |
Hosfield DJ, Guan Y, Haas BJ, Cunningham RP, Tainer
JA |
(1999) "Structure
of the DNA repair enzyme endonuclease IV and its DNA
complex: double-nucleotide flipping at abasic sites and
three-metal-ion catalysis."
Cell(Cambridge,Mass.), 98,
397-408. doi: 10.1016/S0092-8674(00)81968-6.
|
Crystal structure of escherichia coli endonuclease iv
in complex with damaged DNA . SNAP output
|
1qx0
|
transferase-DNA |
X-ray (2.26 Å) |
Guasch A, Lucas M, Moncalian G, Cabezas M, Prez-Luque
R, Gomis-Rth FX, de la Cruz F, Coll M |
(2003) "RECOGNITION
AND PROCESSING OF THE ORIGIN OF TRANSFER DNA BY
CONJUGATIVE RELAXASE TRWC."
Nat.Struct.Biol., 10,
1002-1010. doi: 10.1038/nsb1017.
|
Conjugative relaxase trwc in complex with orit DNA.
metal-bound structure . SNAP output
|
1qzg
|
DNA binding protein-DNA |
X-ray (1.9 Å) |
Lei M, Podell ER, Baumann P, Cech TR |
(2003) "DNA
self-recognition in the structure of Pot1 bound to
telomeric single-stranded DNA." Nature,
426, 198-203. doi: 10.1038/nature02092.
|
Crystal structure of pot1 (protection of telomere)-
ssDNA complex . SNAP
output
|
1qzh
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Lei M, Podell ER, Baumann P, Cech TR |
(2003) "DNA
self-recognition in the structure of Pot1 bound to
telomeric single-stranded DNA." Nature,
426, 198-203. doi: 10.1038/nature02092.
|
Crystal structure of pot1 (protection of telomere)-
ssDNA complex . SNAP
output
|
1r0a
|
transferase-immune system-DNA |
X-ray (2.8 Å) |
Peletskaya EN, Kogon AA, Tuske S, Arnold E, Hughes
SH |
(2004) "Nonnucleoside
inhibitor binding affects the interactions of the
fingers subdomain of human immunodeficiency virus type
1 reverse transcriptase with DNA."
J.Virol., 78, 3387-3397. doi:
10.1128/JVI.78.7.3387-3397.2004.
|
Crystal structure of hiv-1 reverse transcriptase
covalently tethered to DNA template-primer solved to
2.8 angstroms . SNAP
output
|
1r0n
|
transcription-DNA |
X-ray (2.6 Å) |
Devarakonda S, Harp JM, Kim Y, Ozyhar A, Rastinejad
F |
(2003) "Structure
of the heterodimeric Ecdysone Receptor DNA-binding
complex." Embo J., 22,
5827-5840. doi: 10.1093/emboj/cdg569.
|
Crystal structure of heterodimeric ecdsyone receptor
DNA binding complex . SNAP output
|
1r0o
|
transcription-DNA |
X-ray (2.24 Å) |
Devarakonda S, Harp JM, Kim Y, Ozyhar A, Rastinejad
F |
(2003) "Structure
of the Heterodimeric Ecdysone Receptor DNA-binding
Complex." Embo J., 22,
5827-5840. doi: 10.1093/emboj/cdg569.
|
Crystal structure of the heterodimeric ecdysone
receptor DNA-binding complex . SNAP output
|
1r2y
|
hydrolase-DNA |
X-ray (2.34 Å) |
Fromme JC, Verdine GL |
(2003) "DNA
Lesion Recognition by the Bacterial Repair Enzyme
MutM." J.Biol.Chem., 278,
51543-51548. doi: 10.1074/jbc.M307768200.
|
Mutm (fpg) bound to 8-oxoguanine (oxog) containing DNA
. SNAP output
|
1r2z
|
hydrolase-DNA |
X-ray (1.63 Å) |
Fromme JC, Verdine GL |
(2003) "DNA
Lesion Recognition by the Bacterial Repair Enzyme
MutM." J.Biol.Chem., 278,
51543-51548. doi: 10.1074/jbc.M307768200.
|
Mutm (fpg) bound to 5,6-dihydrouracil (dhu) containing
DNA . SNAP output
|
1r49
|
isomerase-DNA |
X-ray (3.13 Å) |
Interthal H, Quigley PM, Hol WG, Champoux JJ |
(2004) "The role
of lysine 532 in the catalytic mechanism of human
topoisomerase I." J.Biol.Chem.,
279, 2984-2992. doi: 10.1074/jbc.M309959200.
|
Human topoisomerase i (topo70) double mutant
k532r-y723f . SNAP
output
|
1r4i
|
transcription-DNA |
X-ray (3.1 Å) |
Shaffer PL, Jivan A, Dollins DE, Claessens F, Gewirth
DT |
(2004) "Structural
basis of androgen receptor binding to selective
androgen response elements."
Proc.Natl.Acad.Sci.USA, 101,
4758-4763. doi: 10.1073/pnas.0401123101.
|
Crystal structure of androgen receptor DNA-binding
domain bound to a direct repeat response element .
SNAP output
|
1r4o
|
transcription-DNA |
X-ray (2.5 Å) |
Luisi BF, Xu WX, Otwinowski Z, Freedman LP, Yamamoto
KR, Sigler PB |
(1991) "Crystallographic
Analysis of the Interaction of The Glucocorticoid
Receptor with DNA." Nature,
352, 497-505. doi: 10.1038/352497a0.
|
Crystallographic analysis of the interaction of the
glucocorticoid receptor with DNA . SNAP output
|
1r4r
|
transcription-DNA |
X-ray (3.0 Å) |
Luisi BF, Xu WX, Otwinowski Z, Freedman LP, Yamamoto
KR, Sigler PB |
(1991) "Crystallographic
Analysis of the Interaction of the Glucocorticoid
Receptor with DNA." Nature,
352, 497-505. doi: 10.1038/352497a0.
|
Crystallographic analysis of the interaction of the
glucocorticoid receptor with DNA . SNAP output
|
1r71
|
transcription-DNA |
X-ray (2.2 Å) |
Khare D, Ziegelin G, Lanka E, Heinemann U |
(2004) "Sequence-specific
DNA binding determined by contacts outside the
helix-turn-helix motif of the ParB homolog KorB."
Nat.Struct.Mol.Biol., 11,
656-663. doi: 10.1038/nsmb773.
|
Crystal structure of the DNA binding domain of korb in
complex with the operator DNA . SNAP output
|
1r7m
|
hydrolase-DNA |
X-ray (2.25 Å) |
Moure CM, Gimble FS, Quiocho FA |
(2003) "The
crystal structure of the gene targeting homing
endonuclease I-SceI reveals the origins of its target
site specificity." J.Mol.Biol.,
334, 685-695. doi: 10.1016/j.jmb.2003.09.068.
|
The homing endonuclease i-scei bound to its DNA
recognition region . SNAP output
|
1r8d
|
transcription-DNA |
X-ray (2.7 Å) |
Newberry KJ, Brennan RG |
(2004) "The
structural mechanism for transcription activation by
MerR family member multidrug transporter activation, N
terminus." J.Biol.Chem.,
279, 20356-20362. doi: 10.1074/jbc.M400960200.
|
Crystal structure of mtan bound to DNA . SNAP output
|
1r8e
|
transcription-DNA |
X-ray (2.4 Å) |
Newberry KJ, Brennan RG |
(2004) "The
structural mechanism for transcription activation by
MerR family member multidrug transporter activation, N
terminus." J.Biol.Chem.,
279, 20356-20362. doi: 10.1074/jbc.M400960200.
|
Crystal structure of bmrr bound to DNA at 2.4a
resolution . SNAP
output
|
1r9s
|
transcription-DNA-RNA hybrid |
X-ray (4.25 Å) |
Westover KD, Bushnell DA, Kornberg RD |
(2004) "Structural
basis of transcription: nucleotide selection by
rotation in the RNA polymerase II active center."
Cell(Cambridge,Mass.), 119,
481-489. doi: 10.1016/j.cell.2004.10.016.
|
RNA polymerase ii strand separated elongation complex,
matched nucleotide . SNAP output
|
1r9t
|
transcription-DNA-RNA hybrid |
X-ray (3.5 Å) |
Westover KD, Bushnell DA, Kornberg RD |
(2004) "Structural
basis of transcription: nucleotide selection by
rotation in the RNA polymerase II active center."
Cell(Cambridge,Mass.), 119,
481-489. doi: 10.1016/j.cell.2004.10.016.
|
RNA polymerase ii strand separated elongation complex,
mismatched nucleotide . SNAP output
|
1ram
|
transcription-DNA |
X-ray (2.7 Å) |
Chen YQ, Ghosh S, Ghosh G |
(1998) "A novel
DNA recognition mode by the NF-kappa B p65
homodimer." Nat.Struct.Biol.,
5, 67-73. doi: 10.1038/nsb0198-67.
|
A novel DNA recognition mode by nf-kb p65 homodimer .
SNAP output
|
1rb8
|
virus-DNA |
X-ray (3.5 Å) |
Bernal RA, Hafenstein S, Esmeralda R, Fane BA,
Rossmann MG |
(2004) "The
phiX174 Protein J Mediates DNA Packaging and Viral
Attachment to Host Cells." J.Mol.Biol.,
337, 1109-1122. doi: 10.1016/j.jmb.2004.02.033.
|
The phix174 DNA binding protein j in two different
capsid environments. . SNAP output
|
1rbj
|
hydrolase-DNA |
X-ray (2.7 Å) |
Ko TP, Williams R, McPherson A |
(1996) "Structure
of a ribonuclease B+d(pA)4 complex." Acta
Crystallogr.,Sect.D, 52, 160-164.
doi: 10.1107/S0907444995009127.
|
Ribonuclease b complex with d(tetra-(deoxy-adenylate))
. SNAP output
|
1rc8
|
transferase-DNA |
X-ray (2.75 Å) |
Eastberg JH, Pelletier J, Stoddard BL |
(2004) "Recognition
of DNA substrates by T4 bacteriophage polynucleotide
kinase." Nucleic Acids Res.,
32, 653-660. doi: 10.1093/nar/gkh212.
|
T4 polynucleotide kinase bound to 5'-gtcac-3' ssDNA .
SNAP output
|
1rcn
|
hydrolase-DNA |
X-ray (2.32 Å) |
Fontecilla-Camps JC, de Llorens R, le Du MH, Cuchillo
CM |
(1994) "Crystal
structure of ribonuclease A.d(ApTpApApG) complex.
Direct evidence for extended substrate
recognition." J.Biol.Chem.,
269, 21526-21531.
|
Crystal structure of the ribonuclease a d(aptpapapg)
complex : direct evidence for extended substrate
recognition . SNAP
output
|
1rcs
|
transcription-DNA |
NMR |
Zhang H, Zhao D, Revington M, Lee W, Jia X,
Arrowsmith C, Jardetzky O |
(1994) "The
solution structures of the trp repressor-operator DNA
complex." J.Mol.Biol.,
238, 592-614. doi: 10.1006/jmbi.1994.1317.
|
NMR study of trp repressor-operator DNA complex .
SNAP output
|
1rep
|
replication-DNA |
X-ray (2.6 Å) |
Komori H, Matsunaga F, Higuchi Y, Ishiai M, Wada C,
Miki K |
(1999) "Crystal
structure of a prokaryotic replication initiator
protein bound to DNA at 2.6 A resolution." EMBO
J., 18, 4597-4607. doi: 10.1093/emboj/18.17.4597.
|
Crystal structure of replication initiator protein
repe54 of mini-f plasmid complexed with an iteron DNA .
SNAP output
|
1rff
|
hydrolase-DNA |
X-ray (1.7 Å) |
Davies DR, Interthal H, Champoux JJ, Hol WG |
(2004) "Explorations
of peptide and oligonucleotide binding sites of
tyrosyl-DNA phosphodiesterase using vanadate
complexes." J.Med.Chem.,
47, 829-837. doi: 10.1021/jm030487x.
|
Crystal structure of human tyrosyl-DNA
phosphodiesterase complexed with vanadate, octapeptide
klnyydpr, and tetranucleotide agtt. . SNAP output
|
1rfi
|
hydrolase-DNA |
X-ray (2.2 Å) |
Davies DR, Interthal H, Champoux JJ, Hol WG |
(2004) "Explorations
of peptide and oligonucleotide binding sites of
tyrosyl-DNA phosphodiesterase using vanadate
complexes." J.Med.Chem.,
47, 829-837. doi: 10.1021/jm030487x.
|
Crystal structure of human tyrosyl-DNA
phosphodiesterase complexed with vanadate, pentapeptide
klnyk, and tetranucleotide agtc . SNAP output
|
1rg1
|
hydrolase-DNA |
X-ray (2.1 Å) |
Davies DR, Interthal H, Champoux JJ, Hol WG |
(2004) "Explorations
of peptide and oligonucleotide binding sites of
tyrosyl-DNA phosphodiesterase using vanadate
complexes." J.Med.Chem.,
47, 829-837. doi: 10.1021/jm030487x.
|
Crystal structure of human tyrosyl-DNA
phosphodiesterase complexed with vanadate, octopamine,
and tetranucleotide agtt . SNAP output
|
1rg2
|
hydrolase-DNA |
X-ray (2.1 Å) |
Davies DR, Interthal H, Champoux JJ, Hol WG |
(2004) "Explorations
of peptide and oligonucleotide binding sites of
tyrosyl-DNA phosphodiesterase using vanadate
complexes." J.Med.Chem.,
47, 829-837. doi: 10.1021/jm030487x.
|
Crystal structure of human tyrosyl-DNA
phosphodiesterase complexed with vanadate, octopamine,
and tetranucleotide agta . SNAP output
|
1rgt
|
hydrolase-DNA |
X-ray (2.0 Å) |
Davies DR, Interthal H, Champoux JJ, Hol WG |
(2004) "Explorations
of peptide and oligonucleotide binding sites of
tyrosyl-DNA phosphodiesterase using vanadate
complexes." J.Med.Chem.,
47, 829-837. doi: 10.1021/jm030487x.
|
Crystal structure of human tyrosyl-DNA
phosphodiesterase complexed with vanadate, octopamine,
and tetranucleotide agtc . SNAP output
|
1rgu
|
hydrolase-DNA |
X-ray (2.22 Å) |
Davies DR, Interthal H, Champoux JJ, Hol WG |
(2004) "Explorations
of peptide and oligonucleotide binding sites of
tyrosyl-DNA phosphodiesterase using vanadate
complexes." J.Med.Chem.,
47, 829-837. doi: 10.1021/jm030487x.
|
The crystal structure of human tyrosyl-DNA
phosphodiesterase complexed with vanadate, octopamine,
and tetranucleotide agtg . SNAP output
|
1rh0
|
hydrolase-DNA |
X-ray (2.3 Å) |
Davies DR, Interthal H, Champoux JJ, Hol WG |
(2004) "Explorations
of peptide and oligonucleotide binding sites of
tyrosyl-DNA phosphodiesterase using vanadate
complexes." J.Med.Chem.,
47, 829-837. doi: 10.1021/jm030487x.
|
Crystal structure of human tyrosyl-DNA
phosphodiesterase complexed with vanadate, octopamine
and trinucleotide gtt . SNAP output
|
1rh6
|
DNA binding protein-DNA |
X-ray (1.7 Å) |
Sam MD, Cascio D, Johnson RC, Clubb RT |
(2004) "Crystal
structure of the excisionase-DNA complex from
bacteriophage lambda." J.Mol.Biol.,
338, 229-240. doi: 10.1016/j.jmb.2004.02.053.
|
Bacteriophage lambda excisionase (xis)-DNA complex .
SNAP output
|
1rio
|
transcription-DNA |
X-ray (2.3 Å) |
Jain D, Nickels BE, Sun L, Hochschild A, Darst
SA |
(2004) "Structure
of a ternary transcription activation complex."
Mol.Cell, 13, 45-53. doi:
10.1016/S1097-2765(03)00483-0.
|
Structure of bacteriophage lambda ci-ntd in complex
with sigma-region4 of thermus aquaticus bound to DNA .
SNAP output
|
1rm1
|
transcription-DNA |
X-ray (2.5 Å) |
Jin X, Gewirth DT, Geiger JH |
"High Resolution Structure of a Yeast
TFIIA/TBP/TATA-box DNA Complex." |
Structure of a yeast tfiia-tbp-tata-box DNA complex .
SNAP output
|
1rnb
|
endonuclease |
X-ray (1.9 Å) |
Baudet S, Janin J |
(1991) "Crystal
structure of a barnase-d(GpC) complex at 1.9 A
resolution." J.Mol.Biol.,
219, 123-132. doi: 10.1016/0022-2836(91)90862-Z.
|
Crystal structure of a barnase-d(*gp*c) complex at 1.9
angstroms resolution . SNAP output
|
1rpe
|
gene regulation-DNA |
X-ray (2.5 Å) |
Shimon LJ, Harrison SC |
(1993) "The phage
434 OR2/R1-69 complex at 2.5 A resolution."
J.Mol.Biol., 232, 826-838.
doi: 10.1006/jmbi.1993.1434.
|
The phage 434 or2-r1-69 complex at 2.5 angstroms
resolution . SNAP
output
|
1rpz
|
transferase-DNA |
X-ray (2.9 Å) |
Eastberg JH, Pelletier J, Stoddard BL |
(2004) "Recognition
of DNA substrates by T4 bacteriophage polynucleotide
kinase." Nucleic Acids Res.,
32, 653-660. doi: 10.1093/nar/gkh212.
|
T4 polynucleotide kinase bound to 5'-tgcac-3' ssDNA .
SNAP output
|
1rr8
|
isomerase-DNA |
X-ray (2.6 Å) |
Chrencik JE, Staker BL, Burgin AB, Pourquier P,
Pommier Y, Stewart L, Redinbo MR |
(2004) "Mechanisms
of camptothecin resistance by human topoisomerase I
mutations." J.Mol.Biol.,
339, 773-784. doi: 10.1016/j.jmb.2004.03.077.
|
Structural mechanisms of camptothecin resistance by
mutations in human topoisomerase i . SNAP output
|
1rrc
|
transferase-DNA |
X-ray (2.46 Å) |
Eastberg JH, Pelletier J, Stoddard BL |
(2004) "Recognition
of DNA substrates by T4 bacteriophage polynucleotide
kinase." Nucleic Acids Res.,
32, 653-660. doi: 10.1093/nar/gkh212.
|
T4 polynucleotide kinase bound to 5'-gtc-3' ssDNA .
SNAP output
|
1rrj
|
isomerase-DNA |
X-ray (2.3 Å) |
Chrencik JE, Staker BL, Burgin AB, Pourquier P,
Pommier Y, Stewart L, Redinbo MR |
(2004) "Mechanisms
of camptothecin resistance by human topoisomerase I
mutations." J.Mol.Biol.,
339, 773-784. doi: 10.1016/j.jmb.2004.03.077.
|
Structural mechanisms of camptothecin resistance by
mutations in human topoisomerase i . SNAP output
|
1rrq
|
hydrolase-DNA |
X-ray (2.22 Å) |
Fromme JC, Banerjee A, Huang SJ, Verdine GL |
(2004) "Structural
basis for removal of adenine mispaired with
8-oxoguanine by MutY adenine DNA glycosylase."
Nature, 427, 652-656. doi:
10.1038/nature02306.
|
Muty adenine glycosylase in complex with DNA containing
an a:oxog pair . SNAP
output
|
1rrs
|
hydrolase-DNA |
X-ray (2.4 Å) |
Fromme JC, Banerjee A, Huang SJ, Verdine GL |
(2004) "Structural
basis for removal of adenine mispaired with
8-oxoguanine by MutY adenine DNA glycosylase."
Nature, 427, 652-656. doi:
10.1038/nature02306.
|
Muty adenine glycosylase in complex with DNA containing
an abasic site . SNAP
output
|
1rta
|
hydrolase-DNA |
X-ray (2.5 Å) |
Birdsall DL, McPherson A |
(1992) "Crystal
structure disposition of thymidylic acid tetramer in
complex with ribonuclease A."
J.Biol.Chem., 267,
22230-22236.
|
Crystal structure disposition of thymidylic acid
tetramer in complex with ribonuclease a . SNAP output
|
1rtd
|
transferase-DNA |
X-ray (3.2 Å) |
Huang H, Chopra R, Verdine GL, Harrison SC |
(1998) "Structure
of a covalently trapped catalytic complex of HIV-1
reverse transcriptase: implications for drug
resistance." Science,
282, 1669-1675. doi: 10.1126/science.282.5394.1669.
|
Structure of a catalytic complex of hiv-1 reverse
transcriptase: implications for nucleoside analog drug
resistance . SNAP
output
|
1run
|
transcription-DNA |
X-ray (2.7 Å) |
Parkinson G, Gunasekera A, Vojtechovsky J, Zhang X,
Kunkel TA, Berman H, Ebright RH |
(1996) "Aromatic
hydrogen bond in sequence-specific protein DNA
recognition." Nat.Struct.Biol.,
3, 837-841. doi: 10.1038/nsb1096-837.
|
Catabolite gene activator protein (cap)-DNA complex +
adenosine-3',5'-cyclic-monophosphate . SNAP output
|
1ruo
|
transcription-DNA |
X-ray (2.7 Å) |
Parkinson G, Gunasekera A, Vojtechovsky J, Zhang X,
Kunkel TA, Berman H, Ebright RH |
(1996) "Aromatic
hydrogen bond in sequence-specific protein DNA
recognition." Nat.Struct.Biol.,
3, 837-841. doi: 10.1038/nsb1096-837.
|
Catabolite gene activator protein (cap) mutant-DNA
complex + adenosine-3',5'-cyclic-monophosphate .
SNAP output
|
1rv5
|
hydrolase-DNA |
X-ray (2.1 Å) |
Horton NC, Perona JJ |
(1998) "Role of
protein-induced bending in the specificity of DNA
recognition: crystal structure of EcoRV endonuclease
complexed with d(AAAGAT) + d(ATCTT)."
J.Mol.Biol., 277, 779-783.
doi: 10.1006/jmbi.1998.1655.
|
Complex of ecorv endonuclease with d(aaagat)-d(atctt) .
SNAP output
|
1rva
|
hydrolase-DNA |
X-ray (2.0 Å) |
Kostrewa D, Winkler FK |
(1995) "Mg2+
binding to the active site of EcoRV endonuclease: a
crystallographic study of complexes with substrate and
product DNA at 2 A resolution."
Biochemistry, 34, 683-696.
doi: 10.1021/bi00002a036.
|
Mg2+ binding to the active site of eco rv endonuclease:
a crystallographic study of complexes with substrate
and product DNA at 2 angstroms resolution . SNAP output
|
1rvb
|
hydrolase-DNA |
X-ray (2.1 Å) |
Kostrewa D, Winkler FK |
(1995) "Mg2+
binding to the active site of EcoRV endonuclease: a
crystallographic study of complexes with substrate and
product DNA at 2 A resolution."
Biochemistry, 34, 683-696.
doi: 10.1021/bi00002a036.
|
Mg2+ binding to the active site of eco rv endonuclease:
a crystallographic study of complexes with substrate
and product DNA at 2 angstroms resolution . SNAP output
|
1rvc
|
hydrolase-DNA |
X-ray (2.1 Å) |
Kostrewa D, Winkler FK |
(1995) "Mg2+
binding to the active site of EcoRV endonuclease: a
crystallographic study of complexes with substrate and
product DNA at 2 A resolution."
Biochemistry, 34, 683-696.
doi: 10.1021/bi00002a036.
|
Mg2+ binding to the active site of eco rv endonuclease:
a crystallographic study of complexes with substrate
and product DNA at 2 angstroms resolution . SNAP output
|
1rxv
|
hydrolase-DNA |
X-ray (2.5 Å) |
Chapados BR, Hosfield DJ, Han S, Qiu J, Yelent B,
Shen B, Tainer JA |
(2004) "Structural
Basis for FEN-1 Substrate Specificity and PCNA-Mediated
Activation in DNA Replication and Repair."
Cell(Cambridge,Mass.), 116,
39-50. doi: 10.1016/S0092-8674(03)01036-5.
|
Crystal structure of a. fulgidus fen-1 bound to DNA .
SNAP output
|
1rxw
|
hydrolase-DNA |
X-ray (2.0 Å) |
Chapados BR, Hosfield DJ, Han S, Qiu J, Yelent B,
Shen B, Tainer JA |
(2004) "Structural
Basis for FEN-1 Substrate Specificity and PCNA-Mediated
Activation in DNA Replication and Repair."
Cell(Cambridge,Mass.), 116,
39-50. doi: 10.1016/S0092-8674(03)01036-5.
|
Crystal structure of a. fulgidus fen-1 bound to DNA .
SNAP output
|
1ryr
|
transferase-DNA |
X-ray (2.28 Å) |
Ling H, Boudsocq F, Plosky B, Woodgate R, Yang W |
(2003) "Replication
of a Cis-Syn Thymine Dimer at Atomic Resolution."
Nature, 424, 1083-1087. doi:
10.1038/nature01919.
|
Replication of a cis-syn thymine dimer at atomic
resolution . SNAP
output
|
1rys
|
transferase-DNA |
X-ray (2.03 Å) |
Ling H, Boudsocq F, Plosky B, Woodgate R, Yang W |
(2003) "Replication
of a Cis-Syn Thymine Dimer at Atomic Resolution."
Nature, 424, 1083-1087. doi:
10.1038/nature01919.
|
Replication of a cis-syn thymine dimer at atomic
resolution . SNAP
output
|
1rz9
|
viral protein-DNA |
X-ray (3.1 Å) |
Hickman AB, Ronning DR, Perez ZN, Kotin RM, Dyda
F |
(2004) "The
nuclease domain of adeno-associated virus rep
coordinates replication initiation using two distinct
DNA recognition interfaces." Mol.Cell,
13, 403-414. doi: 10.1016/S1097-2765(04)00023-1.
|
Crystal structure of aav rep complexed with the
rep-binding sequence . SNAP output
|
1rzr
|
transcription-transport protein-DNA |
X-ray (2.8 Å) |
Schumacher MA, Allen GS, Diel M, Seidel G, Hillen W,
Brennan RG |
(2004) "Structural
basis for allosteric control of the transcription
regulator CcpA by the phosphoprotein HPr-Ser46-P."
Cell(Cambridge,Mass.), 118,
731-741. doi: 10.1016/j.cell.2004.08.027.
|
Crystal structure of transcriptional
regulator-phosphoprotein-DNA complex . SNAP output
|
1rzt
|
transferase-DNA |
X-ray (2.1 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Blanco L, Kunkel
TA, Pedersen LC |
(2004) "A
structural solution for the DNA polymerase
lambda-dependent repair of DNA gaps with minimal
homology." Mol.Cell, 13,
561-572. doi: 10.1016/S1097-2765(04)00061-9.
|
Crystal structure of DNA polymerase lambda complexed
with a two nucleotide gap DNA molecule . SNAP output
|
1s0m
|
transferase-DNA |
X-ray (2.7 Å) |
Ling H, Sayer JM, Plosky BS, Yagi H, Boudsocq F,
Woodgate R, Jerina DM, Yang W |
(2004) "Crystal
structure of a benzo[a]pyrene diol epoxide adduct in a
ternary complex with a DNA polymerase."
Proc.Natl.Acad.Sci.USA, 101,
2265-2269. doi: 10.1073/pnas.0308332100.
|
Crystal structure of a benzo[a]pyrene diol epoxide
adduct in a ternary complex with a DNA polymerase .
SNAP output
|
1s0n
|
transferase-DNA |
X-ray (2.8 Å) |
Ling H, Boudsocq F, Woodgate R, Yang W |
(2004) "Snapshots
of Replication through an Abasic Lesion; Structural
Basis for Base Substitutions and Frameshifts."
Mol.Cell, 13, 751-762. doi:
10.1016/S1097-2765(04)00101-7.
|
Snapshots of replication through an abasic lesion:
structural basis for base substitution and frameshift .
SNAP output
|
1s0o
|
transferase-DNA |
X-ray (2.1 Å) |
Ling H, Boudsocq F, Woodgate R, Yang W |
(2004) "Snapshots
of Replication through an Abasic Lesion; Structural
Basis for Base Substitutions and Frameshifts."
Mol.Cell, 13, 751-762. doi:
10.1016/S1097-2765(04)00101-7.
|
Snapshots of replication through an abasic lesion:
structural basis for base substitution and frameshift .
SNAP output
|
1s0v
|
transferase-DNA-RNA hybrid |
X-ray (3.2 Å) |
Temiakov D, Patlan V, Anikin M, McAllister WT,
Yokoyama S, Vassylyev DG |
(2004) "Structural
basis for substrate selection by t7 RNA
polymerase." Cell(Cambridge,Mass.),
116, 381-391. doi: 10.1016/S0092-8674(04)00059-5.
|
Structural basis for substrate selection by t7 RNA
polymerase . SNAP
output
|
1s10
|
transferase-DNA |
X-ray (2.1 Å) |
Ling H, Boudsocq F, Woodgate R, Yang W |
(2004) "Snapshots
of Replication through an Abasic Lesion; Structural
Basis for Base Substitutions and Frameshifts."
Mol.Cell, 13, 751-762. doi:
10.1016/S1097-2765(04)00101-7.
|
Snapshots of replication through an abasic lesion:
structural basis for base substitution and frameshift .
SNAP output
|
1s32
|
structural protein-DNA |
X-ray (2.05 Å) |
Edayathumangalam RS, Weyermann P, Gottesfeld JM,
Dervan PB, Luger K |
(2004) "Molecular
Recognition of the Nucleosomal 'Supergroove'."
Proc.Natl.Acad.Sci.USA, 101,
6864-6869. doi: 10.1073/pnas.0401743101.
|
Molecular recognition of the nucleosomal 'supergroove'
. SNAP output
|
1s40
|
cell cycle-DNA |
NMR |
Mitton-Fry RM, Anderson EM, Theobald DL, Glustrom LW,
Wuttke DS |
(2004) "Structural
basis for telomeric single-stranded DNA recognition by
yeast Cdc13." J.Mol.Biol.,
338, 241-255. doi: 10.1016/j.jmb.2004.01.063.
|
Solution structure of the cdc13 DNA-binding domain
complexed with a single-stranded telomeric DNA 11-mer .
SNAP output
|
1s6m
|
DNA binding protein-DNA |
X-ray (2.28 Å) |
Boer R, Russi S, Guasch A, Lucas M, Blanco AG,
Perez-Luque R, Coll M, de la Cruz F |
(2006) "Unveiling
the molecular mechanism of a conjugative relaxase: The
structure of TrwC complexed with a 27-mer DNA
comprising the recognition hairpin and the cleavage
site." J.Mol.Biol., 358,
857-869. doi: 10.1016/j.jmb.2006.02.018.
|
Conjugative relaxase trwc in complex with orit DNA.
metal-bound structure . SNAP output
|
1s76
|
transferase |
X-ray (2.88 Å) |
Yin YW, Steitz TA |
(2004) "The
structural mechanism of translocation and helicase
activity in T7 RNA polymerase."
Cell(Cambridge,Mass.), 116,
393-404. doi: 10.1016/S0092-8674(04)00120-5.
|
T7 RNA polymerase alpha beta methylene atp elongation
complex . SNAP
output
|
1s77
|
transferase |
X-ray (2.69 Å) |
Yin YW, Steitz TA |
(2004) "The
structural mechanism of translocation and helicase
activity in T7 RNA polymerase."
Cell(Cambridge,Mass.), 116,
393-404. doi: 10.1016/S0092-8674(04)00120-5.
|
T7 rnap product pyrophosphate elongation complex .
SNAP output
|
1s97
|
transferase-DNA |
X-ray (2.4 Å) |
Trincao J, Johnson RE, Wolfle WT, Escalante CR,
Prakash S, Prakash L, Aggarwal AK |
(2004) "Dpo4 is
hindered in extending a G.T mismatch by a reverse
wobble." Nat.Struct.Mol.Biol.,
11, 457-462. doi: 10.1038/nsmb755.
|
Dpo4 with gt mismatch . SNAP output
|
1s9f
|
transferase-DNA |
X-ray (2.0 Å) |
Trincao J, Johnson RE, Wolfle WT, Escalante CR,
Prakash S, Prakash L, Aggarwal AK |
(2004) "Dpo4 is
hindered in extending a G.T mismatch by a reverse
wobble." Nat.Struct.Mol.Biol.,
11, 457-462. doi: 10.1038/nsmb755.
|
Dpo with at matched . SNAP output
|
1s9k
|
transcription-DNA |
X-ray (3.1 Å) |
Wang D, Stroud JC, Chen L |
"Crystal Structure of Human NFAT1 and Fos-Jun on the
IL-2 ARRE1 Site." |
Crystal structure of human nfat1 and fos-jun on the
il-2 arre1 site . SNAP
output
|
1sa3
|
hydrolase-DNA |
X-ray (1.95 Å) |
Xu QS, Kucera RB, Roberts RJ, Guo HC |
(2004) "An
Asymmetric Complex of Restriction Endonuclease MspI on
Its Palindromic DNA Recognition Site."
STRUCTURE, 12, 1741-1747.
doi: 10.1016/j.str.2004.07.014.
|
An asymmetric complex of restriction endonuclease mspi
on its palindromic DNA recognition site . SNAP output
|
1sax
|
transcription-DNA |
X-ray (2.8 Å) |
Garcia-Castellanos R, Mallorqui-Fernandez G, Marrero
A, Potempa J, Coll M, Gomis-Ruth FX |
(2004) "On the
transcriptional regulation of methicillin resistance:
MecI repressor in complex with its operator."
J.Biol.Chem., 279,
17888-17896. doi: 10.1074/jbc.M313123200.
|
Three-dimensional structure of s.aureus
methicillin-resistance regulating transcriptional
repressor meci in complex with 25-bp ds-DNA . SNAP output
|
1sc7
|
isomerase-DNA |
X-ray (3.0 Å) |
Staker BL, Feese MD, Cushman M, Pommier Y, Zembower
D, Stewart L, Burgin AB |
(2005) "Structures
of three classes of anticancer agents bound to the
human topoisomerase I-DNA covalent complex."
J.Med.Chem., 48, 2336-2345.
doi: 10.1021/jm049146p.
|
Human DNA topoisomerase i (70 kda) in complex with the
indenoisoquinoline mj-ii-38 and covalent complex with a
22 base pair DNA duplex . SNAP output
|
1seu
|
isomerase-DNA |
X-ray (3.0 Å) |
Staker BL, Feese MD, Cushman M, Pommier Y, Zembower
D, Stewart L, Burgin AB |
(2005) "Structures
of three classes of anticancer agents bound to the
human topoisomerase I-DNA covalent complex."
J.Med.Chem., 48, 2336-2345.
doi: 10.1021/jm049146p.
|
Human DNA topoisomerase i (70 kda) in complex with the
indolocarbazole sa315f and covalent complex with a 22
base pair DNA duplex . SNAP output
|
1sfo
|
transcription-DNA-RNA hybrid |
X-ray (3.61 Å) |
Westover KD, Bushnell DA, Kornberg RD |
(2004) "Structural
Basis of Transcription: Separation of RNA from DNA by
RNA Polymerase II." Science,
303, 1014-1016. doi: 10.1126/science.1090839.
|
RNA polymerase ii strand separated elongation complex .
SNAP output
|
1sfu
|
DNA binding protein-DNA |
X-ray (2.0 Å) |
Ha SC, Lokanath NK, Van Quyen D, Wu CA, Lowenhaupt K,
Rich A, Kim YG, Kim KK |
(2004) "A
poxvirus protein forms a complex with left-handed
Z-DNA: crystal structure of a Yatapoxvirus Zalpha bound
to DNA." Proc.Natl.Acad.Sci.USA,
101, 14367-14372. doi: 10.1073/pnas.0405586101.
|
Crystal structure of the viral zalpha domain bound to
left-handed z-DNA . SNAP
output
|
1si2
|
gene regulation-RNA-DNA |
X-ray (2.6 Å) |
Ma JB, Ye K, Patel DJ |
(2004) "Structural
basis for overhang-specific small interfering RNA
recognition by the PAZ domain." Nature,
429, 318-322. doi: 10.1038/nature02519.
|
Crystal structure of the paz domain of human eif2c1 in
complex with a 9-mer sirna-like duplex of
deoxynucleotide overhang . SNAP output
|
1skm
|
transferase-DNA |
X-ray (2.2 Å) |
Horton JR, Ratner G, Banavali NK, Huang N, Choi Y,
Maier MA, Marquez VE, MacKerell AD, Cheng X |
(2004) "Caught
in the act: visualization of an intermediate in the DNA
base-flipping pathway induced by HhaI
methyltransferase." Nucleic Acids Res.,
32, 3877-3886. doi: 10.1093/nar/gkh701.
|
Hhai methyltransferase in complex with DNA containing
an abasic south carbocyclic sugar at its target site .
SNAP output
|
1skn
|
transcription-DNA |
X-ray (2.5 Å) |
Rupert PB, Daughdrill GW, Bowerman B, Matthews
BW |
(1998) "A new
DNA-binding motif in the Skn-1 binding domain-DNA
complex." Nat.Struct.Biol.,
5, 484-491. doi: 10.1038/nsb0698-484.
|
The binding domain of skn-1 in complex with DNA: a new
DNA-binding motif . SNAP
output
|
1skr
|
transferase-electron transport-DNA |
X-ray (2.4 Å) |
Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS,
Ellenberger T |
(2004) "Nucleotide
insertion opposite a cis-syn thymine dimer by a
replicative DNA polymerase from bacteriophage T7."
Nat.Struct.Mol.Biol., 11,
784-790. doi: 10.1038/nsmb792.
|
T7 DNA polymerase complexed to DNA primer-template and
ddatp . SNAP output
|
1sks
|
transferase-electron transport-DNA |
X-ray (2.3 Å) |
Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS,
Ellenberger T |
(2004) "Nucleotide
insertion opposite a cis-syn thymine dimer by a
replicative DNA polymerase from bacteriophage T7."
Nat.Struct.Mol.Biol., 11,
784-790. doi: 10.1038/nsmb792.
|
Binary 3' complex of t7 DNA polymerase with a DNA
primer-template containing a cis-syn thymine dimer on
the template . SNAP
output
|
1skw
|
transferase-electron transport-DNA |
X-ray (2.3 Å) |
Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS,
Ellenberger T |
(2004) "Nucleotide
insertion opposite a cis-syn thymine dimer by a
replicative DNA polymerase from bacteriophage T7."
Nat.Struct.Mol.Biol., 11,
784-790. doi: 10.1038/nsmb792.
|
Binary 3' complex of t7 DNA polymerase with a DNA
primer-template containing a disordered cis-syn thymine
dimer on the template . SNAP output
|
1sl0
|
transferase-electron transport-DNA |
X-ray (3.2 Å) |
Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS,
Ellenberger T |
(2004) "Nucleotide
insertion opposite a cis-syn thymine dimer by a
replicative DNA polymerase from bacteriophage T7."
Nat.Struct.Mol.Biol., 11,
784-790. doi: 10.1038/nsmb792.
|
Ternary 3' complex of t7 DNA polymerase with a DNA
primer-template containing a disordered cis-syn thymine
dimer on the template and an incoming nucleotide .
SNAP output
|
1sl1
|
transferase-electron transport-DNA |
X-ray (2.2 Å) |
Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS,
Ellenberger T |
(2004) "Nucleotide
insertion opposite a cis-syn thymine dimer by a
replicative DNA polymerase from bacteriophage T7."
Nat.Struct.Mol.Biol., 11,
784-790. doi: 10.1038/nsmb792.
|
Binary 5' complex of t7 DNA polymerase with a DNA
primer-template containing a cis-syn thymine dimer on
the template . SNAP
output
|
1sl2
|
transferase-electron transport-DNA |
X-ray (2.3 Å) |
Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS,
Ellenberger T |
(2004) "Nucleotide
insertion opposite a cis-syn thymine dimer by a
replicative DNA polymerase from bacteriophage T7."
Nat.Struct.Mol.Biol., 11,
784-790. doi: 10.1038/nsmb792.
|
Ternary 5' complex of t7 DNA polymerase with a DNA
primer-template containing a cis-syn thymine dimer on
the template and an incoming nucleotide . SNAP output
|
1srs
|
transcription-DNA |
X-ray (3.2 Å) |
Pellegrini L, Tan S, Richmond TJ |
(1995) "Structure
of serum response factor core bound to DNA."
Nature, 376, 490-498. doi:
10.1038/376490a0.
|
Serum response factor (srf) core complexed with
specific sre DNA . SNAP
output
|
1ssp
|
hydrolase-DNA |
X-ray (1.9 Å) |
Parikh SS, Mol CD, Slupphaug G, Bharati S, Krokan HE,
Tainer JA |
(1998) "Base
excision repair initiation revealed by crystal
structures and binding kinetics of human uracil-DNA
glycosylase with DNA." EMBO J.,
17, 5214-5226. doi: 10.1093/emboj/17.17.5214.
|
Wild-type uracil-DNA glycosylase bound to
uracil-containing DNA . SNAP output
|
1stx
|
hydrolase-DNA |
X-ray (2.1 Å) |
Horton NC, Perona JJ |
(2004) "DNA
cleavage by EcoRV endonuclease: two metal ions in three
metal ion binding sites." Biochemistry,
43, 6841-6857. doi: 10.1021/bi0499056.
|
Structure of the k38a mutant of ecorv bound to cognate
DNA and mn2+ . SNAP
output
|
1suz
|
hydrolase-DNA |
X-ray (1.8 Å) |
Horton NC, Perona JJ |
(2004) "DNA
Cleavage by EcoRV Endonuclease: Two Metal Ions in Three
Metal Ion Binding Sites." Biochemistry,
43, 6841-6857. doi: 10.1021/bi0499056.
|
The structure of k92a ecorv bound to cognate DNA and
mg2+ . SNAP output
|
1svc
|
transcription-DNA |
X-ray (2.6 Å) |
Muller CW, Rey FA, Sodeoka M, Verdine GL, Harrison
SC |
(1995) "Structure
of the NF-kappa B p50 homodimer bound to DNA."
Nature, 373, 311-317. doi:
10.1038/373311a0.
|
Nfkb p50 homodimer bound to DNA . SNAP output
|
1sx5
|
hydrolase-DNA |
X-ray (1.5 Å) |
Horton NC, Perona JJ |
(2004) "DNA
cleavage by EcoRV endonuclease: Two metal ions in three
metal ion binding sites." Biochemistry,
43, 6841-6857. doi: 10.1021/bi0499056.
|
K38a ecorv bound to cleaved DNA and mn2+: p1 crystal
form . SNAP output
|
1sx8
|
hydrolase-DNA |
X-ray (2.15 Å) |
Horton NC, Perona JJ |
(2004) "DNA
Cleavage by EcoRV Endonuclease: Two Metal Ions in Three
Metal Ion Binding Sites." Biochemistry,
43, 6841-6857. doi: 10.1021/bi0499056.
|
Ecorv bound to cognate DNA and mn2+ . SNAP output
|
1sxp
|
transferase-DNA |
X-ray (2.5 Å) |
Lariviere L, Morera S |
(2004) "Structural
evidence of a passive base flipping mechanism for
{beta}-Glucosyltransferase." J.Biol.Chem.,
279, 34715-34720. doi: 10.1074/jbc.M404394200.
|
Bgt in complex with a 13mer DNA containing a central
a:g mismatch . SNAP
output
|
1sxq
|
transferase-DNA |
X-ray (1.8 Å) |
Lariviere L, Morera S |
(2004) "Structural
evidence of a passive base flipping mechanism for
{beta}-Glucosyltransferase." J.Biol.Chem.,
279, 34715-34720. doi: 10.1074/jbc.M404394200.
|
Bgt in complex with a 13mer DNA containing a central
c:g base pair and udp . SNAP output
|
1t03
|
transferase-antibody-DNA |
X-ray (3.1 Å) |
Tuske S, Sarafianos SG, Clark Jr AD, Ding J, Naeger
LK, White KL, Miller MD, Gibbs CS, Boyer PL, Clark P,
Wang G, Gaffney BL, Jones RA, Jerina DM, Hughes SH,
Arnold E |
(2004) "Structure
of HIV-1 RT-DNA complexes before and after
incorporation of the anti-AIDS drug tenofovir."
Nat.Struct.Mol.Biol., 11,
469-474. doi: 10.1038/nsmb760.
|
Hiv-1 reverse transcriptase crosslinked to tenofovir
terminated template-primer (complex p) . SNAP output
|
1t05
|
transferase-DNA |
X-ray (3.0 Å) |
Tuske S, Sarafianos SG, Clark Jr AD, Ding J, Naeger
LK, White KL, Miller MD, Gibbs CS, Boyer PL, Clark P,
Wang G, Gaffney BL, Jones RA, Jerina DM, Hughes SH,
Arnold E |
(2004) "Structures
of HIV-1 RT-DNA complexes before and after
incorporation of the anti-AIDS drug tenofovir."
Nat.Struct.Mol.Biol., 11,
469-474. doi: 10.1038/nsmb760.
|
Hiv-1 reverse transcriptase crosslinked to
template-primer with tenofovir-diphosphate bound as the
incoming nucleotide substrate . SNAP output
|
1t2k
|
transcription-DNA |
X-ray (3.0 Å) |
Panne D, Maniatis T, Harrison SC |
(2004) "Crystal
structure of ATF-2/c-Jun and IRF-3 bound to the
interferon-beta enhancer." Embo J.,
23, 4384-4393. doi: 10.1038/sj.emboj.7600453.
|
Structure of the DNA binding domains of irf3, atf-2 and
jun bound to DNA . SNAP
output
|
1t2s
|
nucleic acid binding protein-DNA |
NMR |
Lingel A, Simon B, Izaurralde E, Sattler M |
(2004) "Nucleic
acid 3'-end recognition by the Argonaute2 PAZ
domain." Nat.Struct.Mol.Biol.,
11, 576-577. doi: 10.1038/nsmb777.
|
Structural basis for 3' end recognition of nucleic
acids by the drosophila argonaute 2 paz domain .
SNAP output
|
1t2t
|
hydrolase-DNA |
X-ray (2.5 Å) |
Edgell DR, Derbyshire V, Van Roey P, LaBonne S,
Stanger MJ, Li Z, Boyd TM, Shub DA, Belfort M |
(2004) "Intron-encoded
homing endonuclease I-TevI also functions as a
transcriptional autorepressor."
Nat.Struct.Mol.Biol., 11,
936-944. doi: 10.1038/nsmb823.
|
Crystal structure of the DNA-binding domain of intron
endonuclease i-tevi with operator site . SNAP output
|
1t38
|
transferase-DNA |
X-ray (3.2 Å) |
Daniels DS, Woo TT, Luu KX, Noll DM, Clarke ND, Pegg
AE, Tainer JA |
(2004) "DNA
binding and nucleotide flipping by the human DNA repair
protein AGT." Nat.Struct.Mol.Biol.,
11, 714-720. doi: 10.1038/nsmb791.
|
Human o6-alkylguanine-DNA alkyltransferase bound to DNA
containing o6-methylguanine . SNAP output
|
1t39
|
transferase-DNA |
X-ray (3.3 Å) |
Daniels DS, Woo TT, Luu KX, Noll DM, Clarke ND, Pegg
AE, Tainer JA |
(2004) "DNA
binding and nucleotide flipping by the human DNA repair
protein AGT." Nat.Struct.Mol.Biol.,
11, 714-720. doi: 10.1038/nsmb791.
|
Human o6-alkylguanine-DNA alkyltransferase covalently
crosslinked to DNA . SNAP output
|
1t3n
|
replication-DNA |
X-ray (2.3 Å) |
Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal
AK |
(2004) "Replication
by human DNA polymerase-iota occurs by Hoogsteen
base-pairing." Nature,
430, 377-380. doi: 10.1038/nature02692.
|
Structure of the catalytic core of DNA polymerase iota
in complex with DNA and dttp . SNAP output
|
1t7p
|
transferase-DNA |
X-ray (2.2 Å) |
Doublie S, Tabor S, Long AM, Richardson CC,
Ellenberger T |
(1998) "Crystal
structure of a bacteriophage T7 DNA replication complex
at 2.2 A resolution." Nature,
391, 251-258. doi: 10.1038/34593.
|
T7 DNA polymerase complexed to DNA primer-template,a
nucleoside triphosphate, and its processivity factor
thioredoxin . SNAP
output
|
1t8e
|
transferase-electron transport-DNA |
X-ray (2.54 Å) |
Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel
TA, Ellenberger T |
(2004) "Structural
basis for the dual coding potential of 8-oxoguanosine
by a high-fidelity DNA polymerase." Embo
J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354.
|
T7 DNA polymerase ternary complex with dctp at the
insertion site. . SNAP
output
|
1t8i
|
isomerase-DNA |
X-ray (3.0 Å) |
Staker BL, Feese MD, Cushman M, Pommier Y, Zembower
D, Stewart L, Burgin AB |
(2005) "Structures
of three classes of anticancer agents bound to the
human topoisomerase I-DNA covalent complex."
J.Med.Chem., 48, 2336-2345.
doi: 10.1021/jm049146p.
|
Human DNA topoisomerase i (70 kda) in complex with the
poison camptothecin and covalent complex with a 22 base
pair DNA duplex . SNAP
output
|
1t9i
|
hydrolase-DNA |
X-ray (1.6 Å) |
Chevalier B, Sussman D, Otis C, Noel AJ, Turmel M,
Lemieux C, Stephens K, Monnat Jr RJ, Stoddard BL |
(2004) "Metal-Dependent
DNA Cleavage Mechanism of the I-CreI LAGLIDADG Homing
Endonuclease." Biochemistry,
43, 14015-14026. doi: 10.1021/bi048970c.
|
I-crei(d20n)-DNA complex . SNAP output
|
1t9j
|
hydrolase-DNA |
X-ray (2.0 Å) |
Chevalier B, Sussman D, Otis C, Noel AJ, Turmel M,
Lemieux C, Stephens K, Monnat Jr RJ, Stoddard BL |
(2004) "Metal-Dependent
DNA Cleavage Mechanism of the I-CreI LAGLIDADG Homing
Endonuclease." Biochemistry,
43, 14015-14026. doi: 10.1021/bi048970c.
|
I-crei(q47e)-DNA complex . SNAP output
|
1tau
|
transferase-DNA |
X-ray (3.0 Å) |
Eom SH, Wang J, Steitz TA |
(1996) "Structure
of Taq ploymerase with DNA at the polymerase active
site." Nature, 382,
278-281. doi: 10.1038/382278a0.
|
Taq polymerase (e.c.2.7.7.7)-DNA-b-octylglucoside
complex . SNAP
output
|
1tc3
|
DNA binding protein-DNA |
X-ray (2.45 Å) |
van Pouderoyen G, Ketting RF, Perrakis A, Plasterk
RH, Sixma TK |
(1997) "Crystal
structure of the specific DNA-binding domain of Tc3
transposase of C.elegans in complex with transposon
DNA." EMBO J., 16,
6044-6054. doi: 10.1093/emboj/16.19.6044.
|
Transposase tc3a1-65 from caenorhabditis elegans .
SNAP output
|
1tdz
|
hydrolase-DNA |
X-ray (1.8 Å) |
Coste F, Ober M, Carell T, Boiteux S, Zelwer C,
Castaing B |
(2004) "Structural
basis for the recognition of the FapydG lesion
(2,6-diamino-4-hydroxy-5-formamidopyrimidine) by
formamidopyrimidine-DNA glycosylase."
J.Biol.Chem., 279,
44074-44083. doi: 10.1074/jbc.M405928200.
|
Crystal structure complex between the lactococcus
lactis fpg (mutm) and a fapy-dg containing DNA .
SNAP output
|
1tez
|
lyase-DNA |
X-ray (1.8 Å) |
Mees A, Klar T, Gnau P, Hennecke U, Eker APM, Carell
T, Essen L-O |
(2004) "Crystal
structure of a photolyase bound to a CPD-like DNA
lesion after in situ repair." Science,
306, 1789-1793. doi: 10.1126/science.1101598.
|
Complex between DNA and the DNA photolyase from
anacystis nidulans . SNAP output
|
1tf3
|
transcription-DNA |
NMR |
Foster MP, Wuttke DS, Radhakrishnan I, Case DA,
Gottesfeld JM, Wright PE |
(1997) "Domain
packing and dynamics in the DNA complex of the
N-terminal zinc fingers of TFIIIA."
Nat.Struct.Biol., 4, 605-608.
doi: 10.1038/nsb0897-605.
|
Tfiiia finger 1-3 bound to DNA, NMR, 22 structures .
SNAP output
|
1tf6
|
transcription-DNA |
X-ray (3.1 Å) |
Nolte RT, Conlin RM, Harrison SC, Brown RS |
(1998) "Differing
roles for zinc fingers in DNA recognition: structure of
a six-finger transcription factor IIIA complex."
Proc.Natl.Acad.Sci.USA, 95,
2938-2943. doi: 10.1073/pnas.95.6.2938.
|
Co-crystal structure of xenopus tfiiia zinc finger
domain bound to the 5s ribosomal RNA gene internal
control region . SNAP
output
|
1tgh
|
transcription-DNA |
X-ray (2.9 Å) |
Juo ZS, Chiu TK, Leiberman PM, Baikalov I, Berk AJ,
Dickerson RE |
(1996) "How
proteins recognize the TATA box."
J.Mol.Biol., 261, 239-254.
doi: 10.1006/jmbi.1996.0456.
|
Tata binding protein (tbp)-DNA complex . SNAP output
|
1tk0
|
transferase-electron transport-DNA |
X-ray (2.3 Å) |
Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel
TA, Ellenberger T |
(2004) "Structural
basis for the dual coding potential of 8-oxoguanosine
by a high-fidelity DNA polymerase." Embo
J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354.
|
T7 DNA polymerase ternary complex with 8 oxo guanosine
and ddctp at the insertion site . SNAP output
|
1tk5
|
transferase-electron transport-DNA |
X-ray (2.2 Å) |
Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel
TA, Ellenberger T |
(2004) "Structural
basis for the dual coding potential of 8-oxoguanosine
by a high-fidelity DNA polymerase." Embo
J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354.
|
T7 DNA polymerase binary complex with 8 oxo guanosine
in the templating strand . SNAP output
|
1tk8
|
transferase-electron transport-DNA |
X-ray (2.5 Å) |
Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel
TA, Ellenberger T |
(2004) "Structural
basis for the dual coding potential of 8-oxoguanosine
by a high-fidelity DNA polymerase." Embo
J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354.
|
T7 DNA polymerase ternary complex with 8 oxo guanosine
and damp at the elongation site . SNAP output
|
1tkd
|
transferase-electron transport-DNA |
X-ray (2.49 Å) |
Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel
TA, Ellenberger T |
(2004) "Structural
basis for the dual coding potential of 8-oxoguanosine
by a high-fidelity DNA polymerase." Embo
J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354.
|
T7 DNA polymerase ternary complex with 8 oxo guanosine
and dcmp at the elongation site . SNAP output
|
1tl8
|
isomerase-DNA |
X-ray (3.1 Å) |
Ioanoviciu A, Antony S, Pommier Y, Staker BL, Stewart
L, Cushman M |
(2005) "Synthesis
and Mechanism of Action Studies of a Series of
Norindenoisoquinoline Topoisomerase I Poisons Reveal an
Inhibitor with a Flipped Orientation in the Ternary
DNA-Enzyme-Inhibitor Complex As Determined by X-ray
Crystallographic Analysis." J.Med.Chem.,
48, 4803-4814. doi: 10.1021/jm050076b.
|
Human DNA topoisomerase i (70 kda) in complex with the
indenoisoquinoline ai-iii-52 and covalent complex with
a 22 base pair DNA duplex . SNAP output
|
1tn9
|
integrase-DNA |
NMR |
Wojciak JM, Connolly KM, Clubb RT |
(1999) "NMR
structure of the Tn916 integrase-DNA complex."
Nat.Struct.Biol., 6, 366-373.
doi: 10.1038/7603.
|
The solution structure of tn916 integrase n-terminal
domain-DNA complex . SNAP output
|
1tqe
|
transcription-protein binding-DNA |
X-ray (2.7 Å) |
Han A, He J, Wu Y, Liu JO, Chen L |
(2005) "Mechanism
of Recruitment of Class II Histone Deacetylases by
Myocyte Enhancer Factor-2." J.Mol.Biol.,
345, 91-102. doi: 10.1016/j.jmb.2004.10.033.
|
Mechanism of recruitment of class ii histone
deacetylases by myocyte enhancer factor-2 . SNAP output
|
1tro
|
transcription-DNA |
X-ray (1.9 Å) |
Otwinowski Z, Schevitz RW, Zhang RG, Lawson CL,
Joachimiak A, Marmorstein RQ, Luisi BF, Sigler PB |
(1988) "Crystal
structure of trp repressor/operator complex at atomic
resolution." Nature, 335,
321-329. doi: 10.1038/335321a0.
|
Crystal structure of trp repressor operator complex at
atomic resolution . SNAP
output
|
1trr
|
transcription-DNA |
X-ray (2.4 Å) |
Lawson CL, Carey J |
(1993) "Tandem
binding in crystals of a trp repressor/operator
half-site complex." Nature,
366, 178-182. doi: 10.1038/366178a0.
|
Tandem binding in crystals of a trp repressor-operator
half-site complex . SNAP
output
|
1tsr
|
antitumor protein-DNA |
X-ray (2.2 Å) |
Cho Y, Gorina S, Jeffrey PD, Pavletich NP |
(1994) "Crystal
structure of a p53 tumor suppressor-DNA complex:
understanding tumorigenic mutations."
Science, 265, 346-355.
|
P53 core domain in complex with DNA . SNAP output
|
1ttu
|
transcription |
X-ray (2.85 Å) |
Kovall RA, Hendrickson WA |
(2004) "Crystal
structure of the nuclear effector of Notch signaling,
CSL, bound to DNA." Embo J.,
23, 3441-3451. doi: 10.1038/sj.emboj.7600349.
|
Crystal structure of csl bound to DNA . SNAP output
|
1tup
|
antitumor protein-DNA |
X-ray (2.2 Å) |
Cho Y, Gorina S, Jeffrey PD, Pavletich NP |
(1994) "Crystal
structure of a p53 tumor suppressor-DNA complex:
understanding tumorigenic mutations."
Science, 265, 346-355.
|
Tumor suppressor p53 complexed with DNA . SNAP output
|
1tv9
|
transferase-DNA |
X-ray (2.0 Å) |
Krahn JM, Beard WM, Wilson SH |
(2004) "STRUCTURAL
INSIGHTS INTO DNA POLYMERASE BETA DETERRENTS FOR
MISINCORPORATION SUPPORT OF AN INDUCED-FIT MECHANISM
FOR FIDELITY." Structure,
12, 1823-1832. doi: 10.1016/j.str.2004.08.001.
|
Human DNA polymerase beta complexed with nicked DNA
containing a mismatched template adenine and incoming
cytidine . SNAP
output
|
1tva
|
transferase-DNA |
X-ray (2.6 Å) |
Krahn JM, Beard WA, Wilson SH |
(2004) "Structural
insights into DNA polymerase Beta deterrents for
misincorporation support an induced-fit mechanism for
fidelity." Structure, 12,
1823-1832. doi: 10.1016/j.str.2004.08.001.
|
Human DNA polymerase beta complexed with nicked DNA
containing a mismatched template thymidine and incoming
cytidine . SNAP
output
|
1tw8
|
hydrolase-DNA |
X-ray (2.8 Å) |
Etzkorn C, Horton NC |
(2004) "Ca2+
binding in the active site of HincII: implications for
the catalytic mechanism." Biochemistry,
43, 13256-13270.
|
Hincii bound to ca2+ and cognate DNA gtcgac . SNAP output
|
1tx3
|
hydrolase-DNA |
X-ray (2.5 Å) |
Etzkorn C, Horton NC |
(2004) "Ca2+
binding in the active site of HincII: implications for
the catalytic mechanism." Biochemistry,
43, 13256-13270. doi: 10.1021/bi0490082.
|
Hincii bound to cognate DNA . SNAP output
|
1u0c
|
hydrolase-DNA |
X-ray (2.5 Å) |
Sussman D, Chadsey M, Fauce S, Engel A, Bruett A,
Monnat R, Stoddard BL, Seligman LM |
(2004) "Isolation
and characterization of new homing endonuclease
specificities at individual target site positions."
J.Mol.Biol., 342, 31-41. doi:
10.1016/j.jmb.2004.07.031.
|
Y33c mutant of homing endonuclease i-crei . SNAP output
|
1u0d
|
hydrolase-DNA |
X-ray (2.9 Å) |
Sussman D, Chadsey M, Fauce S, Engel A, Bruett A,
Monnat R, Stoddard BL, Seligman LM |
(2004) "Isolation
and characterization of new homing endonuclease
specificities at individual target site positions."
J.Mol.Biol., 342, 31-41. doi:
10.1016/j.jmb.2004.07.031.
|
Y33h mutant of homing endonuclease i-crei . SNAP output
|
1u1k
|
transport protein-DNA |
X-ray (2.0 Å) |
Myers JC, Shamoo Y |
(2004) "Human
UP1 as a Model for Understanding Purine Recognition in
the Family of Proteins Containing the RNA Recognition
Motif (RRM)." J.Mol.Biol.,
342, 743-756. doi: 10.1016/j.jmb.2004.07.029.
|
Crystal structure of up1 complexed with d(ttagggtt 7da
ggg); a human telomeric repeat containing
7-deaza-adenine . SNAP
output
|
1u1l
|
transport protein-DNA |
X-ray (2.0 Å) |
Myers JC, Shamoo Y |
(2004) "Human
UP1 as a Model for Understanding Purine Recognition in
the Family of Proteins Containing the RNA Recognition
Motif (RRM)." J.Mol.Biol.,
342, 743-756. doi: 10.1016/j.jmb.2004.07.029.
|
Crystal structure of up1 complexed with d(ttagggtt prn
ggg); a human telomeric repeat containing nebularine .
SNAP output
|
1u1m
|
transport protein-DNA |
X-ray (2.0 Å) |
Myers JC, Shamoo Y |
(2004) "Human
UP1 as a Model for Understanding Purine Recognition in
the Family of Proteins Containing the RNA Recognition
Motif (RRM)." J.Mol.Biol.,
342, 743-756. doi: 10.1016/j.jmb.2004.07.029.
|
Crystal structure of up1 complexed with d(ttagggtta 7gu
gg); a human telomeric repeat containing
7-deaza-guanine . SNAP
output
|
1u1n
|
transport protein-DNA |
X-ray (2.1 Å) |
Myers JC, Shamoo Y |
(2004) "Human
UP1 as a Model for Understanding Purine Recognition in
the Family of Proteins Containing the RNA Recognition
Motif (RRM)." J.Mol.Biol.,
342, 743-756. doi: 10.1016/j.jmb.2004.07.029.
|
Crystal structure of up1 complexed with d(ttagggtta
(prn)gg); a human telomeric repeat containing
nebularine . SNAP
output
|
1u1o
|
transport protein-DNA |
X-ray (2.0 Å) |
Myers JC, Shamoo Y |
(2004) "Human
UP1 as a Model for Understanding Purine Recognition in
the Family of Proteins Containing the RNA Recognition
Motif (RRM)." J.Mol.Biol.,
342, 743-756. doi: 10.1016/j.jmb.2004.07.029.
|
Crystal structure of up1 complexed with
d(ttagggttag(di)g); a human telomeric repeat containing
inosine . SNAP
output
|
1u1p
|
transport protein-DNA |
X-ray (1.9 Å) |
Myers JC, Shamoo Y |
(2004) "Human
UP1 as a Model for Understanding Purine Recognition in
the Family of Proteins Containing the RNA Recognition
Motif (RRM)." J.Mol.Biol.,
342, 743-756. doi: 10.1016/j.jmb.2004.07.029.
|
Crystal structure of up1 complexed with d(ttagggtta 2pr
gg); a human telomeric repeat containing 2-aminopurine
. SNAP output
|
1u1q
|
transport protein-DNA |
X-ray (1.8 Å) |
Myers JC, Shamoo Y |
(2004) "Human
UP1 as a Model for Understanding Purine Recognition in
the Family of Proteins Containing the RNA Recognition
Motif (RRM)." J.Mol.Biol.,
342, 743-756. doi: 10.1016/j.jmb.2004.07.029.
|
Crystal structure of up1 complexed with
d(ttagggtta(di)gg); a human telomeric repeat containing
inosine . SNAP
output
|
1u1r
|
transport protein-DNA |
X-ray (1.8 Å) |
Myers JC, Shamoo Y |
(2004) "Human
UP1 as a Model for Understanding Purine Recognition in
the Family of Proteins Containing the RNA Recognition
Motif (RRM)." J.Mol.Biol.,
342, 743-756. doi: 10.1016/j.jmb.2004.07.029.
|
Crystal structure of up1 complexed with
d(ttagggttag(2pr)g); a human telomeric repeat
containing 2-aminopurine . SNAP output
|
1u1y
|
virus-RNA |
X-ray (2.85 Å) |
Horn WT, Convery MA, Stonehouse NJ, Adams CJ, Liljas
L, Phillips SE, Stockley PG |
(2004) "The
crystal structure of a high affinity RNA stem-loop
complexed with the bacteriophage MS2 capsid: further
challenges in the modeling of ligand-RNA
interactions." Rna, 10,
1776-1782. doi: 10.1261/rna.7710304.
|
Crystal structure of a complex between wt bacteriophage
ms2 coat protein and an f5 aptamer RNA stemloop with
2aminopurine substituted at the-10 position . SNAP output
|
1u35
|
structural protein-DNA |
X-ray (3.0 Å) |
Chakravarthy S, Gundimella SK, Caron C, Perche PY,
Pehrson JR, Khochbin S, Luger K |
(2005) "Structural
characterization of the histone variant macroH2A."
Mol.Cell.Biol., 25,
7616-7624. doi: 10.1128/MCB.25.17.7616-7624.2005.
|
Crystal structure of the nucleosome core particle
containing the histone domain of macroh2a . SNAP output
|
1u3e
|
DNA binding protein-DNA |
X-ray (2.92 Å) |
Shen BW, Landthaler M, Shub DA, Stoddard BL |
(2004) "DNA
Binding and Cleavage by the HNH Homing Endonuclease
I-HmuI." J.Mol.Biol.,
342, 43-56. doi: 10.1016/j.jmb.2004.07.032.
|
DNA binding and cleavage by the hnh homing endonuclease
i-hmui . SNAP output
|
1u45
|
transferase-DNA |
X-ray (2.01 Å) |
Hsu GW, Ober M, Carell T, Beese LS |
(2004) "Error-prone
replication of oxidatively damaged DNA by a
high-fidelity DNA polymerase." Nature,
431, 217-221. doi: 10.1038/nature02908.
|
8oxoguanine at the pre-insertion site of the polymerase
active site . SNAP
output
|
1u47
|
transferase-DNA |
X-ray (2.0 Å) |
Hsu GW, Ober M, Carell T, Beese LS |
(2004) "Error-prone
replication of oxidatively damaged DNA by a
high-fidelity DNA polymerase." Nature,
431, 217-221. doi: 10.1038/nature02908.
|
Cytosine-8-oxoguanine base pair at the polymerase
active site . SNAP
output
|
1u48
|
transferase-DNA |
X-ray (2.1 Å) |
Hsu GW, Ober M, Carell T, Beese LS |
(2004) "Error-prone
replication of oxidatively damaged DNA by a
high-fidelity DNA polymerase." Nature,
431, 217-221. doi: 10.1038/nature02908.
|
Extension of a cytosine-8-oxoguanine base pair .
SNAP output
|
1u49
|
transferase-DNA |
X-ray (2.15 Å) |
Hsu GW, Ober M, Carell T, Beese LS |
(2004) "Error-prone
replication of oxidatively damaged DNA by a
high-fidelity DNA polymerase." Nature,
431, 217-221. doi: 10.1038/nature02908.
|
Adenine-8oxoguanine mismatch at the polymerase active
site . SNAP output
|
1u4b
|
transferase-DNA |
X-ray (1.6 Å) |
Hsu GW, Ober M, Carell T, Beese LS |
(2004) "Error-prone
replication of oxidatively damaged DNA by a
high-fidelity DNA polymerase." Nature,
431, 217-221. doi: 10.1038/nature02908.
|
Extension of an adenine-8oxoguanine mismatch . SNAP output
|
1u78
|
DNA binding protein-DNA |
X-ray (2.69 Å) |
Watkins S, van Pouderoyen G, Sixma TK |
(2004) "Structural
analysis of the bipartite DNA-binding domain of Tc3
transposase bound to transposon DNA." Nucleic
Acids Res., 32, 4306-4312. doi:
10.1093/nar/gkh770.
|
Structure of the bipartite DNA-binding domain of tc3
transposase bound to transposon DNA . SNAP output
|
1u8b
|
metal binding protein-DNA |
X-ray (2.1 Å) |
He C, Hus JC, Sun LJ, Zhou P, Norman DP, Dotsch V,
Wei H, Gross JD, Lane WS, Wagner G, Verdine GL |
(2005) "A
methylation-dependent electrostatic switch controls DNA
repair and transcriptional activation by E. coli
ada." Mol.Cell, 20,
117-129. doi: 10.1016/j.molcel.2005.08.013.
|
Crystal structure of the methylated n-ada-DNA complex .
SNAP output
|
1u8r
|
metal-binding protein,transcription-DNA |
X-ray (2.75 Å) |
Wisedchaisri G, Holmes RK, Hol WGJ |
(2004) "Crystal
Structure of an IdeR-DNA Complex Reveals a
Conformational Change in Activated IdeR for
Base-specific Interactions." J.Mol.Biol.,
342, 1155-1169. doi: 10.1016/j.jmb.2004.07.083.
|
Crystal structure of an ider-DNA complex reveals a
conformational change in activated ider for
base-specific interactions . SNAP output
|
1ua0
|
transferase-DNA |
X-ray (2.1 Å) |
Hsu GW, Kiefer JR, Burnouf D, Becherel OJ, Fuchs RPP,
Beese LS |
(2004) "Observing
translesion synthesis of an aromatic amine DNA adduct
by a high-fidelity DNA polymerase."
J.Biol.Chem., 279,
50280-50285. doi: 10.1074/jbc.M409224200.
|
Aminofluorene DNA adduct at the pre-insertion site of a
DNA polymerase . SNAP
output
|
1ua1
|
transferase-DNA |
X-ray (2.0 Å) |
Hsu GW, Kiefer JR, Becherel OJ, Fuchs RPP, Beese
LS |
(2004) "Observing
translesion synthesis of an aromatic amine DNA adduct
by a high-fidelity DNA polymerase."
J.Biol.Chem., 279,
50280-50285. doi: 10.1074/jbc.M409224200.
|
Structure of aminofluorene adduct paired opposite
cytosine at the polymerase active site. . SNAP output
|
1uaa
|
hydrolase-DNA |
X-ray (3.0 Å) |
Korolev S, Hsieh J, Gauss GH, Lohman TM, Waksman
G |
(1997) "Major
domain swiveling revealed by the crystal structures of
complexes of E. coli Rep helicase bound to
single-stranded DNA and ADP."
Cell(Cambridge,Mass.), 90,
635-647. doi: 10.1016/S0092-8674(00)80525-5.
|
E. coli rep helicase-DNA complex . SNAP output
|
1ubd
|
transcription-DNA |
X-ray (2.5 Å) |
Houbaviy HB, Usheva A, Shenk T, Burley SK |
(1996) "Cocrystal
structure of YY1 bound to the adeno-associated virus P5
initiator." Proc.Natl.Acad.Sci.USA,
93, 13577-13582. doi: 10.1073/pnas.93.24.13577.
|
Co-crystal structure of human yy1 zinc finger domain
bound to the adeno-associated virus p5 initiator
element . SNAP
output
|
1unj
|
DNA-antibiotic |
X-ray (2.5 Å) |
Alexopoulos EC, Jares-Erijman EA, Jovin TM, Klement
R, Machinek R, Sheldrick GM, Uson I |
(2005) "Crystal
and Solution Structures of 7-Amino-Actinomycin D
Complexes with D(Ttagbrut), D(Ttagtt) and
D(Tttagttt)." Acta Crystallogr.,Sect.D,
61, 407. doi: 10.1107/S090744490500082X.
|
Crystal structure of a 7-aminoactinomycin d complex
with non-complementary DNA . SNAP output
|
1unm
|
DNA-antibiotic |
X-ray (2.0 Å) |
Alexopoulos EC, Jares-Erijman EA, Jovin TM, Klement
R, Machinek R, Sheldrick GM, Uson I |
(2005) "Crystal
and Solution Structures of 7-Amino-Actinomycin D
Complexes with D(Ttagbrut), D(Ttagtt) and
D(Tttagttt)." Acta Crystallogr.,Sect.D,
61, 407. doi: 10.1107/S090744490500082X.
|
Crystal structure of 7-aminoactinomycin d with
non-complementary DNA . SNAP output
|
1urn
|
transcription-RNA |
X-ray (1.92 Å) |
Oubridge C, Ito N, Evans PR, Teo CH, Nagai K |
(1994) "Crystal
structure at 1.92 A resolution of the RNA-binding
domain of the U1A spliceosomal protein complexed with
an RNA hairpin." Nature,
372, 432-438. doi: 10.1038/372432a0.
|
U1a mutant-RNA complex + glycerol . SNAP output
|
1uut
|
hydrolase-DNA |
X-ray (2.0 Å) |
Hickman AB, Ronning DR, Perez ZN, Kotin RM, Dyda
F |
(2004) "The
Nuclease Domain of Adeno-Associated Virus Rep
Coordinates Replication Initiation Using Two Distinct
DNA Recognition Interfaces." Mol.Cell,
13, 403. doi: 10.1016/S1097-2765(04)00023-1.
|
The nuclease domain of adeno-associated virus rep
complexed with the rbe' stemloop of the viral inverted
terminal repeat . SNAP
output
|
1v14
|
hydrolase |
X-ray (2.9 Å) |
Mate MJ, Kleanthous C |
(2004) "Structure-Based
Analysis of the Metal-Dependent Mechanism of H-N-H
Endonucleases." J.Biol.Chem.,
279, 34763. doi: 10.1074/JBC.M403719200.
|
Crystal structure of the colicin e9, mutant his103ala,
in complex with mg+2 and dsDNA (resolution 2.9a) .
SNAP output
|
1v15
|
hydrolase |
X-ray (2.4 Å) |
Mate MJ, Kleanthous C |
(2004) "Structure-Based
Analysis of the Metal-Dependent Mechanism of H-N-H
Endonucleases." J.Biol.Chem.,
279, 34763. doi: 10.1074/JBC.M403719200.
|
Crystal structure of the colicin e9, mutant his103ala,
in complex with zn+2 and dsDNA (resolution 2.4a) .
SNAP output
|
1vas
|
hydrolase-DNA |
X-ray (2.75 Å) |
Vassylyev DG, Kashiwagi T, Mikami Y, Ariyoshi M, Iwai
S, Ohtsuka E, Morikawa K |
(1995) "Atomic
model of a pyrimidine dimer excision repair enzyme
complexed with a DNA substrate: structural basis for
damaged DNA recognition."
Cell(Cambridge,Mass.), 83,
773-782. doi: 10.1016/0092-8674(95)90190-6.
|
Atomic model of a pyrimidine dimer specific excision
repair enzyme complexed with a DNA substrate:
structural basis for damaged DNA recognition . SNAP output
|
1vfc
|
structural protein-DNA |
NMR |
Hanaoka S, Nagadoi A, Nishimura Y |
(2005) "Comparison
between TRF2 and TRF1 of their telomeric DNA-bound
structures and DNA-binding activities." Protein
Sci., 14, 119-130. doi: 10.1110/ps.04983705.
|
Solution structure of the DNA complex of human trf2 .
SNAP output
|
1vkx
|
transcription-DNA |
X-ray (2.9 Å) |
Chen FE, Huang DB, Chen YQ, Ghosh G |
(1998) "Crystal
structure of p50/p65 heterodimer of transcription
factor NF-kappaB bound to DNA." Nature,
391, 410-413. doi: 10.1038/34956.
|
Crystal structure of the nfkb p50-p65 heterodimer
complexed to the immunoglobulin kb DNA . SNAP output
|
1vol
|
transcription-DNA |
X-ray (2.7 Å) |
Nikolov DB, Chen H, Halay ED, Usheva AA, Hisatake K,
Lee DK, Roeder RG, Burley SK |
(1995) "Crystal
structure of a TFIIB-TBP-TATA-element ternary
complex." Nature, 377,
119-128. doi: 10.1038/377119a0.
|
Tfiib (human core domain)-tbp (a.thaliana)-tata element
ternary complex . SNAP
output
|
1vpw
|
transcription-DNA |
X-ray (2.7 Å) |
Arvidson DN, Lu F, Faber C, Zalkin H, Brennan RG |
(1998) "The
structure of PurR mutant L54M shows an alternative
route to DNA kinking." Nat.Struct.Biol.,
5, 436-441. doi: 10.1038/nsb0698-436.
|
Structure of the purr mutant, l54m, bound to
hypoxanthine and purf operator DNA . SNAP output
|
1vq5
|
ribosome |
X-ray (2.6 Å) |
Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz
TA |
(2005) "Structural
Insights into the Roles of Water and the 2' Hydroxyl of
the P Site tRNA in the Peptidyl Transferase
Reaction." Mol.Cell, 20,
437-448. doi: 10.1016/j.molcel.2005.09.006.
|
The structure of the transition state analogue "raa"
bound to the large ribosomal subunit of haloarcula
marismortui . SNAP
output
|
1vqp
|
ribosome |
X-ray (2.25 Å) |
Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz
TA |
(2005) "Structural
Insights into the Roles of Water and the 2' Hydroxyl of
the P Site tRNA in the Peptidyl Transferase
Reaction." Mol.Cell, 20,
437-448. doi: 10.1016/j.molcel.2005.09.006.
|
The structure of the transition state analogue "rap"
bound to the large ribosomal subunit of haloarcula
marismortui . SNAP
output
|
1vrl
|
hydrolase-DNA |
X-ray (2.5 Å) |
Fromme JC, Banerjee A, Huang SJ, Verdine GL |
(2004) "Structural
basis for removal of adenine mispaired with
8-oxoguanine by MutY adenine DNA glycosylase."
Nature, 427, 652-656. doi:
10.1038/nature02306.
|
Muty adenine glycosylase in complex with DNA and soaked
adenine free base . SNAP
output
|
1vrr
|
hydrolase-DNA |
X-ray (2.7 Å) |
Townson SA, Samuelson JC, Xu SY, Aggarwal AK |
(2005) "Implications
for Switching Restriction Enzyme Specificities from the
Structure of BstYI Bound to a BglII DNA Sequence."
Structure, 13, 791-801. doi:
10.1016/j.str.2005.02.018.
|
Crystal structure of the restriction endonuclease bstyi
complex with DNA . SNAP
output
|
1vs2
|
DNA-antibiotic |
X-ray (2.0 Å) |
Wang AH, Ughetto G, Quigley GJ, Rich A |
(1986) "Interactions
of Quinoxaline Antibiotic and DNA: The Molecular
Structure of a Triostin A-D(Gcgtacgc) Complex."
J.Biomol.Struct.Dyn., 4, 319.
|
Interactions of quinoxaline antibiotic and DNA: the
molecular structure of a triostin a-d(gcgtacgc) complex
. SNAP output
|
1vtg
|
DNA-antibiotic |
X-ray (1.67 Å) |
Wang AH, Ughetto G, Quigley GJ, Hakoshima T, van der
Marel GA, van Boom JH, Rich A |
(1984) "The
molecular structure of a DNA-triostin A complex."
Science, 225, 1115-1121.
|
The molecular structure of a DNA-triostin a complex .
SNAP output
|
1vtl
|
transcription-DNA |
X-ray (2.25 Å) |
Kim JL, Nikolov DB, Burley SK |
(1993) "Co-Crystal
Structure of TBP Recognizing the Minor Groove of a TATA
Element." Nature, 365,
520-527. doi: 10.1038/365520a0.
|
Co-crystal structure of tbp recognizing the minor
groove of a tata element . SNAP output
|
1vtn
|
transcription-DNA |
X-ray (2.5 Å) |
Clark KL, Halay ED, Lai E, Burley SK |
(1993) "Co-Crystal
Structure of the HNF-3/Fork Head DNA-Recognition Motif
Resembles Histone H5." Nature,
364, 412-420. doi: 10.1038/364412a0.
|
Co-crystal structure of the hnf-3-fork head
DNA-recognition motif resembles histone h5 . SNAP output
|
1vto
|
transcription-DNA |
X-ray (1.9 Å) |
Kim JL, Burley SK |
(1994) "1.9 A
Resolution Refined Structure of TBP Recognizing the
Minor Groove of TATAAAAG."
Nat.Struct.Biol., 1, 638-653.
|
1.9 Å resolution refined structure of tbp recognizing
the minor groove of tataaaag . SNAP output
|
1w0t
|
DNA binding protein |
X-ray (2.0 Å) |
Court RI, Chapman LM, Fairall L, Rhodes D |
(2005) "How the
Human Telomeric Proteins Trf1 and Trf2 Recognize
Telomeric DNA: A View from High-Resolution Crystal
Structures." Embo Rep.,
6, 39. doi: 10.1038/SJ.EMBOR.7400314.
|
Htrf1 DNA-binding domain in complex with telomeric DNA.
. SNAP output
|
1w0u
|
DNA binding protein |
X-ray (1.8 Å) |
Court RI, Chapman LM, Fairall L, Rhodes D |
(2005) "How the
Human Telomeric Proteins Trf1 and Trf2 Recognize
Telomeric DNA: A View from High-Resolution Crystal
Structures." Embo Rep.,
6, 39. doi: 10.1038/SJ.EMBOR.7400314.
|
Htrf2 DNA-binding domain in complex with telomeric DNA.
. SNAP output
|
1w36
|
recombination |
X-ray (3.1 Å) |
Singleton MR, Dillingham MS, Gaudier M,
Kowalczykowski SC, Wigley DB |
(2004) "Crystal
Structure of Recbcd Enzyme Reveals a Machine for
Processing DNA Breaks." Nature,
432, 187. doi: 10.1038/NATURE02988.
|
Recbcd:DNA complex . SNAP output
|
1w7a
|
DNA binding |
X-ray (2.27 Å) |
Lamers MH, Georgijevic D, Lebbink J, Winterwerp HHK,
Agianian B, De Wind N, Sixma TK |
(2004) "ATP
Increases the Affinity between Muts ATPase Domains:
Implications for ATP Hydrolysis and Conformational
Changes." J.Biol.Chem.,
279, 43879. doi: 10.1074/JBC.M406380200.
|
Atp bound muts . SNAP
output
|
1wb9
|
DNA-binding |
X-ray (2.1 Å) |
Lebbink JHG, Georgijevic D, Natrajan G, Fish A,
Winterwerp HHK, Sixma TK, De Wind N |
(2006) "Dual
Role of Muts Glutamate 38 in DNA Mismatch
Discrimination and in the Authorization of Repair."
Embo J., 25, 409. doi:
10.1038/SJ.EMBOJ.7600936.
|
Crystal structure of e. coli DNA mismatch repair enzyme
muts, e38t mutant, in complex with a g.t mismatch .
SNAP output
|
1wbb
|
DNA-binding |
X-ray (2.5 Å) |
Lebbink JHG, Georgijevic D, Natrajan G, Fish A,
Winterwerp HHK, Sixma TK, De Wind N |
(2006) "Dual
Role of Muts Glutamate 38 in DNA Mismatch
Discrimination and in the Authorization of Repair."
Embo J., 25, 409. doi:
10.1038/SJ.EMBOJ.7600936.
|
Crystal structure of e. coli DNA mismatch repair enzyme
muts, e38a mutant, in complex with a g.t mismatch .
SNAP output
|
1wbd
|
DNA-binding |
X-ray (2.4 Å) |
Lebbink JHG, Georgijevic D, Natrajan G, Fish A,
Winterwerp HHK, Sixma TK, De Wind N |
(2006) "Dual
Role of Muts Glutamate 38 in DNA Mismatch
Discrimination and in the Authorization of Repair."
Embo J., 25, 409. doi:
10.1038/SJ.EMBOJ.7600936.
|
Crystal structure of e. coli DNA mismatch repair enzyme
muts, e38q mutant, in complex with a g.t mismatch .
SNAP output
|
1wd0
|
structural protein-DNA |
X-ray (1.9 Å) |
Ko TP, Chu HM, Chen CY, Chou CC, Wang AH |
(2004) "Structures
of the hyperthermophilic chromosomal protein Sac7d in
complex with DNA decamers." Acta
Crystallogr.,Sect.D, 60,
1381-1387. doi: 10.1107/S0907444904012065.
|
Crystal structures of the hyperthermophilic chromosomal
protein sac7d in complex with DNA decamers . SNAP output
|
1wd1
|
structural protein-DNA |
X-ray (2.2 Å) |
Ko TP, Chu HM, Chen CY, Chou CC, Wang AH |
(2004) "Structures
of the hyperthermophilic chromosomal protein Sac7d in
complex with DNA decamers." Acta
Crystallogr.,Sect.D, 60,
1381-1387. doi: 10.1107/S0907444904012065.
|
Crystal structures of the hyperthermophilic chromosomal
protein sac7d in complex with DNA decamers . SNAP output
|
1wet
|
transcription-DNA |
X-ray (2.6 Å) |
Schumacher MA, Glasfeld A, Zalkin H, Brennan RG |
(1997) "The X-ray
structure of the PurR-guanine-purF operator complex
reveals the contributions of complementary
electrostatic surfaces and a water-mediated hydrogen
bond to corepressor specificity and binding
affinity." J.Biol.Chem.,
272, 22648-22653. doi: 10.1074/jbc.272.36.22648.
|
Structure of the purr-guanine-purf operator complex .
SNAP output
|
1wtb
|
transcription-DNA |
NMR |
Enokizono Y, Konishi Y, Nagata K, Ouhashi K, Uesugi
S, Ishikawa F, Katahira M |
(2005) "Structure
of hnRNP D complexed with single-stranded telomere DNA
and unfolding of the quadruplex by heterogeneous
nuclear ribonucleoprotein D."
J.Biol.Chem., 280,
18862-18870. doi: 10.1074/jbc.M411822200.
|
Complex structure of the c-terminal RNA-binding domain
of hnrnp d (auf1) with telomere DNA . SNAP output
|
1wte
|
hydrolase-DNA |
X-ray (1.9 Å) |
Hashimoto H, Shimizu T, Imasaki T, Kato M, Shichijo
N, Kita K, Sato M |
(2005) "Crystal
structures of type II restriction endonuclease EcoO109I
and its complex with cognate DNA."
J.Biol.Chem., 280, 5605-5610.
doi: 10.1074/jbc.M411684200.
|
Crystal structure of type ii restrcition endonuclease,
ecoo109i complexed with cognate DNA . SNAP output
|
1wto
|
DNA binding protein-DNA |
X-ray (1.5 Å) |
Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang
AH-J |
(2005) "Probing
the DNA kink structure induced by the hyperthermophilic
chromosomal protein Sac7d." NUCLEIC ACIDS
RES., 33, 430-438. doi: 10.1093/nar/gki191.
|
Hyperthermophile chromosomal protein sac7d double
mutant v26f-m29f in complex with DNA gcgatcgc .
SNAP output
|
1wtp
|
DNA binding protein-DNA |
X-ray (1.9 Å) |
Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang
AH-J |
(2005) "Probing
the DNA kink structure induced by the hyperthermophilic
chromosomal protein Sac7d." NUCLEIC ACIDS
RES., 33, 430-438. doi: 10.1093/nar/gki191.
|
Hyperthermophile chromosomal protein sac7d single
mutant m29f in complex with DNA gcga(ubr)cgc . SNAP output
|
1wtq
|
DNA binding protein-DNA |
X-ray (1.7 Å) |
Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang
AH-J |
(2005) "Probing
the DNA kink structure induced by the hyperthermophilic
chromosomal protein Sac7d." NUCLEIC ACIDS
RES., 33, 430-438. doi: 10.1093/nar/gki191.
|
Hyperthermophile chromosomal protein sac7d single
mutant m29f in complex with DNA gtaattac . SNAP output
|
1wtr
|
DNA binding protein-DNA |
X-ray (1.8 Å) |
Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang
AH-J |
(2005) "Probing
the DNA kink structure induced by the hyperthermophilic
chromosomal protein Sac7d." NUCLEIC ACIDS
RES., 33, 430-438. doi: 10.1093/nar/gki191.
|
Hyperthermophile chromosomal protein sac7d single
mutant m29a in complex with DNA gcgatcgc . SNAP output
|
1wtv
|
DNA binding protein-DNA |
X-ray (1.6 Å) |
Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang
AH-J |
(2005) "Probing
the DNA kink structure induced by the hyperthermophilic
chromosomal protein Sac7d." NUCLEIC ACIDS
RES., 33, 430-438. doi: 10.1093/nar/gki191.
|
Hyperthermophile chromosomal protein sac7d single
mutant m29a in complex with DNA gtaattac . SNAP output
|
1wtw
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang
AH-J |
(2005) "Probing
the DNA kink structure induced by the hyperthermophilic
chromosomal protein Sac7d." NUCLEIC ACIDS
RES., 33, 430-438. doi: 10.1093/nar/gki191.
|
Hyperthermophile chromosomal protein sac7d single
mutant v26a in complex with DNA gcgatcgc . SNAP output
|
1wtx
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang
AH-J |
(2005) "Probing
the DNA kink structure induced by the hyperthermophilic
chromosomal protein Sac7d." NUCLEIC ACIDS
RES., 33, 430-438. doi: 10.1093/nar/gki191.
|
Hyperthermophile chromosomal protein sac7d single
mutant v26a in complex with DNA gtaattac . SNAP output
|
1wvl
|
structural protein-DNA |
X-ray (2.6 Å) |
Wu SW, Ko TP, Chou CC, Wang AH |
(2005) "Design
and characterization of a multimeric DNA binding
protein using Sac7d and GCN4 as templates."
Proteins, 60, 617-628. doi:
10.1002/prot.20524.
|
Crystal structure of multimeric DNA-binding protein
sac7d-gcn4 with DNA decamer . SNAP output
|
1x0f
|
transcription-DNA |
NMR |
Enokizono Y, Konishi Y, Nagata K, Ouhashi K, Uesugi
S, Ishikawa F, Katahira M |
(2005) "Structure
of hnRNP D complexed with single-stranded telomere DNA
and unfolding of the quadruplex by heterogeneous
nuclear ribonucleoprotein D."
J.Biol.Chem., 280,
18862-18870. doi: 10.1074/jbc.M411822200.
|
Complex structure of the c-terminal RNA-binding domain
of hnrnp d(auf1) with telomeric DNA . SNAP output
|
1x9m
|
transferase-electron transport-DNA |
X-ray (2.1 Å) |
Dutta S, Li Y, Johnson D, Dzantiev L, Richardson CC,
Romano LJ, Ellenberger T |
(2004) "Crystal
structures of 2-acetylaminofluorene and 2-aminofluorene
in complex with T7 DNA polymerase reveal mechanisms of
mutagenesis." Proc.Natl.Acad.Sci.USA,
101, 16186-16191. doi: 10.1073/pnas.0406516101.
|
T7 DNA polymerase in complex with an
n-2-acetylaminofluorene-adducted DNA . SNAP output
|
1x9n
|
ligase-DNA |
X-ray (3.0 Å) |
Pascal JM, O'Brien PJ, Tomkinson AE, Ellenberger
T |
(2004) "Human
DNA ligase I completely encircles and partially unwinds
nicked DNA." Nature, 432,
473-478. doi: 10.1038/nature03082.
|
Crystal structure of human DNA ligase i bound to
5'-adenylated, nicked DNA . SNAP output
|
1x9s
|
transferase-electron transport-DNA |
X-ray (2.7 Å) |
Dutta S, Li Y, Johnson D, Dzantiev L, Richardson CC,
Romano LJ, Ellenberger T |
(2004) "Crystal
structures of 2-acetylaminofluorene and 2-aminofluorene
in complex with T7 DNA polymerase reveal mechanisms of
mutagenesis." Proc.Natl.Acad.Sci.Usa,
101, 16186-16191. doi: 10.1073/pnas.0406516101.
|
T7 DNA polymerase in complex with a primer-template DNA
containing a disordered n-2 aminofluorene on the
template, crystallized with dideoxy-ctp as the incoming
nucleotide. . SNAP
output
|
1x9w
|
transferase-electron transport-DNA |
X-ray (2.3 Å) |
Dutta S, Li Y, Johnson D, Dzantiev L, Richardson CC,
Romano LJ, Ellenberger T |
(2004) "Crystal
structures of 2-acetylaminofluorene and 2-aminofluorene
in complex with T7 DNA polymerase reveal mechanisms of
mutagenesis." Proc.Natl.Acad.Sci.Usa,
101, 16186-16191. doi: 10.1073/pnas.0406516101.
|
T7 DNA polymerase in complex with a primer-template DNA
containing a disordered n-2 aminofluorene on the
template, crystallized with dideoxy-atp as the incoming
nucleotide. . SNAP
output
|
1xbr
|
transcription-DNA |
X-ray (2.5 Å) |
Muller CW, Herrmann BG |
(1997) "Crystallographic
structure of the T domain-DNA complex of the Brachyury
transcription factor." Nature,
389, 884-888. doi: 10.1038/39929.
|
T domain from xenopus laevis bound to DNA . SNAP output
|
1xc8
|
hydrolase-DNA |
X-ray (1.95 Å) |
Coste F, Ober M, Carell T, Boiteux S, Zelwer C,
Castaing B |
(2004) "Structural
basis for the recognition of the FapydG lesion
(2,6-diamino-4-hydroxy-5-formamidopyrimidine) by
formamidopyrimidine-DNA glycosylase."
J.Biol.Chem., 279,
44074-44083. doi: 10.1074/jbc.M405928200.
|
Crystal structure complex between the wild-type
lactococcus lactis fpg (mutm) and a fapy-dg containing
DNA . SNAP output
|
1xc9
|
transferase-DNA |
X-ray (1.9 Å) |
Hsu GW, Huang X, Luneva NP, Geacintov NE, Beese
LS |
(2005) "Structure
of a High Fidelity DNA Polymerase Bound to a
Benzo[a]pyrene Adduct That Blocks Replication."
J.Biol.Chem., 280, 3764-3770.
doi: 10.1074/jbc.M411276200.
|
Structure of a high-fidelity polymerase bound to a
benzo[a]pyrene adduct that blocks replication .
SNAP output
|
1xf2
|
immune system-DNA |
X-ray (2.3 Å) |
Schuermann JP, Prewitt SP, Davies C, Deutscher SL,
Tanner JJ |
(2005) "Evidence
for Structural Plasticity of Heavy Chain
Complementarity-determining Region 3 in Antibody-ssDNA
Recognition." J.Mol.Biol.,
347, 965-978. doi: 10.1016/j.jmb.2005.02.008.
|
Structure of fab DNA-1 complexed with dt3 . SNAP output
|
1xhu
|
hydrolase-DNA |
X-ray (2.95 Å) |
Etzkorn C, Horton NC |
(2004) "Mechanistic
Insights from the Structures of HincII Bound to Cognate
DNA Cleaved from Addition of Mg(2+) and Mn(2+)."
J.Mol.Biol., 343, 833-849.
doi: 10.1016/j.jmb.2004.08.082.
|
Hincii bound to cleaved, cognate DNA containing gtcgac
. SNAP output
|
1xhv
|
hydrolase-DNA |
X-ray (2.5 Å) |
Etzkorn C, Horton NC |
(2004) "Mechanistic
Insights from the Structures of HincII Bound to Cognate
DNA Cleaved from Addition of Mg(2+) and Mn(2+)."
J.Mol.Biol., 343, 833-849.
doi: 10.1016/j.jmb.2004.08.082.
|
Hincii bound to cleaved cognate DNA gtcgac and mn2+ .
SNAP output
|
1xhz
|
transferase-DNA |
X-ray (2.7 Å) |
Kamtekar S, Berman AJ, Wang J, Lazaro JM, de Vega M,
Blanco L, Salas M, Steitz TA |
(2004) "Insights
into Strand Displacement and Processivity from the
Crystal Structure of the Protein-Primed DNA Polymerase
of Bacteriophage phi29." Mol.Cell,
16, 609-618. doi: 10.1016/j.molcel.2004.10.019.
|
Phi29 DNA polymerase, orthorhombic crystal form, ssDNA
complex . SNAP
output
|
1xi1
|
transferase-DNA |
X-ray (2.2 Å) |
Wang J, Kamtekar S, Berman AJ, Steitz TA |
(2005) "Correction
of X-ray intensities from single crystals containing
lattice-translocation defects." Acta
Crystallogr.,Sect.D, 61, 67-74.
doi: 10.1107/S0907444904026721.
|
Phi29 DNA polymerase ssDNA complex, monoclinic crystal
form . SNAP output
|
1xjv
|
transcription-DNA |
X-ray (1.73 Å) |
Lei M, Podell ER, Cech TR |
(2004) "Structure
of human POT1 bound to telomeric single-stranded DNA
provides a model for chromosome end-protection."
Nat.Struct.Mol.Biol., 11,
1223-1229. doi: 10.1038/nsmb867.
|
Crystal structure of human pot1 bound to telomeric
single-stranded DNA (ttagggttag) . SNAP output
|
1xns
|
hydrolase, ligase-DNA |
X-ray (2.8 Å) |
Ghosh K, Lau CK, Guo F, Segall AM, Van Duyne GD |
(2005) "Peptide
trapping of the Holliday junction intermediate in
Cre-loxP site-specific recombination."
J.Biol.Chem., 280, 8290-8299.
doi: 10.1074/jbc.M411668200.
|
Peptide trapped holliday junction intermediate in
cre-loxp recombination . SNAP output
|
1xo0
|
hydrolase, ligase-DNA |
X-ray (2.0 Å) |
Ghosh K, Lau CK, Guo F, Segall AM, Van Duyne GD |
(2005) "Peptide
trapping of the Holliday junction intermediate in
Cre-loxP site-specific recombination."
J.Biol.Chem., 280, 8290-8299.
doi: 10.1074/jbc.M411668200.
|
High resolution structure of the holliday junction
intermediate in cre-loxp site-specific recombination .
SNAP output
|
1xpx
|
transcription regulation-DNA |
X-ray (2.8 Å) |
Yousef MS, Matthews BW |
(2005) "Structural
Basis of Prospero-DNA Interaction: Implications for
Transcription Regulationin Developing Cells."
STRUCTURE, 13, 601-607. doi:
10.1016/j.str.2005.01.023.
|
Structural basis of prospero-DNA interaction;
implications for transcription regulation in developing
cells . SNAP output
|
1xs9
|
transcription-DNA |
NMR |
Dangi B, Gronenborn AM, Rosner JL, Martin RG |
(2004) "Versatility
of the carboxy-terminal domain of the alpha subunit of
RNA polymerase in transcriptional activation: use of
the DNA contact site as a protein contact site for
MarA." Mol.Microbiol.,
54, 45-59. doi: 10.1111/j.1365-2958.2004.04250.x.
|
A model of the ternary complex formed between mara, the
alpha-ctd of RNA polymerase and DNA . SNAP output
|
1xsd
|
transcription-DNA |
X-ray (2.7 Å) |
Safo MK, Zhao Q, Ko T-P, Musayev FN, Robinson H,
Scarsdale N, Wang AH-J, Archer GL |
(2005) "Crystal
structures of the BlaI repressor from Staphylococcus
aureus and its complex with DNA: insights into
transcriptional regulation of the bla and mec
operons." J.Bacteriol.,
187, 1833-1844. doi: 10.1128/JB.187.5.1833-1844.2005.
|
Crystal structure of the blai repressor in complex with
DNA . SNAP output
|
1xsl
|
transferase-DNA |
X-ray (2.3 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Kunkel TA,
Pedersen LC |
(2005) "A closed
conformation for the Pol lambda catalytic cycle."
Nat.Struct.Mol.Biol., 12,
97-98. doi: 10.1038/nsmb876.
|
Crystal structure of human DNA polymerase lambda in
complex with a one nucleotide DNA gap . SNAP output
|
1xsn
|
transferase-DNA |
X-ray (1.95 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Kunkel TA,
Pedersen LC |
(2005) "A closed
conformation for the Pol lambda catalytic cycle."
Nat.Struct.Mol.Biol., 12,
97-98. doi: 10.1038/nsmb876.
|
Crystal structure of human DNA polymerase lambda in
complex with a one nucleotide DNA gap and ddttp .
SNAP output
|
1xsp
|
transferase-DNA |
X-ray (2.2 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Kunkel TA,
Pedersen LC |
(2005) "A closed
conformation for the Pol lambda catalytic cycle."
Nat.Struct.Mol.Biol., 12,
97-98. doi: 10.1038/nsmb876.
|
Crystal structure of human DNA polymerase lambda in
complex with nicked DNA and pyrophosphate . SNAP output
|
1xvk
|
DNA-antibiotic |
X-ray (1.26 Å) |
Cuesta-Seijo JA, Sheldrick GM |
(2005) "Structures
of Complexes between Echinomycin and Duplex DNA."
Acta Crystallogr.,Sect.D, 61,
442. doi: 10.1107/S090744490500137X.
|
X-ray structure of an echinomycin-(gcgtacgc)2 complex .
SNAP output
|
1xvn
|
DNA-antibiotic |
X-ray (1.5 Å) |
Cuesta-Seijo JA, Sheldrick GM |
(2005) "Structures
of Complexes between Echinomycin and Duplex DNA."
Acta Crystallogr.,Sect.D, 61,
442. doi: 10.1107/S090744490500137X.
|
Echinomycin (acgtacgt)2 complex . SNAP output
|
1xvr
|
DNA-antibiotic |
X-ray (1.4 Å) |
Cuesta-Seijo JA, Sheldrick GM |
(2005) "Structures
of Complexes between Echinomycin and Duplex DNA."
Acta Crystallogr.,Sect.D, 61,
442. doi: 10.1107/S090744490500137X.
|
Echinomycin (cgtacg)2 complex . SNAP output
|
1xyi
|
structural protein-DNA |
X-ray (1.45 Å) |
Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang
AH-J |
(2005) "Probing
the DNA kink structure induced by the hyperthermophilic
chromosomal protein Sac7d." Nucleic Acids
Res., 33, 430-438. doi: 10.1093/nar/gki191.
|
Hyperthermophile chromosomal protein sac7d double
mutant val26ala-met29ala in complex with DNA gcgatcgc .
SNAP output
|
1y1w
|
transcription,transferase-DNA-RNA hybrid |
X-ray (4.0 Å) |
Kettenberger H, Armache K-J, Cramer P |
(2004) "Complete
RNA Polymerase II Elongation Complex Structure and Its
Interactions with NTP and TFIIS."
Mol.Cell, 16, 955-965. doi:
10.1016/j.molcel.2004.11.040.
|
Complete RNA polymerase ii elongation complex .
SNAP output
|
1y6f
|
transferase-DNA |
X-ray (2.4 Å) |
Lariviere L, Sommer N, Morera S |
(2005) "Structural
evidence of a passive base-flipping mechanism for AGT,
an unusual GT-B glycosyltransferase."
J.Mol.Biol., 352, 139-150.
doi: 10.1016/j.jmb.2005.07.007.
|
Alpha-glucosyltransferase in complex with udp-glucose
and DNA containing an abasic site . SNAP output
|
1y6g
|
transferase-DNA |
X-ray (2.8 Å) |
Lariviere L, Sommer N, Morera S |
(2005) "Structural
evidence of a passive base-flipping mechanism for AGT,
an unusual GT-B glycosyltransferase."
J.Mol.Biol., 352, 139-150.
doi: 10.1016/j.jmb.2005.07.007.
|
Alpha-glucosyltransferase in complex with udp and a
13_mer DNA containing a hmu base at 2.8 Å resolution .
SNAP output
|
1y77
|
transcription,transferase-DNA-RNA hybrid |
X-ray (4.5 Å) |
Kettenberger H, Armache K-J, Cramer P |
(2004) "Complete
RNA Polymerase II Elongation Complex Structure and Its
Interactions with NTP and TFIIS."
Mol.Cell, 16, 955-965. doi:
10.1016/j.molcel.2004.11.040.
|
Complete RNA polymerase ii elongation complex with
substrate analogue gmpcpp . SNAP output
|
1y8z
|
transferase-DNA |
X-ray (1.9 Å) |
Lariviere L, Sommer N, Morera S |
(2005) "Structural
evidence of a passive base-flipping mechanism for AGT,
an unusual GT-B glycosyltransferase."
J.Mol.Biol., 352, 139-150.
doi: 10.1016/j.jmb.2005.07.007.
|
Alpha-glucosyltransferase in complex with udp and a
13-mer DNA containing a hmu base at 1.9 Å resolution .
SNAP output
|
1ya6
|
transferase-DNA |
X-ray (2.4 Å) |
Lariviere L, Sommer N, Morera S |
(2005) "Structural
evidence of a passive base-flipping mechanism for AGT,
an unusual GT-B glycosyltransferase."
J.Mol.Biol., 352, 139-150.
doi: 10.1016/j.jmb.2005.07.007.
|
Alpha-glucosyltransferase in complex with udp and a
13-mer DNA containing a central a:g mismatch . SNAP output
|
1yf3
|
transferase-DNA |
X-ray (2.29 Å) |
Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng
X |
(2005) "Transition
from Nonspecific to Specific DNA Interactions along the
Substrate-Recognition Pathway of Dam
Methyltransferase." Cell(Cambridge,Mass.),
121, 349-361. doi: 10.1016/j.cell.2005.02.021.
|
T4dam in complex with adohcy and 13-mer oligonucleotide
making non- and semi-specific (~1-4) contact . SNAP output
|
1yfh
|
transferase-DNA |
X-ray (3.01 Å) |
Duguid EM, Rice PA, He C |
(2005) "The
structure of the human AGT protein bound to DNA and its
implications for damage detection."
J.Mol.Biol., 350, 657-666.
doi: 10.1016/j.jmb.2005.05.028.
|
Wt human o6-alkylguanine-DNA alkyltransferase bound to
DNA containing an alkylated cytosine . SNAP output
|
1yfi
|
hydrolase-DNA |
X-ray (2.7 Å) |
Xu QS, Roberts RJ, Guo H-C |
(2005) "Two
crystal forms of the restriction enzyme MspI-DNA
complex show the same novel structure." Protein
Sci., 14, 2590-2600. doi:
10.1110/ps.051565105.
|
Crystal structure of restriction endonuclease mspi in
complex with its cognate DNA in p212121 space group .
SNAP output
|
1yfj
|
transferase-DNA |
X-ray (2.69 Å) |
Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng
X |
(2005) "Transition
from Nonspecific to Specific DNA Interactions along the
Substrate-Recognition Pathway of Dam
Methyltransferase." Cell(Cambridge,Mass.),
121, 349-361. doi: 10.1016/j.cell.2005.02.021.
|
T4dam in complex with adohcy and 15-mer oligonucleotide
showing semi-specific and specific contact . SNAP output
|
1yfl
|
transferase-DNA |
X-ray (3.09 Å) |
Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng
X |
(2005) "Transition
from Nonspecific to Specific DNA Interactions along the
Substrate-Recognition Pathway of Dam
Methyltransferase." Cell(Cambridge,Mass.),
121, 349-361. doi: 10.1016/j.cell.2005.02.021.
|
T4dam in complex with sinefungin and 16-mer
oligonucleotide showing semi-specific and specific
contact and flipped base . SNAP output
|
1ynw
|
transcription-DNA |
X-ray (3.0 Å) |
Shaffer PL, Gewirth DT |
(2004) "Structural
analysis of RXR-VDR interactions on DR3 DNA."
J.Steroid Biochem.Mol.Biol.,
89-90, 215-219. doi: 10.1016/j.jsbmb.2004.03.084.
|
Crystal structure of vitamin d receptor and 9-cis
retinoic acid receptor DNA-binding domains bound to a
dr3 response element . SNAP output
|
1yo5
|
transcription-DNA |
X-ray (2.0 Å) |
Wang Y, Feng L, Said M, Balderman S, Fayazi Z, Liu Y,
Ghosh D, Gulick AM |
(2005) "Analysis
of the 2.0 A Crystal Structure of the Protein-DNA
Complex of the Human PDEF Ets Domain Bound to the
Prostate Specific Antigen Regulatory Site."
Biochemistry, 44, 7095-7106.
doi: 10.1021/bi047352t.
|
Analysis of the 2.0a crystal structure of the
protein-DNA complex of human pdef ets domain bound to
the prostate specific antigen regulatory site .
SNAP output
|
1yqk
|
hydrolase-DNA |
X-ray (2.5 Å) |
Banerjee A, Yang W, Karplus M, Verdine GL |
(2005) "Structure
of a repair enzyme interrogating undamaged DNA
elucidates recognition of damaged DNA."
Nature, 434, 612-618. doi:
10.1038/nature03458.
|
Human 8-oxoguanine glycosylase crosslinked with guanine
containing DNA . SNAP
output
|
1yql
|
hydrolase-DNA |
X-ray (2.6 Å) |
Banerjee A, Yang W, Karplus M, Verdine GL |
(2005) "Structure
of a repair enzyme interrogating undamaged DNA
elucidates recognition of damaged DNA."
Nature, 434, 612-618. doi:
10.1038/nature03458.
|
Catalytically inactive hogg1 crosslinked with
7-deaza-8-azaguanine containing DNA . SNAP output
|
1yqm
|
hydrolase-DNA |
X-ray (2.5 Å) |
Banerjee A, Yang W, Karplus M, Verdine GL |
(2005) "Structure
of a repair enzyme interrogating undamaged DNA
elucidates recognition of damaged DNA."
Nature, 434, 612-618. doi:
10.1038/nature03458.
|
Catalytically inactive human 8-oxoguanine glycosylase
crosslinked to 7-deazaguanine containing DNA . SNAP output
|
1yqr
|
hydrolase-DNA |
X-ray (2.43 Å) |
Banerjee A, Yang W, Karplus M, Verdine GL |
(2005) "Structure
of a repair enzyme interrogating undamaged DNA
elucidates recognition of damaged DNA."
Nature, 434, 612-618. doi:
10.1038/nature03458.
|
Catalytically inactive human 8-oxoguanine glycosylase
crosslinked to oxog containing DNA . SNAP output
|
1yrn
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Li T, Stark MR, Johnson AD, Wolberger C |
(1995) "Crystal
structure of the MATa1/MAT alpha 2 homeodomain
heterodimer bound to DNA." Science,
270, 262-269.
|
Crystal structure of the mata1-matalpha2 homeodomain
heterodimer bound to DNA . SNAP output
|
1ysa
|
transcription-DNA |
X-ray (2.9 Å) |
Ellenberger TE, Brandl CJ, Struhl K, Harrison SC |
(1992) "The GCN4
basic region leucine zipper binds DNA as a dimer of
uninterrupted alpha helices: crystal structure of the
protein-DNA complex."
Cell(Cambridge,Mass.), 71,
1223-1237. doi: 10.1016/S0092-8674(05)80070-4.
|
The gcn4 basic region leucine zipper binds DNA as a
dimer of uninterrupted alpha helices: crystal structure
of the protein-DNA complex . SNAP output
|
1ytb
|
transcription-DNA |
X-ray (1.8 Å) |
Kim Y, Geiger JH, Hahn S, Sigler PB |
(1993) "Crystal
structure of a yeast TBP/TATA-box complex."
Nature, 365, 512-520. doi:
10.1038/365512a0.
|
Crystal structure of a yeast tbp-tata-box complex .
SNAP output
|
1ytf
|
transcription-DNA |
X-ray (2.5 Å) |
Tan S, Hunziker Y, Sargent DF, Richmond TJ |
(1996) "Crystal
structure of a yeast TFIIA/TBP/DNA complex."
Nature, 381, 127-134. doi:
10.1038/381127a0.
|
Yeast tfiia-tbp-DNA complex . SNAP output
|
1yui
|
DNA binding protein-DNA |
NMR |
Omichinski JG, Pedone PV, Felsenfeld G, Gronenborn
AM, Clore GM |
(1997) "The
solution structure of a specific GAGA factor-DNA
complex reveals a modular binding mode."
Nat.Struct.Biol., 4, 122-132.
doi: 10.1038/nsb0297-122.
|
Solution NMR structure of the gaga factor-DNA complex,
regularized mean structure . SNAP output
|
1yuj
|
DNA binding protein-DNA |
NMR |
Omichinski JG, Pedone PV, Felsenfeld G, Gronenborn
AM, Clore GM |
(1997) "The
solution structure of a specific GAGA factor-DNA
complex reveals a modular binding mode."
Nat.Struct.Biol., 4, 122-132.
doi: 10.1038/nsb0297-122.
|
Solution NMR structure of the gaga factor-DNA complex,
50 structures . SNAP
output
|
1z19
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Biswas T, Aihara H, Radman-Livaja M, Filman D, Landy
A, Ellenberger T |
(2005) "A
structural basis for allosteric control of DNA
recombination by lambda integrase."
Nature, 435, 1059-1066. doi:
10.1038/nature03657.
|
Crystal structure of a lambda integrase(75-356) dimer
bound to a coc' core site . SNAP output
|
1z1b
|
DNA binding protein-DNA |
X-ray (3.8 Å) |
Biswas T, Aihara H, Radman-Livaja M, Filman D, Landy
A, Ellenberger T |
(2005) "A
structural basis for allosteric control of DNA
recombination by lambda integrase."
Nature, 435, 1059-1066. doi:
10.1038/nature03657.
|
Crystal structure of a lambda integrase dimer bound to
a coc' core site . SNAP
output
|
1z1c
|
virus-DNA |
X-ray (3.5 Å) |
Kontou M, Govindasamy L, Nam HJ, Bryant N,
Llamas-Saiz AL, Foces-Foces C, Hernando E, Rubio MP,
McKenna R, Almendral JM, Agbandje-McKenna M |
(2005) "Structural
determinants of tissue tropism and in vivo
pathogenicity for the parvovirus minute virus of
mice." J.Virol., 79,
10931-10943. doi: 10.1128/JVI.79.17.10931-10943.2005.
|
Structural determinants of tissue tropism and in vivo
pathogenicity for the parvovirus minute virus of mice .
SNAP output
|
1z1g
|
DNA binding protein-DNA |
X-ray (4.4 Å) |
Biswas T, Aihara H, Radman-Livaja M, Filman D, Landy
A, Ellenberger T |
(2005) "A
structural basis for allosteric control of DNA
recombination by lambda integrase."
Nature, 435, 1059-1066. doi:
10.1038/nature03657.
|
Crystal structure of a lambda integrase tetramer bound
to a holliday junction . SNAP output
|
1z63
|
hydrolase-DNA complex |
X-ray (3.0 Å) |
Durr H, Korner C, Muller M, Hickmann V, Hopfner
KP |
(2005) "X-ray
structures of the Sulfolobus solfataricus SWI2/SNF2
ATPase core and its complex with DNA."
Cell(Cambridge,Mass.), 121,
363-373. doi: 10.1016/j.cell.2005.03.026.
|
Sulfolobus solfataricus swi2-snf2 atpase core in
complex with dsDNA . SNAP output
|
1z9c
|
transcription-DNA |
X-ray (2.64 Å) |
Hong M, Fuangthong M, Helmann JD, Brennan RG |
(2005) "Structure
of an OhrR-ohrA Operator Complex Reveals the DNA
Binding Mechanism of the MarR Family."
Mol.Cell, 20, 131-141. doi:
10.1016/j.molcel.2005.09.013.
|
Crystal structure of ohrr bound to the ohra promoter:
structure of marr family protein with operator DNA .
SNAP output
|
1zaa
|
transcription-DNA |
X-ray (2.1 Å) |
Pavletich NP, Pabo CO |
(1991) "Zinc
finger-DNA recognition: crystal structure of a
Zif268-DNA complex at 2.1 A." Science,
252, 809-817.
|
Zinc finger-DNA recognition: crystal structure of a
zif268-DNA complex at 2.1 angstroms . SNAP output
|
1zay
|
transcription-DNA |
X-ray (2.7 Å) |
Zheleznova EE, Brennan RG |
"The Roles of Exocyclic Groups in the Central
Base-Pair Step in Modulating the Affinity of PurR for its
Operator." |
Purine repressor-hypoxanthine-modified-purf-operator
complex . SNAP
output
|
1zbb
|
structural protein-DNA |
X-ray (9.0 Å) |
Schalch T, Duda S, Sargent DF, Richmond TJ |
(2005) "X-ray
structure of a tetranucleosome and its implications for
the chromatin fibre." Nature,
436, 138-141. doi: 10.1038/nature03686.
|
Structure of the 4_601_167 tetranucleosome . SNAP output
|
1zbi
|
hydrolase-RNA-DNA |
X-ray (1.85 Å) |
Nowotny M, Gaidamakov SA, Crouch RJ, Yang W |
(2005) "Crystal
Structures of RNase H Bound to an RNA/DNA Hybrid:
Substrate Specificity and Metal-Dependent
Catalysis." Cell(Cambridge,Mass.),
121, 1005-1016. doi: 10.1016/j.cell.2005.04.024.
|
Bacillus halodurans rnase h catalytic domain mutant
d132n in complex with 12-mer RNA-DNA hybrid . SNAP output
|
1zbl
|
hydrolase-RNA-DNA |
X-ray (2.2 Å) |
Nowotny M, Gaidamakov SA, Crouch RJ, Yang W |
(2005) "Crystal
Structures of RNase H Bound to an RNA/DNA Hybrid:
Substrate Specificity and Metal-Dependent
Catalysis." Cell(Cambridge,Mass.),
121, 1005-1016. doi: 10.1016/j.cell.2005.04.024.
|
Bacillus halodurans rnase h catalytic domain mutant
d192n in complex with 12-mer RNA-DNA hybrid . SNAP output
|
1zet
|
replication-DNA |
X-ray (2.3 Å) |
Wang J |
(2005) "DNA
polymerases: Hoogsteen base-pairing in DNA
replication?." Nature,
437, E6-7; discussion E7. doi:
10.1038/nature04199.
|
X-ray data do not support hoogsteen base-pairing during
replication by human polymerase iota . SNAP output
|
1zg1
|
transcription-DNA |
X-ray (2.3 Å) |
Maris AE, Kaczor-Grzeskowiak M, Ma Z, Kopka ML,
Gunsalus RP, Dickerson RE |
(2005) "Primary
and Secondary Modes of DNA Recognition by the NarL
Two-Component Response Regulator."
Biochemistry, 44,
14538-14552. doi: 10.1021/bi050734u.
|
Narl complexed to nirb promoter non-palindromic
tail-to-tail DNA site . SNAP output
|
1zg5
|
transcription-DNA |
X-ray (2.3 Å) |
Maris AE, Kaczor-Grzeskowiak M, Ma Z, Kopka ML,
Gunsalus RP, Dickerson RE |
(2005) "Primary
and Secondary Modes of DNA Recognition by the NarL
Two-Component Response Regulator."
Biochemistry, 44,
14538-14552. doi: 10.1021/bi050734u.
|
Narl complexed to narg-89 promoter palindromic
tail-to-tail DNA site . SNAP output
|
1zgw
|
transcription regulator-DNA |
NMR |
He C, Hus JC, Sun LJ, Zhou P, Norman DP, Doetsch V,
Wei H, Gross JD, Lane WS, Wagner G, Verdine GL |
(2005) "A
Methylation-Dependent Electrostatic Switch Controls DNA
Repair and Transcriptional Activation by E. coli
Ada." Mol.Cell, 20,
117-129. doi: 10.1016/j.molcel.2005.08.013.
|
NMR structure of e. coli ada protein in complex with
DNA . SNAP output
|
1zjm
|
DNA-lyase-transferase |
X-ray (2.1 Å) |
Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson
SH |
(2005) "Nucleotide-induced
DNA polymerase active site motions accommodating a
mutagenic DNA intermediate." STRUCTURE,
13, 1225-1233. doi: 10.1016/j.str.2005.05.010.
|
Human DNA polymerase beta complexed with DNA containing
an a-a mismatched primer terminus . SNAP output
|
1zjn
|
DNA-lyase-transferase |
X-ray (2.61 Å) |
Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson
SH |
(2005) "Nucleotide-induced
DNA polymerase active site motions accommodating a
mutagenic DNA intermediate." STRUCTURE,
13, 1225-1233. doi: 10.1016/j.str.2005.05.010.
|
Human DNA polymerase beta complexed with DNA containing
an a-a mismatched primer terminus with dgtp . SNAP output
|
1zla
|
structural protein-DNA |
X-ray (2.9 Å) |
Barbera AJ, Chodaparambil JV, Kelley-Clarke B, Joukov
V, Walter JC, Luger K, Kaye KM |
(2006) "The
nucleosomal surface as a docking station for Kaposi's
sarcoma herpesvirus LANA." Science,
311, 856-861. doi: 10.1126/science.1120541.
|
X-ray structure of a kaposi's sarcoma herpesvirus lana
peptide bound to the nucleosomal core . SNAP output
|
1zlk
|
transcription-DNA |
X-ray (3.1 Å) |
Wisedchaisri G, Wu M, Rice AE, Roberts DM, Sherman
DR, Hol WGJ |
(2005) "Structures
of Mycobacterium tuberculosis DosR and DosR-DNA complex
involved in gene activation during adaptation to
hypoxic latency." J.Mol.Biol.,
354, 630-641. doi: 10.1016/j.jmb.2005.09.048.
|
Crystal structure of the mycobacterium tuberculosis
hypoxic response regulator dosr c-terminal domain-DNA
complex . SNAP
output
|
1zm5
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Boer R, Russi S, Guasch A, Lucas M, Blanco AG,
Perez-Luque R, Coll M, de la Cruz F |
(2006) "Unveiling
the Molecular Mechanism of a Conjugative Relaxase: The
Structure of TrwC Complexed with a 27-mer DNA
Comprising the Recognition Hairpin and the Cleavage
Site." J.Mol.Biol., 358,
857-869. doi: 10.1016/j.jmb.2006.02.018.
|
Conjugative relaxase trwc in complex with orit DNA,
cooper-bound structure . SNAP output
|
1zme
|
transcription-DNA |
X-ray (2.5 Å) |
Swaminathan K, Flynn P, Reece RJ, Marmorstein R |
(1997) "Crystal
structure of a PUT3-DNA complex reveals a novel
mechanism for DNA recognition by a protein containing a
Zn2Cys6 binuclear cluster."
Nat.Struct.Biol., 4, 751-759.
doi: 10.1038/nsb0997-751.
|
Crystal structure of put3-DNA complex . SNAP output
|
1zns
|
hydrolase-DNA |
X-ray (2.5 Å) |
Doudeva LG, Huang H, Hsia KC, Shi Z, Li CL, Shen Y,
Cheng YS, Yuan HS |
(2006) "Crystal
structural analysis and metal-dependent stability and
activity studies of the ColE7 endonuclease domain in
complex with DNA/Zn2+ or inhibitor/Ni2+."
Protein Sci., 15, 269-280.
doi: 10.1110/ps.051903406.
|
Crystal structure of n-cole7-12-bp DNA-zn complex .
SNAP output
|
1zq3
|
transcription-DNA |
NMR |
Baird-Titus JM, Clark-Baldwin K, Dave V, Caperelli
CA, Ma J, Rance M |
(2006) "The
solution structure of the native K50 Bicoid homeodomain
bound to the consensus TAATCC DNA-binding site."
J.Mol.Biol., 356, 1137-1151.
doi: 10.1016/j.jmb.2005.12.007.
|
NMR solution structure of the bicoid homeodomain bound
to the consensus DNA binding site taatcc . SNAP output
|
1zqa
|
transferase-DNA |
X-ray (3.2 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
kcl (150 millimolar) at ph 7.5 . SNAP output
|
1zqb
|
transferase-DNA |
X-ray (3.2 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
bacl2 (150 millimolar) . SNAP output
|
1zqc
|
transferase-DNA |
X-ray (3.2 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
cacl2 (15 millimolar) . SNAP output
|
1zqd
|
transferase-DNA |
X-ray (3.5 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
cacl2 (150 millimolar) . SNAP output
|
1zqe
|
transferase-DNA |
X-ray (3.7 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
crcl3 (saturated solution) . SNAP output
|
1zqf
|
transferase-DNA |
X-ray (2.9 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
cscl (150 millimolar) . SNAP output
|
1zqg
|
transferase-DNA |
X-ray (3.1 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
a sodium-free artificial mother liquor at ph 6.5 .
SNAP output
|
1zqh
|
transferase-DNA |
X-ray (3.1 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
a sodium-free artificial mother liquor at ph 7.5 .
SNAP output
|
1zqi
|
transferase-DNA |
X-ray (2.7 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
kcl (150 millimolar) . SNAP output
|
1zqj
|
transferase-DNA |
X-ray (3.3 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
cacl2 (15 millimolar) and mgcl2 (15 millimolar) .
SNAP output
|
1zqk
|
transferase-DNA |
X-ray (3.2 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
kcl (75 millimolar) and mgcl2 (75 millimolar) .
SNAP output
|
1zql
|
transferase-DNA |
X-ray (3.3 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
mncl2 (15 millimolar) and mgcl2 (15 millimolar) .
SNAP output
|
1zqm
|
transferase-DNA |
X-ray (3.2 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
mncl2 (15 millimolar) . SNAP output
|
1zqn
|
transferase-DNA |
X-ray (3.0 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
bacl2 (15 millimolar) and nacl (15 millimolar) .
SNAP output
|
1zqo
|
transferase-DNA |
X-ray (3.2 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
cacl2 (15 millimolar) and nacl (15 millimolar) .
SNAP output
|
1zqp
|
transferase-DNA |
X-ray (2.8 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
kcl (75 millimolar) and nacl (75 millimolar) . SNAP output
|
1zqq
|
transferase-DNA |
X-ray (3.3 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
mncl2 (15 millimolar) and nacl (15 millimolar) .
SNAP output
|
1zqr
|
transferase-DNA |
X-ray (3.7 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (e.c.2.7.7.7)-DNA complex, soaked
in the presence of nicl2 . SNAP output
|
1zqs
|
transferase-DNA |
X-ray (3.3 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
tlcl (0.5 millimolar) . SNAP output
|
1zqt
|
transferase-DNA |
X-ray (3.4 Å) |
Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut
J |
(1996) "A
structural basis for metal ion mutagenicity and
nucleotide selectivity in human DNA polymerase
beta." Biochemistry, 35,
12762-12777. doi: 10.1021/bi9529566.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
datp (0.01 millimolar) and zncl2 (0.02 millimolar) .
SNAP output
|
1zr2
|
recombination-DNA |
X-ray (3.9 Å) |
Li W, Kamtekar S, Xiong Y, Sarkis GJ, Grindley ND,
Steitz TA |
(2005) "Structure
of a synaptic gamma delta resolvase tetramer covalently
linked to two cleaved DNAs." Science,
309, 1210-1215. doi: 10.1126/science.1112064.
|
Structure of a synaptic gamma-delta resolvase tetramer
covalently linked to two cleaved dnas . SNAP output
|
1zr4
|
recombination-DNA |
X-ray (3.4 Å) |
Li W, Kamtekar S, Xiong Y, Sarkis GJ, Grindley ND,
Steitz TA |
(2005) "Structure
of a synaptic gamma delta resolvase tetramer covalently
linked to two cleaved DNAs." Science,
309, 1210-1215. doi: 10.1126/science.1112064.
|
Structure of a synaptic gamma-delta resolvase tetramer
covalently linked to two cleaved dnas . SNAP output
|
1zrc
|
gene regulation-DNA |
X-ray (2.8 Å) |
Napoli AA, Lawson CL, Ebright RH, Berman HM |
(2006) "Indirect
readout of DNA sequence at the primary-kink site in the
CAP-DNA complex: recognition of pyrimidine-purine and
purine-purine steps." J.Mol.Biol.,
357, 173-183. doi: 10.1016/j.jmb.2005.12.051.
|
4 crystal structures of cap-DNA with all base-pair
substitutions at position 6, cap-icap38 DNA . SNAP output
|
1zrd
|
gene regulation-DNA |
X-ray (2.8 Å) |
Napoli AA, Lawson CL, Ebright RH, Berman HM |
(2006) "Indirect
readout of DNA sequence at the primary-kink site in the
CAP-DNA complex: recognition of pyrimidine-purine and
purine-purine steps." J.Mol.Biol.,
357, 173-183. doi: 10.1016/j.jmb.2005.12.051.
|
4 crystal structures of cap-DNA with all base-pair
substitutions at position 6, cap-[6a;17t]icap38 DNA .
SNAP output
|
1zre
|
gene regulation-DNA |
X-ray (2.8 Å) |
Napoli AA, Lawson CL, Ebright RH, Berman HM |
(2006) "Indirect
readout of DNA sequence at the primary-kink site in the
CAP-DNA complex: recognition of pyrimidine-purine and
purine-purine steps." J.Mol.Biol.,
357, 173-183. doi: 10.1016/j.jmb.2005.12.051.
|
4 crystal structures of cap-DNA with all base-pair
substitutions at position 6, cap-[6g;17c]icap38 DNA .
SNAP output
|
1zrf
|
gene regulation-DNA |
X-ray (2.1 Å) |
Napoli AA, Lawson CL, Ebright RH, Berman HM |
(2006) "Indirect
readout of DNA sequence at the primary-kink site in the
CAP-DNA complex: recognition of pyrimidine-purine and
purine-purine steps." J.Mol.Biol.,
357, 173-183. doi: 10.1016/j.jmb.2005.12.051.
|
4 crystal structures of cap-DNA with all base-pair
substitutions at position 6, cap-[6c;17g]icap38 DNA .
SNAP output
|
1zs4
|
transcription-DNA |
X-ray (1.7 Å) |
Jain D, Kim Y, Maxwell KL, Beasley S, Zhang R, Gussin
GN, Edwards AM, Darst SA |
(2005) "Crystal
Structure of Bacteriophage lambdacII and Its DNA
Complex." Mol.Cell, 19,
259-269. doi: 10.1016/j.molcel.2005.06.006.
|
Structure of bacteriophage lambda cii protein in
complex with DNA . SNAP
output
|
1ztg
|
DNA, RNA binding protein-DNA |
X-ray (3.0 Å) |
Yoga YMK, Traore DAK, Sidiqi M, Szeto C, Pendini NR,
Barker A, Leedman PJ, Wilce JA, Wilce MCJ |
(2012) "Contribution
of the first K-homology domain of poly(C)-binding
protein 1 to its affinity and specificity for C-rich
oligonucleotides." Nucleic Acids Res.,
40, 5101-5114. doi: 10.1093/nar/gks058.
|
Human alpha polyc binding protein kh1 . SNAP output
|
1ztt
|
transferase-DNA |
X-ray (1.85 Å) |
Goodwin KD, Long EC, Georgiadis MM |
(2005) "A
host-guest approach for determining drug-DNA
interactions: an example using netropsin."
Nucleic Acids Res., 33,
4106-4116. doi: 10.1093/nar/gki717.
|
Netropsin bound to d(cttaattcgaattaag) in complex with
mmlv rt catalytic fragment . SNAP output
|
1ztw
|
transferase-DNA |
X-ray (1.8 Å) |
Goodwin KD, Long EC, Georgiadis MM |
(2005) "A
host-guest approach for determining drug-DNA
interactions: an example using netropsin."
Nucleic Acids Res., 33,
4106-4116. doi: 10.1093/nar/gki717.
|
D(cttaattcgaattaag) complexed with moloney murine
leukemia virus reverse transcriptase catalytic fragment
. SNAP output
|
1zvv
|
transcription-DNA |
X-ray (2.98 Å) |
Schumacher MA, Seidel G, Hillen W, Brennan RG |
(2006) "Phosphoprotein
Crh-Ser46-P displays altered binding to CcpA to effect
carbon catabolite regulation."
J.Biol.Chem., 281, 6793-6800.
doi: 10.1074/jbc.M509977200.
|
Crystal structure of a ccpa-crh-DNA complex . SNAP output
|
1zx4
|
cell cycle |
X-ray (2.98 Å) |
Schumacher MA, Funnell BE |
(2005) "Structures
of ParB bound to DNA reveal mechanism of partition
complex formation." Nature,
438, 516-519. doi: 10.1038/nature04149.
|
Structure of parb bound to DNA . SNAP output
|
1zyq
|
transferase-electron transport-DNA |
X-ray (2.7 Å) |
Brieba LG, Kokoska RJ, Bebenek K, Kunkel TA,
Ellenberger T |
(2005) "A lysine
residue in the fingers subdomain of t7 DNA polymerase
modulates the miscoding potential of
8-oxo-7,8-dihydroguanosine." Structure,
13, 1653-1659. doi: 10.1016/j.str.2005.07.020.
|
T7 DNA polymerase in complex with 8og and incoming
ddatp . SNAP output
|
1zzi
|
structural protein-DNA |
X-ray (1.8 Å) |
Backe PH, Messias AC, Ravelli RB, Sattler M, Cusack
S |
(2005) "X-Ray
Crystallographic and NMR Studies of the Third KH Domain
of hnRNP K in Complex with Single-Stranded Nucleic
Acids." STRUCTURE, 13,
1055-1067. doi: 10.1016/j.str.2005.04.008.
|
Crystal structure analysis of the third kh domain of
hnrnp k in complex with ssDNA . SNAP output
|
1zzj
|
structural protein-DNA |
X-ray (2.3 Å) |
Backe PH, Messias AC, Ravelli RB, Sattler M, Cusack
S |
(2005) "X-Ray
Crystallographic and NMR Studies of the Third KH Domain
of hnRNP K in Complex with Single-Stranded Nucleic
Acids." STRUCTURE, 13,
1055-1067. doi: 10.1016/j.str.2005.04.008.
|
Structure of the third kh domain of hnrnp k in complex
with 15-mer ssDNA . SNAP
output
|
209d
|
DNA-antibiotic |
X-ray (3.0 Å) |
Shinomiya M, Chu W, Carlson RG, Weaver RF, Takusagawa
F |
(1995) "Structural,
Physical, and Biological Characteristics of RNA.DNA
Binding Agent N8-Actinomycin D."
Biochemistry, 34, 8481. doi:
10.1021/BI00026A032.
|
Structural, physical and biological characteristics of
RNA:DNA binding agent n8-actinomycin d . SNAP output
|
2a07
|
transcription-DNA |
X-ray (1.9 Å) |
Stroud JC, Wu Y, Bates DL, Han A, Nowick K, Paabo S,
Tong H, Chen L |
(2006) "Structure
of the Forkhead Domain of FOXP2 Bound to DNA."
Structure, 14, 159-166. doi:
10.1016/j.str.2005.10.005.
|
Crystal structure of foxp2 bound specifically to DNA. .
SNAP output
|
2a0i
|
hydrolase-DNA |
X-ray (2.72 Å) |
Larkin C, Datta S, Harley MJ, Anderson BJ, Ebie A,
Hargreaves V, Schildbach JF |
(2005) "Inter-
and intramolecular determinants of the specificity of
single-stranded DNA binding and cleavage by the f
factor relaxase." Structure,
13, 1533-1544. doi: 10.1016/j.str.2005.06.013.
|
F factor trai relaxase domain bound to f orit
single-stranded DNA . SNAP output
|
2a3v
|
recombination |
X-ray (2.8 Å) |
MacDonald D, Demarre G, Bouvier M, Mazel D, Gopaul
DN |
(2006) "Structural
basis for broad DNA-specificity in integron
recombination." Nature,
440, 1157-1162. doi: 10.1038/nature04643.
|
Structural basis for broad DNA-specificity in integron
recombination . SNAP
output
|
2a66
|
transcription-DNA |
X-ray (2.2 Å) |
Solomon IH, Hager JM, Safi R, McDonnell DP, Redinbo
MR, Ortlund EA |
(2005) "Crystal
Structure of the Human LRH-1 DBD-DNA Complex Reveals
Ftz-F1 Domain Positioning is Required for Receptor
Activity." J.Mol.Biol.,
354, 1091-1102. doi: 10.1016/j.jmb.2005.10.009.
|
Human liver receptor homologue DNA-binding domain
(hlrh-1 dbd) in complex with dsDNA from the hcyp7a1
promoter . SNAP
output
|
2a6o
|
transcription-DNA |
X-ray (2.6 Å) |
Ronning DR, Guynet C, Ton-Hoang B, Perez ZN,
Ghirlando R, Chandler M, Dyda F |
(2005) "Active
site sharing and subterminal hairpin recognition in a
new class of DNA transposases." Mol.Cell,
20, 143-154. doi: 10.1016/j.molcel.2005.07.026.
|
Crystal structure of the ishp608 transposase in complex
with stem-loop DNA . SNAP output
|
2ac0
|
apoptosis-DNA |
X-ray (1.8 Å) |
Kitayner M, Rozenberg H, Kessler N, Rabinovich D,
Shaulov L, Haran TE, Shakked Z |
(2006) "Structural
Basis of DNA Recognition by p53 Tetramers."
Mol.Cell, 22, 741-753. doi:
10.1016/j.molcel.2006.05.015.
|
Structural basis of DNA recognition by p53 tetramers
(complex i) . SNAP
output
|
2acj
|
hydrolase-DNA |
X-ray (2.6 Å) |
Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK |
(2005) "Crystal
structure of a junction between B-DNA and Z-DNA reveals
two extruded bases." Nature,
437, 1183-1186. doi: 10.1038/nature04088.
|
Crystal structure of the b-z junction containing DNA
bound to z-DNA binding proteins . SNAP output
|
2adw
|
DNA-antibiotic |
X-ray (1.6 Å) |
Cuesta-Seijo JA, Weiss MS, Sheldrick GM |
(2006) "Serendipitous
Sad Phasing of an Echinomycin-(Acgtacgt)2
Bisintercalation Complex." Acta
Crystallogr.,Sect.D, 62, 417.
doi: 10.1107/S0907444906003763.
|
Crystal structure of echinomycin-(acgtacgt)2 solved by
sad . SNAP output
|
2ady
|
apoptosis-DNA |
X-ray (2.5 Å) |
Kitayner M, Rozenberg H, Kessler N, Rabinovich D,
Shaulov L, Haran TE, Shakked Z |
(2006) "Structural
Basis of DNA Recognition by p53 Tetramers."
Mol.Cell, 22, 741-753. doi:
10.1016/j.molcel.2006.05.015.
|
Structural basis of DNA recognition by p53 tetramers
(complex iv) . SNAP
output
|
2ago
|
transferase-DNA |
X-ray (2.85 Å) |
Vaisman A, Ling H, Woodgate R, Yang W |
(2005) "Fidelity
of Dpo4: effect of metal ions, nucleotide selection and
pyrophosphorolysis." Embo J.,
24, 2957-2967. doi: 10.1038/sj.emboj.7600786.
|
Fidelity of dpo4: effect of metal ions, nucleotide
selection and pyrophosphorolysis . SNAP output
|
2agp
|
transferase-DNA |
X-ray (2.9 Å) |
Vaisman A, Ling H, Woodgate R, Yang W |
(2005) "Fidelity
of Dpo4: effect of metal ions, nucleotide selection and
pyrophosphorolysis." Embo J.,
24, 2957-2967. doi: 10.1038/sj.emboj.7600786.
|
Fidelity of dpo4: effect of metal ions, nucleotide
selection and pyrophosphorolysis . SNAP output
|
2agq
|
transferase-DNA |
X-ray (2.1 Å) |
Vaisman A, Ling H, Woodgate R, Yang W |
(2005) "Fidelity
of Dpo4: effect of metal ions, nucleotide selection and
pyrophosphorolysis." Embo J.,
24, 2957-2967. doi: 10.1038/sj.emboj.7600786.
|
Fidelity of dpo4: effect of metal ions, nucleotide
selection and pyrophosphorolysis . SNAP output
|
2ahi
|
apoptosis-DNA |
X-ray (1.85 Å) |
Kitayner M, Rozenberg H, Kessler N, Rabinovich D,
Shaulov L, Haran TE, Shakked Z |
(2006) "Structural
Basis of DNA Recognition by p53 Tetramers."
Mol.Cell, 22, 741-753. doi:
10.1016/j.molcel.2006.05.015.
|
Structural basis of DNA recognition by p53 tetramers
(complex iii) . SNAP
output
|
2ajq
|
transferase,transcription-DNA |
X-ray (2.6 Å) |
Brieba L, Ellenberger T |
"Structure of replicative DNA polymerase provides
insigts into the mechanisms for processivity,
frameshifting and editing." |
Structure of replicative DNA polymerase provides
insigts into the mechanisms for processivity,
frameshifting and editing . SNAP output
|
2alz
|
transferase-DNA |
X-ray (2.5 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2005) "Human
DNA Polymerase iota Incorporates dCTP Opposite Template
G via a G.C+ Hoogsteen Base Pair."
Structure, 13, 1569-1577.
doi: 10.1016/j.str.2005.08.010.
|
Ternary complex of hpoli with DNA and dctp . SNAP output
|
2aoq
|
hydrolase-DNA |
X-ray (2.2 Å) |
Lee JY, Chang J, Joseph N, Ghirlando R, Rao DN, Yang
W |
(2005) "MutH
complexed with hemi- and unmethylated DNAs: coupling
base recognition and DNA cleavage."
Mol.Cell, 20, 155-166. doi:
10.1016/j.molcel.2005.08.019.
|
Crystal structure of muth-unmethylated DNA complex .
SNAP output
|
2aor
|
hydrolase-DNA |
X-ray (2.0 Å) |
Lee JY, Chang J, Joseph N, Ghirlando R, Rao DN, Yang
W |
(2005) "MutH
complexed with hemi- and unmethylated DNAs: coupling
base recognition and DNA cleavage."
Mol.Cell, 20, 155-166. doi:
10.1016/j.molcel.2005.08.019.
|
Crystal structure of muth-hemimethylated DNA complex .
SNAP output
|
2aq4
|
transferase |
X-ray (2.32 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2005) "Rev1
employs a novel mechanism of DNA synthesis using a
protein template." Science,
309, 2219-2222. doi: 10.1126/science.1116336.
|
Ternary complex of the catalytic core of rev1 with DNA
and dctp. . SNAP
output
|
2as5
|
transcription-DNA |
X-ray (2.7 Å) |
Wu Y, Borde M, Heissmeyer V, Feuerer M, Lapan AD,
Stroud JC, Bates DL, Guo L, Han A, Ziegler SF, Mathis D,
Benoist C, Chen L, Rao A |
(2006) "FOXP3
Controls Regulatory T Cell Function through Cooperation
with NFAT." Cell(Cambridge,Mass.),
126, 375-387. doi: 10.1016/j.cell.2006.05.042.
|
Structure of the DNA binding domains of nfat and foxp2
bound specifically to DNA. . SNAP output
|
2asd
|
transferase-DNA |
X-ray (1.95 Å) |
Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde
S, Geacintov NE, Patel DJ |
(2006) "Stepwise
Translocation of Dpo4 Polymerase during Error-Free
Bypass of an oxoG Lesion." Plos Biol.,
4, 1-18. doi: 10.1371/journal.pbio.0040011.
|
Oxog-modified insertion ternary complex . SNAP output
|
2asj
|
transferase-DNA |
X-ray (2.35 Å) |
Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde
S, Geacintov NE, Patel DJ |
(2006) "Stepwise
Translocation of Dpo4 Polymerase during Error-Free
Bypass of an oxoG Lesion." Plos Biol.,
4, 1-18. doi: 10.1371/journal.pbio.0040011.
|
Oxog-modified preinsertion binary complex . SNAP output
|
2asl
|
transferase-DNA |
X-ray (2.65 Å) |
Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde
S, Geacintov NE, Patel DJ |
(2006) "Stepwise
Translocation of Dpo4 Polymerase during Error-Free
Bypass of an oxoG Lesion." Plos Biol.,
4, 1-18. doi: 10.1371/journal.pbio.0040011.
|
Oxog-modified postinsertion binary complex . SNAP output
|
2ata
|
apoptosis-DNA |
X-ray (2.2 Å) |
Kitayner M, Rozenberg H, Kessler N, Rabinovich D,
Shaulov L, Haran TE, Shakked Z |
(2006) "Structural
Basis of DNA Recognition by p53 Tetramers."
Mol.Cell, 22, 741-753. doi:
10.1016/j.molcel.2006.05.015.
|
Structural basis of DNA recognition by p53 tetramers
(complex ii) . SNAP
output
|
2atl
|
transferase-DNA |
X-ray (2.8 Å) |
Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde
S, Geacintov NE, Patel DJ |
(2006) "Stepwise
Translocation of Dpo4 Polymerase during Error-Free
Bypass of an oxoG Lesion." Plos Biol.,
4, 1-18. doi: 10.1371/journal.pbio.0040011.
|
Unmodified insertion ternary complex . SNAP output
|
2au0
|
transferase-DNA |
X-ray (2.7 Å) |
Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde
S, Geacintov NE, Patel DJ |
(2006) "Stepwise
Translocation of Dpo4 Polymerase during Error-Free
Bypass of an oxoG Lesion." Plos Biol.,
4, 1-18. doi: 10.1371/journal.pbio.0040011.
|
Unmodified preinsertion binary complex . SNAP output
|
2axy
|
DNA binding protein-DNA |
X-ray (1.7 Å) |
Du Z, Lee JK, Tjhen R, Li S, Pan H, Stroud RM, James
TL |
(2005) "Crystal
Structure of the First KH Domain of Human
Poly(C)-binding Protein-2 in Complex with a C-rich
Strand of Human Telomeric DNA at 1.7 A."
J.Biol.Chem., 280,
38823-38830. doi: 10.1074/jbc.M508183200.
|
Crystal structure of kh1 domain of human
poly(c)-binding protein-2 with c-rich strand of human
telomeric DNA . SNAP
output
|
2ayb
|
transcription-DNA |
X-ray (3.2 Å) |
Hooley E, Fairweather V, Clarke AR, Gaston K, Brady
RL |
(2006) "The
recognition of local DNA conformation by the human
papillomavirus type 6 E2 protein." Nucleic
Acids Res., 34, 3897-3908. doi:
10.1093/nar/gkl466.
|
Crystal structure of hpv6a e2 DNA binding domain bound
to a 16 base pair DNA target . SNAP output
|
2ayg
|
transcription-DNA |
X-ray (3.1 Å) |
Hooley E, Fairweather V, Clarke AR, Gaston K, Brady
RL |
(2006) "The
recognition of local DNA conformation by the human
papillomavirus type 6 E2 protein." Nucleic
Acids Res., 34, 3897-3908. doi:
10.1093/nar/gkl466.
|
Crystal structure of hpv6a e2 DNA binding domain bound
to an 18 base pair DNA target . SNAP output
|
2b0d
|
hydrolase-DNA |
X-ray (2.0 Å) |
Hiller DA, Rodriguez AM, Perona JJ |
(2005) "Non-cognate
Enzyme-DNA Complex: Structural and Kinetic Analysis of
EcoRV Endonuclease Bound to the EcoRI Recognition Site
GAATTC." J.Mol.Biol.,
354, 121-136. doi: 10.1016/j.jmb.2005.09.046.
|
Ecorv restriction endonuclease-gaattc-ca2+ . SNAP output
|
2b0e
|
hydrolase-DNA |
X-ray (1.9 Å) |
Hiller DA, Rodriguez AM, Perona JJ |
(2005) "Non-cognate
Enzyme-DNA Complex: Structural and Kinetic Analysis of
EcoRV Endonuclease Bound to the EcoRI Recognition Site
GAATTC." J.Mol.Biol.,
354, 121-136. doi: 10.1016/j.jmb.2005.09.046.
|
Ecorv restriction endonuclease-gaautc-ca2+ . SNAP output
|
2b9s
|
isomerase-DNA |
X-ray (2.27 Å) |
Davies DR, Mushtaq A, Interthal H, Champoux JJ, Hol
WG |
(2006) "The
Structure of the Transition State of the Heterodimeric
Topoisomerase I of Leishmania donovani as a Vanadate
Complex with Nicked DNA." J.Mol.Biol.,
357, 1202-1210. doi: 10.1016/j.jmb.2006.01.022.
|
Crystal structure of heterodimeric l. donovani
topoisomerase i-vanadate-DNA complex . SNAP output
|
2bam
|
hydrolase-DNA |
X-ray (2.0 Å) |
Viadiu H, Aggarwal AK |
(1998) "The role
of metals in catalysis by the restriction endonuclease
BamHI." Nat.Struct.Biol.,
5, 910-916. doi: 10.1038/2352.
|
Restriction endonuclease bamhi complex with DNA and
calcium ions (pre-reactive complex). . SNAP output
|
2bcq
|
transferase, lyase-DNA |
X-ray (1.65 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC,
Kunkel TA |
(2006) "Structural
analysis of strand misalignment during DNA synthesis by
a human DNA polymerase."
Cell(Cambridge,Mass.), 124,
331-342. doi: 10.1016/j.cell.2005.10.039.
|
DNA polymerase lambda in complex with a DNA duplex
containing an unpaired dtmp . SNAP output
|
2bcr
|
transferase, lyase-DNA |
X-ray (1.75 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC,
Kunkel TA |
(2006) "Structural
analysis of strand misalignment during DNA synthesis by
a human DNA polymerase."
Cell(Cambridge,Mass.), 124,
331-342. doi: 10.1016/j.cell.2005.10.039.
|
DNA polymerase lambda in complex with a DNA duplex
containing an unpaired damp . SNAP output
|
2bcs
|
transferase, lyase-DNA |
X-ray (2.2 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC,
Kunkel TA |
(2006) "Structural
analysis of strand misalignment during DNA synthesis by
a human DNA polymerase."
Cell(Cambridge,Mass.), 124,
331-342. doi: 10.1016/j.cell.2005.10.039.
|
DNA polymerase lambda in complex with a DNA duplex
containing an unpaired dcmp . SNAP output
|
2bcu
|
transferase, lyase-DNA |
X-ray (2.2 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC,
Kunkel TA |
(2006) "Structural
analysis of strand misalignment during DNA synthesis by
a human DNA polymerase."
Cell(Cambridge,Mass.), 124,
331-342. doi: 10.1016/j.cell.2005.10.039.
|
DNA polymerase lambda in complex with a DNA duplex
containing an unpaired damp and a t:t mismatch .
SNAP output
|
2bcv
|
transferase, lyase-DNA |
X-ray (2.0 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC,
Kunkel TA |
(2006) "Structural
analysis of strand misalignment during DNA synthesis by
a human DNA polymerase."
Cell(Cambridge,Mass.), 124,
331-342. doi: 10.1016/j.cell.2005.10.039.
|
DNA polymerase lambda in complex with dttp and a DNA
duplex containing an unpaired dtmp . SNAP output
|
2bdp
|
transferase-DNA |
X-ray (1.8 Å) |
Kiefer JR, Mao C, Braman JC, Beese LS |
(1998) "Visualizing
DNA replication in a catalytically active Bacillus DNA
polymerase crystal." Nature,
391, 304-307. doi: 10.1038/34693.
|
Crystal structure of bacillus DNA polymerase i fragment
complexed to 9 base pairs of duplex DNA . SNAP output
|
2bgw
|
hydrolase |
X-ray (2.8 Å) |
Newman M, Murray-Rust J, Lally J, Rudolf J, Fadden A,
Knowles PP, White MF, McDonald NQ |
(2005) "Structure
of an XPF endonuclease with and without DNA suggests a
model for substrate recognition." EMBO J.,
24, 895-905. doi: 10.1038/sj.emboj.7600581.
|
Xpf from aeropyrum pernix, complex with DNA . SNAP output
|
2bjc
|
transcription regulator |
NMR |
Salinas RK, Folkers GE, Bonvin AMJJ, Das D, Boelens
R, Kaptein R |
(2005) "Altered
Specificity in DNA Binding by the Lac Repressor: A
Mutant Lac Headpiece that Mimics the Gal
Repressor." Chembiochem,
6, 1628. doi: 10.1002/CBIC.200500049.
|
NMR structure of a protein-DNA complex of an altered
specificity mutant of the lac repressor headpiece that
mimics the gal repressor . SNAP output
|
2bnw
|
DNA-binding-regulatory protein |
X-ray (2.45 Å) |
Weihofen WA, Cicek A, Pratto F, Alonso JC, Saenger
W |
(2006) "Structures
of Omega Repressors Bound to Direct and Inverted DNA
Repeats Explain Modulation of Transcription."
Nucleic Acids Res., 34, 1450.
doi: 10.1093/NAR/GKL015.
|
Structural basis for cooperative binding of
ribbon-helix-helix omega repressor to direct DNA heptad
repeats . SNAP
output
|
2bnz
|
DNA binding protein-DNA |
X-ray (2.6 Å) |
Weihofen WA, Cicek A, Pratto F, Alonso JC, Saenger
W |
(2006) "Structures
of Omega Repressors Bound to Direct and Inverted DNA
Repeats Explain Modulation of Transcription."
Nucleic Acids Res., 34, 1450.
doi: 10.1093/NAR/GKL015.
|
Structural basis for cooperative binding of
ribbon-helix-helix omega repressor to inverted DNA
heptad repeats . SNAP
output
|
2bop
|
transcription-DNA |
X-ray (1.7 Å) |
Hegde RS, Grossman SR, Laimins LA, Sigler PB |
(1992) "Crystal
structure at 1.7 A of the bovine papillomavirus-1 E2
DNA-binding domain bound to its DNA target."
Nature, 359, 505-512. doi:
10.1038/359505a0.
|
Crystal structure at 1.7 angstroms of the bovine
papillomavirus-1 e2 DNA-binding domain bound to its DNA
target . SNAP output
|
2bpa
|
virus-DNA |
X-ray (3.0 Å) |
McKenna R, Xia D, Willingmann P, Ilag LL,
Krishnaswamy S, Rossmann MG, Olson NH, Baker TS,
Incardona NL |
(1992) "Atomic
structure of single-stranded DNA bacteriophage phi X174
and its functional implications." Nature,
355, 137-143. doi: 10.1038/355137a0.
|
Atomic structure of single-stranded DNA bacteriophage
phix174 and its functional implications . SNAP output
|
2bpf
|
transferase-DNA |
X-ray (2.9 Å) |
Pelletier H, Sawaya MR, Kumar A, Wilson SH, Kraut
J |
(1994) "Structures
of ternary complexes of rat DNA polymerase beta, a DNA
template-primer, and ddCTP." Science,
264, 1891-1903.
|
Structures of ternary complexes of rat DNA polymerase
beta, a DNA template-primer, and ddctp . SNAP output
|
2bpg
|
transferase-DNA |
X-ray (3.6 Å) |
Pelletier H, Sawaya MR, Kumar A, Wilson SH, Kraut
J |
(1994) "Structures
of ternary complexes of rat DNA polymerase beta, a DNA
template-primer, and ddCTP." Science,
264, 1891-1903.
|
Structures of ternary complexes of rat DNA polymerase
beta, a DNA template-primer, and ddctp . SNAP output
|
2bq3
|
transferase |
X-ray (2.0 Å) |
Zang H, Goodenough AK, Choi JY, Irimia A,
Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M,
Guengerich FP |
(2005) "DNA
Adduct Bypass Polymerization by Sulfolobus Solfataricus
DNA Polymerase Dpo4: Analysis and Crystal Structures of
Multiple Base Pair Substitution and Frameshift Products
with the Adduct 1,N2-Ethenoguanine."
J.Biol.Chem., 280, 29750.
doi: 10.1074/JBC.M504756200.
|
DNA adduct bypass polymerization by sulfolobus
solfataricus dpo4. analysis and crystal structures of
multiple base-pair substitution and frameshift products
with the adduct 1,n2-ethenoguanine . SNAP output
|
2bqr
|
transferase |
X-ray (2.37 Å) |
Zang H, Goodenough AK, Choi JY, Irimia A,
Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M,
Guengerich FP |
(2005) "DNA
Adduct Bypass Polymerization by Sulfolobus Solfataricus
DNA Polymerase Dpo4: Analysis and Crystal Structures of
Multiple Base Pair Substitution and Frameshift Products
with the Adduct 1,N2-Ethenoguanine."
J.Biol.Chem., 280, 29750.
doi: 10.1074/JBC.M504756200.
|
DNA adduct bypass polymerization by sulfolobus
solfataricus dpo4. analysis and crystal structures of
multiple base-pair substitution and frameshift products
with the adduct 1,n2-ethenoguanine . SNAP output
|
2bqu
|
transferase |
X-ray (2.5 Å) |
Zang H, Goodenough AK, Choi JY, Irimia A,
Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M,
Guengerich FP |
(2005) "DNA
Adduct Bypass Polymerization by Sulfolobus Solfataricus
DNA Polymerase Dpo4: Analysis and Crystal Structures of
Multiple Base Pair Substitution and Frameshift Products
with the Adduct 1,N2-Ethenoguanine."
J.Biol.Chem., 280, 29750.
doi: 10.1074/JBC.M504756200.
|
DNA adduct bypass polymerization by sulfolobus
solfataricus dpo4. analysis and crystal structures of
multiple base-pair substitution and frameshift products
with the adduct 1,n2-ethenoguanine . SNAP output
|
2br0
|
transferase |
X-ray (2.17 Å) |
Zang H, Goodenough AK, Choi JY, Irimia A,
Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M,
Guengerich FP |
(2005) "DNA
Adduct Bypass Polymerization by Sulfolobus Solfataricus
DNA Polymerase Dpo4: Analysis and Crystal Structures of
Multiple Base Pair Substitution and Frameshift Products
with the Adduct 1,N2-Ethenoguanine."
J.Biol.Chem., 280, 29750.
doi: 10.1074/JBC.M504756200.
|
DNA adduct bypass polymerization by sulfolobus
solfataricus dpo4. analysis and crystal structures of
multiple base-pair substitution and frameshift products
with the adduct 1,n2-ethenoguanine . SNAP output
|
2bsq
|
transcription |
X-ray (3.0 Å) |
Mattison K, Wilbur JS, So M, Brennan RG |
(2006) "Structure
of Fitab from Neisseria Gonorrhoeae Bound to DNA
Reveals a Tetramer of Toxin-Antitoxin Heterodimers
Containing Pin Domains and Ribbon-Helix-Helix
Motifs." J.Biol.Chem.,
281, 37942. doi: 10.1074/JBC.M605198200.
|
Fitab bound to DNA . SNAP output
|
2bzf
|
DNA binding protein |
X-ray (2.87 Å) |
Bradley CM, Ronning DR, Ghirlando R, Craigie R, Dyda
F |
(2005) "Structural
Basis for DNA Bridging by Barrier-to-Autointegration
Factor." Nat.Struct.Mol.Biol.,
12, 935. doi: 10.1038/NSMB989.
|
Structural basis for DNA bridging by
barrier-to-autointegration factor (baf) . SNAP output
|
2c22
|
polymerase |
X-ray (2.56 Å) |
Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch
LV, Egli M, Guengerich FP |
(2006) "Efficient
and High Fidelity Incorporation of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus
Solfataricus DNA Polymerase Dpo4."
J.Biol.Chem., 281, 2358. doi:
10.1074/JBC.M510889200.
|
Efficient and high fidelity incorporation of dctp
opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus
solfataricus DNA polymerase dpo4 . SNAP output
|
2c28
|
polymerase |
X-ray (2.27 Å) |
Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch
LV, Egli M, P Guengerich F |
(2006) "Efficient
and High Fidelity Incorporation of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus
Solfataricus DNA Polymerase Dpo4."
J.Biol.Chem., 281, 2358. doi:
10.1074/JBC.M510889200.
|
Efficient and high fidelity incorporation of dctp
opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus
solfataricus DNA polymerase dpo4 . SNAP output
|
2c2d
|
polymerase |
X-ray (2.57 Å) |
Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch
LV, Egli M, P Guengerich F |
(2006) "Efficient
and High Fidelity Incorporation of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus
Solfataricus DNA Polymerase Dpo4."
J.Biol.Chem., 281, 2358. doi:
10.1074/JBC.M510889200.
|
Efficient and high fidelity incorporation of dctp
opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus
solfataricus DNA polymerase dpo4 . SNAP output
|
2c2e
|
polymerase |
X-ray (2.61 Å) |
Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch
LV, Egli M, P Guengerich F |
(2006) "Efficient
and High Fidelity Incorporation of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus
Solfataricus DNA Polymerase Dpo4."
J.Biol.Chem., 281, 2358. doi:
10.1074/JBC.M510889200.
|
Efficient and high fidelity incorporation of dctp
opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus
solfataricus DNA polymerase dpo4 . SNAP output
|
2c2r
|
polymerase |
X-ray (2.55 Å) |
Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch
LV, Egli M, Guengerich FP |
(2006) "Efficient
and High Fidelity Incorporation of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus
Solfataricus DNA Polymerase Dpo4."
J.Biol.Chem., 281, 2358. doi:
10.1074/JBC.M510889200.
|
Efficient and high fidelity incorporation of dctp
opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus
solfataricus DNA polymerase dpo4 . SNAP output
|
2c5r
|
DNA-binding protein-DNA |
X-ray (2.9 Å) |
Albert A, Munoz-Espin D, Jimenez M, Asensio JL,
Hermoso JA, Salas M, Meijer WJJ |
(2005) "Structural
Basis for Membrane Anchorage of Viral Phi 29 DNA During
Replication." J.Biol.Chem.,
280, 42486. doi: 10.1074/JBC.C500429200.
|
The structure of phage phi29 replication organizer
protein p16.7 in complex with double stranded DNA .
SNAP output
|
2c62
|
transcription |
X-ray (1.74 Å) |
Werten S, Moras D |
(2006) "A Global
Transcription Cofactor Bound to Juxtaposed Strands of
Unwound DNA." Nat.Struct.Mol.Biol.,
13, 181. doi: 10.1038/NSMB1044.
|
Crystal structure of the human transcription cofactor
pc4 in complex with single-stranded DNA . SNAP output
|
2c6y
|
transcription regulation |
X-ray (2.4 Å) |
Tsai K-L, Huang C-Y, Chang C-H, Sun Y-J, Chuang W-J,
Hsiao C-D |
(2006) "Crystal
Structure of the Human Foxk1A-DNA Complex and its
Implications on the Diverse Binding Specificity of
Winged Helix/Forkhead Proteins."
J.Biol.Chem., 281, 17400.
doi: 10.1074/JBC.M600478200.
|
Crystal structure of interleukin enhancer-binding
factor 1 bound to DNA . SNAP output
|
2c7a
|
receptor-DNA |
X-ray (2.5 Å) |
Roemer SC, Donham DC, Sherman L, Pon VH, Edwards DP,
Churchill MEA |
(2006) "Structure
of the Progesterone Receptor-Deoxyribonucleic Acid
Complex: Novel Interactions Required for Binding to
Half-Site Response Elements."
Mol.Endocrinol., 20, 3042.
doi: 10.1210/ME.2005-0511.
|
Structure of the progesterone receptor-DNA complex .
SNAP output
|
2c7o
|
transferase-DNA |
X-ray (1.9 Å) |
Neely RK, Daujotyte D, Grazulis S, Magennis SW,
Dryden DTF, Klimasauskas S, Jones AC |
(2005) "Time-Resolved
Fluorescence of 2-Aminopurine as a Probe of Base
Flipping in M.HhaI-DNA Complexes." Nucleic
Acids Res., 33, 6953. doi:
10.1093/NAR/GKI995.
|
Hhai DNA methyltransferase complex with 13mer
oligonucleotide containing 2-aminopurine adjacent to
the target base (pcgc:gmgc) and sah . SNAP output
|
2c7p
|
transferase-DNA |
X-ray (1.7 Å) |
Neely RK, Daujotyte D, Grazulis S, Magennis SW,
Dryden DTF, Klimasauskas S, Jones AC |
(2005) "Time-Resolved
Fluorescence of 2-Aminopurine as a Probe of Base
Flipping in M.HhaI-DNA Complexes." Nucleic
Acids Res., 33, 6953. doi:
10.1093/NAR/GKI995.
|
Hhai DNA methyltransferase complex with oligonucleotide
containing 2- aminopurine opposite to the target base
(gcgc:gmpc) and sah . SNAP output
|
2c7q
|
transferase-DNA |
X-ray (1.85 Å) |
Neely RK, Daujotyte D, Grazulis S, Magennis SW,
Dryden DTF, Klimasauskas S, Jones AC |
(2005) "Time-Resolved
Fluorescence of 2-Aminopurine as a Probe of Base
Flipping in M.HhaI-DNA Complexes." Nucleic
Acids Res., 33, 6953. doi:
10.1093/NAR/GKI995.
|
Hhai DNA methyltransferase complex with oligonucleotide
containing 2- aminopurine outside the recognition
sequence (paired with g) and sah . SNAP output
|
2c7r
|
transferase-DNA |
X-ray (1.9 Å) |
Neely RK, Daujotyte D, Grazulis S, Magennis SW,
Dryden DTF, Klimasauskas S, Jones AC |
(2005) "Time-Resolved
Fluorescence of 2-Aminopurine as a Probe of Base
Flipping in M.HhaI-DNA Complexes." Nucleic
Acids Res., 33, 6953. doi:
10.1093/NAR/GKI995.
|
Hhai DNA methyltransferase (t250g mutant) complex with
oligonucleotide containing 2-aminopurine as a target
base (gpgc:gmgc) and sah . SNAP output
|
2c9l
|
viral protein |
X-ray (2.25 Å) |
Petosa C, Morand P, Baudin F, Moulin M, Artero JB,
Muller CW |
(2006) "Structural
Basis of Lytic Cycle Activation by the Epstein-Barr
Virus Zebra Protein." Mol.Cell,
21, 565. doi: 10.1016/J.MOLCEL.2006.01.006.
|
Structure of the epstein-barr virus zebra protein .
SNAP output
|
2c9n
|
viral protein |
X-ray (3.3 Å) |
Petosa C, Morand P, Baudin F, Moulin M, Artero JB,
Muller CW |
(2006) "Structural
Basis of Lytic Cycle Activation by the Epstein-Barr
Virus Zebra Protein." Mol.Cell,
21, 565. doi: 10.1016/J.MOLCEL.2006.01.006.
|
Structure of the epstein-barr virus zebra protein at
approximately 3. 5 angstrom resolution . SNAP output
|
2cax
|
transcriptional repressor |
X-ray (2.9 Å) |
Weihofen WA, Cicek A, Pratto F, Alonso JC, Saenger
W |
(2006) "Structures
of Omega Repressors Bound to Direct and Inverted DNA
Repeats Explain Modulation of Transcription."
Nucleic Acids Res., 34, 1450.
doi: 10.1093/NAR/GKL015.
|
Structural basis for cooperative binding of
ribbon-helix-helix repressor omega to mutated direct
DNA heptad repeats . SNAP output
|
2ccz
|
DNA-replication |
X-ray (2.7 Å) |
Huang C-Y, Hsu C-H, Sun Y-J, Wu H-N, Hsiao C-D |
(2006) "Complexed
Crystal Structure of Replication Restart Primsome
Protein Prib Reveals a Novel Single-Stranded
DNA-Binding Mode." Nucleic Acids Res.,
34, 3878. doi: 10.1093/NAR/GKL536.
|
Crystal structure of e. coli primosomol protein prib
bound to ssDNA . SNAP
output
|
2cdm
|
DNA-DNA-binding protein |
X-ray (2.7 Å) |
Boer R, Russi S, Guasch A, Lucas M, Blanco AG,
Perez-Luque R, Coll M, De La Cruz F |
(2006) "Unveiling
the Molecular Mechanism of a Conjugative Relaxase: The
Structure of Trwc Complexed with a 27-mer DNA
Comprising the Recognition Hairpin and the Cleavage
Site." J.Mol.Biol., 358,
857. doi: 10.1016/J.JMB.2006.02.018.
|
The structure of trwc complexed with a 27-mer DNA
comprising the recognition hairpin and the cleavage
site . SNAP output
|
2cgp
|
transcription-DNA |
X-ray (2.2 Å) |
Passner JM, Steitz TA |
(1997) "The
structure of a CAP-DNA complex having two cAMP
molecules bound to each monomer."
Proc.Natl.Acad.Sci.USA, 94,
2843-2847. doi: 10.1073/pnas.94.7.2843.
|
Catabolite gene activator protein-DNA complex,
adenosine-3',5'-cyclic-monophosphate . SNAP output
|
2crx
|
hydrolase, ligase-DNA |
X-ray (2.5 Å) |
Gopaul DN, Guo F, Van Duyne GD |
(1998) "Structure
of the Holliday junction intermediate in Cre-loxP
site-specific recombination." EMBO J.,
17, 4175-4187. doi: 10.1093/emboj/17.14.4175.
|
Structure of the holliday junction intermediate in
cre-loxp site-specific recombination . SNAP output
|
2cv5
|
structural protein-DNA |
X-ray (2.5 Å) |
Tsunaka Y, Kajimura N, Tate S, Morikawa K |
(2005) "Alteration
of the nucleosomal DNA path in the crystal structure of
a human nucleosome core particle." Nucleic
Acids Res., 33, 3424-3434. doi:
10.1093/nar/gki663.
|
Crystal structure of human nucleosome core particle .
SNAP output
|
2d45
|
transcription-DNA |
X-ray (3.8 Å) |
Safo MK, Ko TP, Musayev FN, Zhao Q, Wang AH, Archer
GL |
(2006) "Structure
of the MecI repressor from Staphylococcus aureus in
complex with the cognate DNA operator of mec."
Acta Crystallogr.,Sect.F, 62,
320-324. doi: 10.1107/S1744309106009742.
|
Crystal structure of the meci-meca repressor-operator
complex . SNAP
output
|
2d55
|
DNA-antibiotic |
X-ray (3.0 Å) |
Kamitori S, Takusagawa F |
(1992) "Crystal
Structure of the 2:1 Complex between D(Gaagcttc) and
the Anticancer Drug Actinomycin D."
J.Mol.Biol., 225, 445. doi:
10.1016/0022-2836(92)90931-9.
|
Structural, physical and biological characteristics of
RNA.DNA binding agent n8-actinomycin d . SNAP output
|
2d5v
|
transcription-DNA |
X-ray (2.0 Å) |
Iyaguchi D, Yao M, Watanabe N, Nishihira J, Tanaka
I |
(2007) "DNA
recognition mechanism of the ONECUT homeodomain of
transcription factor HNF-6." Structure,
15, 75-83. doi: 10.1016/j.str.2006.11.004.
|
Crystal structure of hnf-6alpha DNA-binding domain in
complex with the ttr promoter . SNAP output
|
2d7d
|
hydrolase-DNA |
X-ray (2.1 Å) |
Eryilmaz J, Ceschini S, Ryan J, Geddes S, Waters TR,
Barrett TE |
(2006) "Structural
insights into the cryptic DNA-dependent ATPase activity
of UvrB." J.Mol.Biol.,
357, 62-72. doi: 10.1016/j.jmb.2005.12.059.
|
Structural insights into the cryptic DNA dependent
atp-ase activity of uvrb . SNAP output
|
2d7g
|
hydrolase |
X-ray (3.3 Å) |
Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T,
Masai H, Saito M, Shirai T, Kohda D |
(2007) "Structural
basis of the 3'-end recognition of a leading strand in
stalled replication forks by PriA." EMBO
J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697.
|
Crystal structure of the aa complex of the n-terminal
domain of pria . SNAP
output
|
2d7h
|
hydrolase |
X-ray (3.0 Å) |
Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T,
Masai H, Saito M, Shirai T, Kohda D |
(2007) "Structural
basis of the 3'-end recognition of a leading strand in
stalled replication forks by PriA." EMBO
J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697.
|
Crystal structure of the ccc complex of the n-terminal
domain of pria . SNAP
output
|
2da8
|
DNA-antibiotic |
NMR |
Addess KJ, Sinsheimer JS, Feigon J |
(1993) "Solution
Structure of a Complex between
[N-Mecys3,N-Mecys7]Tandem and [D(Gatatc)]2."
Biochemistry, 32, 2498. doi:
10.1021/BI00061A006.
|
Solution structure of a complex between
(n-mecys3,n-mecys7)tandem and (d(gatatc))2 . SNAP output
|
2db3
|
hydrolase-RNA |
X-ray (2.2 Å) |
Sengoku T, Nureki O, Nakamura A, Kobayashi S,
Yokoyama S |
(2006) "Structural
basis for RNA unwinding by the DEAD-box protein
Drosophila Vasa." Cell(Cambridge,Mass.),
125, 287-300. doi: 10.1016/j.cell.2006.01.054.
|
Structural basis for RNA unwinding by the dead-box
protein drosophila vasa . SNAP output
|
2ddg
|
hydrolase-DNA |
X-ray (2.1 Å) |
Kosaka H, Hoseki J, Nakagawa N, Kuramitsu S, Masui
R |
(2007) "Crystal
structure of family 5 uracil-DNA glycosylase bound to
DNA." J.Mol.Biol., 373,
839-850. doi: 10.1016/j.jmb.2007.08.022.
|
Crystal structure of uracil-DNA glycosylase in complex
with ap:g containing DNA . SNAP output
|
2dem
|
hydrolase-DNA |
X-ray (1.95 Å) |
Kosaka H, Hoseki J, Nakagawa N, Kuramitsu S, Masui
R |
(2007) "Crystal
structure of family 5 uracil-DNA glycosylase bound to
DNA." J.Mol.Biol., 373,
839-850. doi: 10.1016/j.jmb.2007.08.022.
|
Crystal structure of uracil-DNA glycosylase in complex
with ap:a containing DNA . SNAP output
|
2dgc
|
transcription-DNA |
X-ray (2.2 Å) |
Keller W, Konig P, Richmond TJ |
(1995) "Crystal
structure of a bZIP/DNA complex at 2.2 A: determinants
of DNA specific recognition." J.Mol.Biol.,
254, 657-667. doi: 10.1006/jmbi.1995.0645.
|
Gcn4 basic domain, leucine zipper complexed with
atf-creb site DNA . SNAP
output
|
2dlc
|
ligase-trna |
X-ray (2.4 Å) |
Tsunoda M, Kusakabe Y, Tanaka N, Ohno S, Nakamura M,
Senda T, Moriguchi T, Asai N, Sekine M, Yokogawa T,
Nishikawa K, Nakamura KT |
(2007) "Structural
basis for recognition of cognate tRNA by tyrosyl-tRNA
synthetase from three kingdoms." Nucleic Acids
Res., 35, 4289-4300. doi:
10.1093/nar/gkm417.
|
Crystal structure of the ternary complex of yeast
tyrosyl-trna synthetase . SNAP output
|
2dnj
|
hydrolase-DNA |
X-ray (2.0 Å) |
Lahm A, Suck D |
(1991) "DNase
I-induced DNA conformation. 2 A structure of a DNase
I-octamer complex." J.Mol.Biol.,
222, 645-667. doi: 10.1016/0022-2836(91)90502-W.
|
Dnase i-induced DNA conformation. 2 angstroms structure
of a dnase i-octamer complex . SNAP output
|
2dp6
|
hydrolase-DNA |
X-ray (1.8 Å) |
Kosaka H, Nakagawa N, Masui R, Kuramitsu S |
"Structure of Family 5 Uracil-DNA Glycosylase Bound
to DNA Reveals Insights into the Mechanism for Substrate
Recognition and Catalysis." |
Crystal structure of uracil-DNA glycosylase in complex
with ap:c containing DNA . SNAP output
|
2dpd
|
DNA binding protein-DNA |
X-ray (3.17 Å) |
Vivian JP, Wilce J, Wilce MCJ |
"Crystal structure of the Replication Termination
Protein in complex with a pseudosymmetric B-site." |
Crystal structure of the replication termination
protein in complex with a pseudosymmetric b-site .
SNAP output
|
2dpi
|
transferase-DNA |
X-ray (2.3 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2006) "Hoogsteen
base pair formation promotes synthesis opposite the
1,N(6)-ethenodeoxyadenosine lesion by human DNA
polymerase iota." Nat.Struct.Mol.Biol.,
13, 619-625. doi: 10.1038/nsmb1118.
|
Ternary complex of hpoli with DNA and dctp . SNAP output
|
2dpj
|
transferase-DNA |
X-ray (2.3 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2006) "Hoogsteen
base pair formation promotes synthesis opposite the
1,N(6)-ethenodeoxyadenosine lesion by human DNA
polymerase iota." Nat.Struct.Mol.Biol.,
13, 619-625. doi: 10.1038/nsmb1118.
|
Structure of hpoli with DNA and dttp . SNAP output
|
2dpu
|
DNA binding protein-DNA |
X-ray (3.1 Å) |
Vivian JP, Wilce J, Wilce MCJ |
"Crystal structure of the replication termination
protein in complex with a pseudosymmetric 21mer B-site
DNA." |
Crystal structure of the replication termination
protein in complex with a pseudosymmetric 21mer b-site
DNA . SNAP output
|
2drp
|
transcription-DNA |
X-ray (2.8 Å) |
Fairall L, Schwabe JW, Chapman L, Finch JT, Rhodes
D |
(1993) "The
crystal structure of a two zinc-finger peptide reveals
an extension to the rules for zinc-finger/DNA
recognition." Nature,
366, 483-487. doi: 10.1038/366483a0.
|
The crystal structure of a two zinc-finger peptide
reveals an extension to the rules for zinc-finger-DNA
recognition . SNAP
output
|
2dtu
|
transferase-DNA |
X-ray (2.37 Å) |
Hogg M, Aller P, Konigsberg W, Wallace SS, Doublie
S |
(2007) "Structural
and biochemical investigation of the role in
proofreading of a beta hairpin loop found in the
exonuclease domain of a replicative DNA polymerase of
the B family." J.Biol.Chem.,
282, 1432-1444. doi: 10.1074/jbc.M605675200.
|
Crystal structure of the beta hairpin loop deletion
variant of rb69 gp43 in complex with DNA containing an
abasic site analog . SNAP output
|
2dwl
|
hydrolase-DNA |
X-ray (3.2 Å) |
Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T,
Masai H, Saito M, Shirai T, Kohda D |
(2007) "Structural
basis of the 3'-end recognition of a leading strand in
stalled replication forks by PriA." EMBO
J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697.
|
Crystal structure of the pria protein complexed with
oligonucleotides . SNAP
output
|
2dwm
|
hydrolase-DNA |
X-ray (3.15 Å) |
Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T,
Masai H, Saito M, Shirai T, Kohda D |
(2007) "Structural
basis of the 3'-end recognition of a leading strand in
stalled replication forks by PriA." EMBO
J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697.
|
Crystal structure of the pria protein complexed with
oligonucleotides . SNAP
output
|
2dwn
|
hydrolase-DNA |
X-ray (3.35 Å) |
Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T,
Masai H, Saito M, Shirai T, Kohda D |
(2007) "Structural
basis of the 3'-end recognition of a leading strand in
stalled replication forks by PriA." EMBO
J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697.
|
Crystal structure of the pria protein complexed with
oligonucleotides . SNAP
output
|
2dy4
|
transferase-DNA |
X-ray (2.65 Å) |
Aller P, Rould MA, Hogg M, Wallace SS, Doublie S |
(2007) "A
structural rationale for stalling of a replicative DNA
polymerase at the most common oxidative thymine lesion,
thymine glycol." Proc.Natl.Acad.Sci.USA,
104, 814-818. doi: 10.1073/pnas.0606648104.
|
Crystal structure of rb69 gp43 in complex with DNA
containing thymine glycol . SNAP output
|
2e1c
|
transcription-DNA |
X-ray (2.1 Å) |
Yokoyama K, Ishijima SA, Koike H, Kurihara C,
Shimowasa A, Kabasawa M, Kawashima T, Suzuki M |
(2007) "Feast/Famine
Regulation by Transcription Factor FL11 for the
Survival of the Hyperthermophilic Archaeon Pyrococcus
OT3." Structure, 15,
1542-1554. doi: 10.1016/j.str.2007.10.015.
|
Structure of putative hth-type transcriptional
regulator ph1519-DNA complex . SNAP output
|
2e2h
|
transcription,transferase-DNA-RNA hybrid |
X-ray (3.95 Å) |
Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg
RD |
(2006) "Structural
basis of transcription: role of the trigger loop in
substrate specificity and catalysis."
Cell(Cambridge,Mass.), 127,
941-954. doi: 10.1016/j.cell.2006.11.023.
|
RNA polymerase ii elongation complex at 5 mm mg2+ with
gtp . SNAP output
|
2e2i
|
transcription,transferase-DNA-RNA hybrid |
X-ray (3.41 Å) |
Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg
RD |
(2006) "Structural
basis of transcription: role of the trigger loop in
substrate specificity and catalysis."
Cell(Cambridge,Mass.), 127,
941-954. doi: 10.1016/j.cell.2006.11.023.
|
RNA polymerase ii elongation complex in 5 mm mg+2 with
2'-dgtp . SNAP
output
|
2e2j
|
transcription,transferase-DNA-RNA hybrid |
X-ray (3.5 Å) |
Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg
RD |
(2006) "Structural
basis of transcription: role of the trigger loop in
substrate specificity and catalysis."
Cell(Cambridge,Mass.), 127,
941-954. doi: 10.1016/j.cell.2006.11.023.
|
RNA polymerase ii elongation complex in 5 mm mg+2 with
gmpcpp . SNAP output
|
2e42
|
transcription-DNA |
X-ray (1.8 Å) |
Tahirov TH, Inoue-Bungo T, Sato K, Shiina M, Hamada
K, Ogata K |
"Structural Basis for Flexible Base Recognition by
C/Ebpbeta." |
Crystal structure of c-ebpbeta bzip homodimer v285a
mutant bound to a high affinity DNA fragment . SNAP output
|
2e43
|
transcription-DNA |
X-ray (2.1 Å) |
Tahirov TH, Inoue-Bungo T, Sato K, Shiina M, Hamada
K, Ogata K |
"Structural Basis for Flexible Base Recognition by
C/Ebpbeta." |
Crystal structure of c-ebpbeta bzip homodimer k269a
mutant bound to a high affinity DNA fragment . SNAP output
|
2e52
|
hydrolase-DNA |
X-ray (2.0 Å) |
Watanabe N, Takasaki Y, Sato C, Ando S, Tanaka I |
(2009) "Structures
of restriction endonuclease HindIII in complex with its
cognate DNA and divalent cations." Acta
Crystallogr.,Sect.D, 65,
1326-1333. doi: 10.1107/S0907444909041134.
|
Crystal structural analysis of hindiii restriction
endonuclease in complex with cognate DNA at 2.0
angstrom resolution . SNAP output
|
2ea0
|
hydrolase-DNA |
X-ray (1.4 Å) |
Golan G, Zharkov DO, Grollman AP, Shoham G |
"Active site plasticity of endonuclease VIII:
Conformational changes compensating for different
substrate and mutations of critical residues." |
Crystal structure of the DNA repair enzyme
endonuclease-viii (nei) from e. coli in complex with
ap-site containing DNA substrate . SNAP output
|
2efw
|
replication-DNA |
X-ray (2.5 Å) |
Vivian JP, Porter CJ, Wilce JA, Wilce MCJ |
(2007) "An
asymmetric structure of the Bacillus subtilis
replication terminator protein in complex with
DNA." J.Mol.Biol., 370,
481-491. doi: 10.1016/j.jmb.2007.02.067.
|
Crystal structure of the rtp:nrb complex from bacillus
subtilis . SNAP
output
|
2er8
|
transcription activator-DNA |
X-ray (2.85 Å) |
Fitzgerald MX, Rojas JR, Kim JM, Kohlhaw GB,
Marmorstein R |
(2006) "Structure
of a Leu3-DNA complex: recognition of everted CGG
half-sites by a Zn2Cys6 binuclear cluster protein."
Structure, 14, 725-735. doi:
10.1016/j.str.2005.11.025.
|
Crystal structure of leu3 DNA-binding domain complexed
with a 12mer DNA duplex . SNAP output
|
2ere
|
transcription activator-DNA |
X-ray (3.0 Å) |
Fitzgerald MX, Rojas JR, Kim JM, Kohlhaw GB,
Marmorstein R |
(2006) "Structure
of a Leu3-DNA complex: recognition of everted CGG
half-sites by a Zn2Cys6 binuclear cluster protein."
Structure, 14, 725-735. doi:
10.1016/j.str.2005.11.025.
|
Crystal structure of a leu3 DNA-binding domain
complexed with a 15mer DNA duplex . SNAP output
|
2erg
|
transcription activator-DNA |
X-ray (3.15 Å) |
Fitzgerald MX, Rojas JR, Kim JM, Kohlhaw GB,
Marmorstein R |
(2006) "Structure
of a Leu3-DNA complex: recognition of everted CGG
half-sites by a Zn2Cys6 binuclear cluster protein."
Structure, 14, 725-735. doi:
10.1016/j.str.2005.11.025.
|
Crystal structure of leu3 DNA-binding domain with a
single h50c mutation complexed with a 15mer DNA duplex
. SNAP output
|
2es2
|
gene regulation |
X-ray (1.78 Å) |
Max KE, Zeeb M, Bienert R, Balbach J, Heinemann
U |
(2006) "T-rich
DNA single strands bind to a preformed site on the
bacterial cold shock protein Bs-CspB."
J.Mol.Biol., 360, 702-714.
doi: 10.1016/j.jmb.2006.05.044.
|
Crystal structure analysis of the bacillus subtilis
cold shock protein bs-cspb in complex with
hexathymidine . SNAP
output
|
2etw
|
cell cycle-DNA |
X-ray (1.67 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Principles of protein-DNA recognition revealed in the
structural analysis of ndt80-mse DNA complexes .
SNAP output
|
2euv
|
cell cycle-DNA |
X-ray (1.94 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Principles of protein-DNA recognition revealed in the
structural analysis of ndt80-mse DNA complexes .
SNAP output
|
2euw
|
cell cycle-DNA |
X-ray (1.68 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Structure of a ndt80-DNA complex (mse mutant ma4t) .
SNAP output
|
2eux
|
cell cycle-DNA |
X-ray (1.57 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Structure of a ndt80-DNA complex (mse variant va4g) .
SNAP output
|
2euz
|
cell cycle-DNA |
X-ray (1.56 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Structure of a ndt80-DNA complex (mse mutant mc5t) .
SNAP output
|
2evf
|
cell cycle-DNA |
X-ray (1.56 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Structure of a ndt80-DNA complex (mse mutant ma6t) .
SNAP output
|
2evg
|
cell cycle-DNA |
X-ray (1.55 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Structure of a ndt80-DNA complex (mse mutant ma7t) .
SNAP output
|
2evh
|
cell cycle-DNA |
X-ray (1.989 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Structure of a ndt80-DNA complex (mse mutant ma7g) .
SNAP output
|
2evi
|
cell cycle-DNA |
X-ray (1.8 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Structure of a ndt80-DNA complex (mse mutant ma8t) .
SNAP output
|
2evj
|
cell cycle-DNA |
X-ray (1.89 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Structure of an ndt80-DNA complex (mse mutant ma9c) .
SNAP output
|
2ewj
|
replication-DNA |
X-ray (2.7 Å) |
Mulcair MD, Schaeffer PM, Oakley AJ, Cross HF, Neylon
C, Hill TM, Dixon NE |
(2006) "A
molecular mousetrap determines polarity of termination
of DNA replication in E. coli."
Cell(Cambridge,Mass.), 125,
1309-1319. doi: 10.1016/j.cell.2006.04.040.
|
Escherichia coli replication terminator protein (tus)
complexed with DNA- locked form . SNAP output
|
2ex5
|
hydrolase-DNA |
X-ray (2.2 Å) |
Spiegel PC, Chevalier B, Sussman D, Turmel M, Lemieux
C, Stoddard BL |
(2006) "The
structure of I-CeuI homing endonuclease: Evolving
asymmetric DNA recognition from a symmetric protein
scaffold." Structure, 14,
869-880. doi: 10.1016/j.str.2006.03.009.
|
Group i intron-encoded homing endonuclease i-ceui
complexed with DNA . SNAP output
|
2exf
|
viral protein-DNA |
NMR |
Bourbigot S, Ramalanjaona N, Boudier C, Salgado GF,
Roques BP, Mely Y, Bouaziz S, Morellet N |
(2008) "How the
HIV-1 nucleocapsid protein binds and destabilises the
(-)primer binding site during reverse
transcription." J.Mol.Biol.,
383, 1112-1128. doi: 10.1016/j.jmb.2008.08.046.
|
Solution structure of the hiv-1 nucleocapsid
(ncp7(12-55)) complexed with the DNA (-) primer binding
site . SNAP output
|
2ezd
|
DNA binding protein-DNA |
NMR |
Huth JR, Bewley CA, Nissen MS, Evans JN, Reeves R,
Gronenborn AM, Clore GM |
(1997) "The
solution structure of an HMG-I(Y)-DNA complex defines a
new architectural minor groove binding motif."
Nat.Struct.Biol., 4, 657-665.
doi: 10.1038/nsb0897-657.
|
Solution structure of a complex of the second DNA
binding domain of human hmg-i(y) bound to DNA dodecamer
containing the prdii site of the interferon-beta
promoter, NMR, minimized average structure . SNAP output
|
2eze
|
DNA binding protein-DNA |
NMR |
Huth JR, Bewley CA, Nissen MS, Evans JN, Reeves R,
Gronenborn AM, Clore GM |
(1997) "The
solution structure of an HMG-I(Y)-DNA complex defines a
new architectural minor groove binding motif."
Nat.Struct.Biol., 4, 657-665.
doi: 10.1038/nsb0897-657.
|
Solution structure of a complex of the second DNA
binding domain of human hmg-i(y) bound to DNA dodecamer
containing the prdii site of the interferon-beta
promoter, NMR, 35 structures . SNAP output
|
2ezf
|
DNA binding protein-DNA |
NMR |
Huth JR, Bewley CA, Nissen MS, Evans JN, Reeves R,
Gronenborn AM, Clore GM |
(1997) "The
solution structure of an HMG-I(Y)-DNA complex defines a
new architectural minor groove binding motif."
Nat.Struct.Biol., 4, 657-665.
doi: 10.1038/nsb0897-657.
|
Solution structure of a complex of the third DNA
binding domain of human hmg-i(y) bound to DNA dodecamer
containing the prdii site of the interferon-beta
promoter, NMR, minimized average structure . SNAP output
|
2ezg
|
DNA binding protein-DNA |
NMR |
Huth JR, Bewley CA, Nissen MS, Evans JN, Reeves R,
Gronenborn AM, Clore GM |
(1997) "The
solution structure of an HMG-I(Y)-DNA complex defines a
new architectural minor groove binding motif."
Nat.Struct.Biol., 4, 657-665.
doi: 10.1038/nsb0897-657.
|
Solution structure of a complex of the third DNA
binding domain of human hmg-i(y) bound to DNA dodecamer
containing the prdii site of the interferon-beta
promoter, NMR, 35 structures . SNAP output
|
2ezv
|
hydrolase-DNA |
X-ray (2.4 Å) |
Vanamee ES, Viadiu H, Kucera R, Dorner L, Picone S,
Schildkraut I, Aggarwal AK |
(2005) "A view
of consecutive binding events from structures of
tetrameric endonuclease SfiI bound to DNA."
Embo J., 24, 4198-4208. doi:
10.1038/sj.emboj.7600880.
|
Crystal structure of tetrameric restriction
endonuclease sfii bound to cognate DNA. . SNAP output
|
2f03
|
hydrolase-DNA |
X-ray (3.05 Å) |
Vanamee ES, Viadiu H, Kucera R, Dorner L, Picone S,
Schildkraut I, Aggarwal AK |
(2005) "A view
of consecutive binding events from structures of
tetrameric endonuclease SfiI bound to DNA."
Embo J., 24, 4198-4208. doi:
10.1038/sj.emboj.7600880.
|
Crystal structure of tetrameric restriction
endonuclease sfii in complex with cognate DNA (partial
bound form) . SNAP
output
|
2f55
|
hydrolase-DNA |
X-ray (3.3 Å) |
Mackintosh SG, Lu JZ, Jordan JB, Harrison MK, Sikora
B, Sharma SD, Cameron CE, Raney KD, Sakon J |
(2006) "Structural
and biological identification of residues on the
surface of NS3 helicase required for optimal
replication of the hepatitis C virus."
J.Biol.Chem., 281, 3528-3535.
doi: 10.1074/jbc.M512100200.
|
Two hepatitis c virus ns3 helicase domains complexed
with the same strand of DNA . SNAP output
|
2f5n
|
hydrolase-DNA |
X-ray (2.0 Å) |
Banerjee A, Santos WL, Verdine GL |
(2006) "Structure
of a DNA glycosylase searching for lesions."
Science, 311, 1153-1157. doi:
10.1126/science.1120288.
|
Mutm crosslinked to undamaged DNA sampling a:t base
pair ic1 . SNAP
output
|
2f5o
|
hydrolase-DNA |
X-ray (2.05 Å) |
Banerjee A, Santos WL, Verdine GL |
(2006) "Structure
of a DNA glycosylase searching for lesions."
Science, 311, 1153-1157. doi:
10.1126/science.1120288.
|
Mutm crosslinked to undamaged DNA sampling g:c base
pair ic3 . SNAP
output
|
2f5p
|
hydrolase-DNA |
X-ray (2.0 Å) |
Banerjee A, Santos WL, Verdine GL |
(2006) "Structure
of a DNA glycosylase searching for lesions."
Science, 311, 1153-1157. doi:
10.1126/science.1120288.
|
Mutm crosslinked to undamaged DNA sampling a:t base
pair ic2 . SNAP
output
|
2f5q
|
hydrolase-DNA |
X-ray (2.35 Å) |
Banerjee A, Santos WL, Verdine GL |
(2006) "Structure
of a DNA glycosylase searching for lesions."
Science, 311, 1153-1157. doi:
10.1126/science.1120288.
|
Catalytically inactive (e3q) mutm crosslinked to oxog:c
containing DNA cc2 . SNAP output
|
2f5s
|
hydrolase-DNA |
X-ray (2.35 Å) |
Banerjee A, Santos WL, Verdine GL |
(2006) "Structure
of a DNA glycosylase searching for lesions."
Science, 311, 1153-1157. doi:
10.1126/science.1120288.
|
Catalytically inactive (e3q) mutm crosslinked to oxog:c
containing DNA cc1 . SNAP output
|
2f8n
|
structural protein-DNA |
X-ray (2.9 Å) |
Chakravarthy S, Luger K |
"Nucleosomes containing the histone domain of
macroH2A: In vitro possibilities." |
2.9 angstrom x-ray structure of hybrid macroh2a
nucleosomes . SNAP
output
|
2f8x
|
transcription-DNA |
X-ray (3.25 Å) |
Nam Y, Sliz P, Song L, Aster JC, Blacklow SC |
(2006) "Structural
basis for cooperativity in recruitment of MAML
coactivators to Notch transcription complexes."
Cell(Cambridge,Mass.), 124,
973-983. doi: 10.1016/j.cell.2005.12.037.
|
Crystal structure of activated notch, csl and maml on
hes-1 promoter DNA sequence . SNAP output
|
2fcc
|
hydrolase |
X-ray (2.3 Å) |
Golan G, Zharkov DO, Grollman AP, Dodson ML,
McCullough AK, Lloyd RS, Shoham G |
(2006) "Structure
of T4 Pyrimidine Dimer Glycosylase in a Reduced Imine
Covalent Complex with Abasic Site-containing DNA."
J.Mol.Biol., 362, 241-258.
doi: 10.1016/j.jmb.2006.06.059.
|
Crystal structure of t4 pyrimidine dimer glycosylase
(t4-pdg) covalently complexed with a DNA substrate
containing abasic site . SNAP output
|
2fd8
|
oxidoreductase-DNA |
X-ray (2.3 Å) |
Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC,
Gibney BR, Hunt JF |
(2006) "Crystal
structures of catalytic complexes of the oxidative
DNA/RNA repair enzyme AlkB." Nature,
439, 879-884. doi: 10.1038/nature04561.
|
Crystal structure of alkb in complex with fe(ii),
2-oxoglutarate, and methylated trinucleotide t-mea-t .
SNAP output
|
2fdc
|
DNA binding protein-DNA |
X-ray (3.3 Å) |
Truglio JJ, Karakas E, Rhau B, Wang H, DellaVecchia
MJ, Van Houten B, Kisker C |
(2006) "Structural
basis for DNA recognition and processing by UvrB."
Nat.Struct.Mol.Biol., 13,
360-364. doi: 10.1038/nsmb1072.
|
Structural basis of DNA damage recognition and
processing by uvrb: crystal structure of a uvrb-DNA
complex . SNAP
output
|
2fdf
|
oxidoreductase-DNA |
X-ray (2.1 Å) |
Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC,
Gibney BR, Hunt JF |
(2006) "Crystal
structures of catalytic complexes of the oxidative
DNA/RNA repair enzyme AlkB." Nature,
439, 879-884. doi: 10.1038/nature04561.
|
Crystal structure of alkb in complex with co(ii),
2-oxoglutarate, and methylated trinucleotide t-mea-t .
SNAP output
|
2fdg
|
oxidoreductase-DNA |
X-ray (2.2 Å) |
Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC,
Gibney BR, Hunt JF |
(2006) "Crystal
structures of catalytic complexes of the oxidative
DNA/RNA repair enzyme AlkB." Nature,
439, 879-884. doi: 10.1038/nature04561.
|
Crystal structure of alkb in complex with fe(ii),
succinate, and methylated trinucleotide t-mea-t .
SNAP output
|
2fdh
|
oxidoreductase-DNA |
X-ray (2.1 Å) |
Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC,
Gibney BR, Hunt JF |
(2006) "Crystal
structures of catalytic complexes of the oxidative
DNA/RNA repair enzyme AlkB." Nature,
439, 879-884. doi: 10.1038/nature04561.
|
Crystal structure of alkb in complex with mn(ii),
2-oxoglutarate, and methylated trinucleotide t-mea-t .
SNAP output
|
2fdi
|
oxidoreductase-DNA |
X-ray (1.8 Å) |
Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC,
Gibney BR, Hunt JF |
(2006) "Crystal
structures of catalytic complexes of the oxidative
DNA/RNA repair enzyme AlkB." Nature,
439, 879-884. doi: 10.1038/nature04561.
|
Crystal structure of alkb in complex with fe(ii),
2-oxoglutarate, and methylated trinucleotide t-mea-t
(air 3 hours) . SNAP
output
|
2fdk
|
oxidoreductase-DNA |
X-ray (2.3 Å) |
Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC,
Gibney BR, Hunt JF |
(2006) "Crystal
structures of catalytic complexes of the oxidative
DNA/RNA repair enzyme AlkB." Nature,
439, 879-884. doi: 10.1038/nature04561.
|
Crystal structure of alkb in complex with fe(ii),
2-oxoglutarate, and methylated trinucleotide t-mea-t
(air 9 days) . SNAP
output
|
2ff0
|
hormone-growth factor-DNA |
NMR |
Little TH, Zhang Y, Matulis CK, Weck J, Zhang Z,
Ramachandran A, Mayo KE, Radhakrishnan I |
(2006) "Sequence-specific
deoxyribonucleic Acid (DNA) recognition by
steroidogenic factor 1: a helix at the carboxy terminus
of the DNA binding domain is necessary for complex
stability." Mol.Endocrinol.,
20, 831-843. doi: 10.1210/me.2005-0384.
|
Solution structure of steroidogenic factor 1 DNA
binding domain bound to its target sequence in the
inhibin alpha-subunit promoter . SNAP output
|
2fio
|
transcription-DNA |
X-ray (2.7 Å) |
Badia D, Camacho A, Perez-Lago L, Escandon C, Salas
M, Coll M |
(2006) "The
structure of phage phi29 transcription regulator p4-DNA
complex reveals an N-hook motif for DNA."
Mol.Cell, 22, 73-81. doi:
10.1016/j.molcel.2006.02.019.
|
Phage phi29 transcription regulator p4-DNA complex .
SNAP output
|
2fj7
|
structural protein-DNA |
X-ray (3.2 Å) |
Bao Y, White CL, Luger K |
(2006) "Nucleosome
Core Particles Containing a Poly(dA.dT) Sequence
Element Exhibit a Locally Distorted DNA Structure."
J.Mol.Biol., 361, 617-624.
doi: 10.1016/j.jmb.2006.06.051.
|
Crystal structure of nucleosome core particle
containing a poly (da.dt) sequence element . SNAP output
|
2fjv
|
transferase-DNA |
X-ray (2.05 Å) |
Goodwin KD, Lewis MA, Tanious FA, Tidwell RR, Wilson
WD, Georgiadis MM, Long EC |
(2006) "A
High-Throughput, High-Resolution Strategy for the Study
of Site-Selective DNA Binding Agents: Analysis of a
"Highly Twisted" Benzimidazole-Diamidine."
J.Am.Chem.Soc., 128,
7846-7854. doi: 10.1021/ja0600936.
|
Rt29 bound to d(cttaattcgaattaag) in complex with mmlv
rt catalytic fragment . SNAP output
|
2fjw
|
transferase-DNA |
X-ray (1.95 Å) |
Goodwin KD, Lewis MA, Tanious FA, Tidwell RR, Wilson
WD, Georgiadis MM, Long EC |
(2006) "A
High-Throughput, High-Resolution Strategy for the Study
of Site-Selective DNA Binding Agents: Analysis of a
"Highly Twisted" Benzimidazole-Diamidine."
J.Am.Chem.Soc., 128,
7846-7854. doi: 10.1021/ja0600936.
|
D(cttgaatgcattcaag) in complex with mmlv rt catalytic
fragment . SNAP
output
|
2fjx
|
transferase-DNA |
X-ray (1.8 Å) |
Goodwin KD, Lewis MA, Tanious FA, Tidwell RR, Wilson
WD, Georgiadis MM, Long EC |
(2006) "A
High-Throughput, High-Resolution Strategy for the Study
of Site-Selective DNA Binding Agents: Analysis of a
"Highly Twisted" Benzimidazole-Diamidine."
J.Am.Chem.Soc., 128,
7846-7854. doi: 10.1021/ja0600936.
|
Rt29 bound to d(cttgaatgcattcaag) in complex with mmlv
rt catalytic fragment . SNAP output
|
2fkc
|
hydrolase-DNA |
X-ray (2.39 Å) |
Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG,
Roberts RJ, Cheng X |
(2006) "DNA
nicking by HinP1I endonuclease: bending, base flipping
and minor groove expansion." Nucleic Acids
Res., 34, 939-948. doi: 10.1093/nar/gkj484.
|
Crystal form i of pre-reactive complex of restriction
endonuclease hinp1i with cognate DNA and calcium ion .
SNAP output
|
2fkh
|
hydrolase-DNA |
X-ray (3.09 Å) |
Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG,
Roberts RJ, Cheng X |
(2006) "DNA
nicking by HinP1I endonuclease: bending, base flipping
and minor groove expansion." Nucleic Acids
Res., 34, 939-948. doi: 10.1093/nar/gkj484.
|
Crystal form ii of pre-reactive complex of restriction
endonuclease hinp1i with cognate DNA and calcium ions .
SNAP output
|
2fl3
|
hydrolase-DNA |
X-ray (2.39 Å) |
Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG,
Roberts RJ, Cheng X |
(2006) "DNA
nicking by HinP1I endonuclease: bending, base flipping
and minor groove expansion." Nucleic Acids
Res., 34, 939-948. doi: 10.1093/nar/gkj484.
|
Binary complex of restriction endonuclease hinp1i with
cognate DNA . SNAP
output
|
2flc
|
hydrolase-DNA |
X-ray (2.59 Å) |
Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG,
Roberts RJ, Cheng X |
(2006) "DNA
nicking by HinP1I endonuclease: bending, base flipping
and minor groove expansion." Nucleic Acids
Res., 34, 939-948. doi: 10.1093/nar/gkj484.
|
Post-reactive complex of restriction endonuclease
hinp1i with nicked cognate DNA and magnesium ions .
SNAP output
|
2fld
|
hydrolase-DNA |
X-ray (2.0 Å) |
Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat
RJ, Stoddard BL, Baker D |
(2006) "Computational
redesign of endonuclease DNA binding and cleavage
specificity." Nature,
441, 656-659. doi: 10.1038/nature04818.
|
I-msoi re-designed for altered DNA cleavage specificity
. SNAP output
|
2fll
|
replication-DNA |
X-ray (2.6 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2006) "An
incoming nucleotide imposes an anti to syn
conformational change on the templating purine in the
human DNA polymerase-iota active site."
Structure, 14, 749-755. doi:
10.1016/j.str.2006.01.010.
|
Ternary complex of human DNA polymerase iota with DNA
and dttp . SNAP
output
|
2fln
|
replication-DNA |
X-ray (2.5 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2006) "An
incoming nucleotide imposes an anti to syn
conformational change on the templating purine in the
human DNA polymerase-iota active site."
Structure, 14, 749-755. doi:
10.1016/j.str.2006.01.010.
|
Binary complex of catalytic core of human DNA
polymerase iota with DNA (template a) . SNAP output
|
2flp
|
replication-DNA |
X-ray (2.4 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2006) "An
incoming nucleotide imposes an anti to syn
conformational change on the templating purine in the
human DNA polymerase-iota active site."
Structure, 14, 749-755. doi:
10.1016/j.str.2006.01.010.
|
Binary complex of the catalytic core of human DNA
polymerase iota with DNA (template g) . SNAP output
|
2fmp
|
transferase-DNA |
X-ray (1.65 Å) |
Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC,
Wilson SH |
(2006) "Magnesium-induced
assembly of a complete DNA polymerase catalytic
complex." Structure, 14,
757-766. doi: 10.1016/j.str.2006.01.011.
|
DNA polymerase beta with a terminated gapped DNA
substrate and ddctp with sodium in the catalytic site .
SNAP output
|
2fmq
|
transferase-DNA |
X-ray (2.2 Å) |
Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC,
Wilson SH |
(2006) "Magnesium-induced
assembly of a complete DNA polymerase catalytic
complex." Structure, 14,
757-766. doi: 10.1016/j.str.2006.01.011.
|
Sodium in active site of DNA polymerase beta . SNAP output
|
2fms
|
transferase-DNA |
X-ray (2.0 Å) |
Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC,
Wilson SH |
(2006) "Magnesium-induced
assembly of a complete DNA polymerase catalytic
complex." Structure, 14,
757-766. doi: 10.1016/j.str.2006.01.011.
|
DNA polymerase beta with a gapped DNA substrate and
dumpnpp with magnesium in the catalytic site . SNAP output
|
2fo1
|
gene regulation-signalling protein-DNA |
X-ray (3.12 Å) |
Wilson JJ, Kovall RA |
(2006) "Crystal
structure of the CSL-Notch-Mastermind ternary complex
bound to DNA." Cell(Cambridge,Mass.),
124, 985-996. doi: 10.1016/j.cell.2006.01.035.
|
Crystal structure of the csl-notch-mastermind ternary
complex bound to DNA . SNAP output
|
2fqz
|
hydrolase-DNA |
X-ray (2.0 Å) |
Bochtler M, Szczepanowski RH, Tamulaitis G, Grazulis
S, Czapinska H, Manakova E, Siksnys V |
(2006) "Nucleotide
flips determine the specificity of the Ecl18kI
restriction endonuclease." Embo J.,
25, 2219-2229. doi: 10.1038/sj.emboj.7601096.
|
Metal-depleted ecl18ki in complex with uncleaved DNA .
SNAP output
|
2fr4
|
immune system-DNA |
X-ray (1.95 Å) |
Ou Z, Bottoms CA, Henzl MT, Tanner JJ |
(2007) "Impact
of DNA hairpin folding energetics on antibody-ssDNA
association." J.Mol.Biol.,
374, 1029-1040. doi: 10.1016/j.jmb.2007.09.084.
|
Structure of fab DNA-1 complexed with a stem-loop DNA
ligand . SNAP output
|
2fvp
|
transferase-DNA |
X-ray (2.25 Å) |
Montano SP, Cote ML, Roth MJ, Georgiadis MM |
(2006) "Crystal
structures of oligonucleotides including the integrase
processing site of the Moloney murine leukemia
virus." Nucleic Acids Res.,
34, 5353-5360. doi: 10.1093/nar/gkl693.
|
A structural study of the ca dinucleotide step in the
integrase processing site of moloney murine leukemia
virus . SNAP output
|
2fvq
|
transferase-DNA |
X-ray (2.3 Å) |
Montano SP, Cote ML, Roth MJ, Georgiadis MM |
(2006) "Crystal
structures of oligonucleotides including the integrase
processing site of the Moloney murine leukemia
virus." Nucleic Acids Res.,
34, 5353-5360. doi: 10.1093/nar/gkl693.
|
A structural study of the ca dinucleotide step in the
integrase processing site of moloney murine leukemia
virus . SNAP output
|
2fvr
|
transferase-DNA |
X-ray (2.2 Å) |
Montano SP, Cote ML, Roth MJ, Georgiadis MM |
(2006) "Crystal
structures of oligonucleotides including the integrase
processing site of the Moloney murine leukemia
virus." Nucleic Acids Res.,
34, 5353-5360. doi: 10.1093/nar/gkl693.
|
A structural study of the ca dinucleotide step in the
integrase processing site of moloney murine leukemia
virus . SNAP output
|
2fvs
|
transferase-DNA |
X-ray (2.35 Å) |
Montano SP, Cote ML, Roth MJ, Georgiadis MM |
(2006) "Crystal
structures of oligonucleotides including the integrase
processing site of the Moloney murine leukemia
virus." Nucleic Acids Res.,
34, 5353-5360. doi: 10.1093/nar/gkl693.
|
A structural study of the ca dinucleotide step in the
integrase processing site of moloney murine leukemia
virus . SNAP output
|
2g1p
|
transferase-DNA |
X-ray (1.89 Å) |
Horton JR, Liebert K, Bekes M, Jeltsch A, Cheng
X |
(2006) "Structure
and substrate recognition of the Escherichia coli DNA
adenine methyltransferase." J.Mol.Biol.,
358, 559-570. doi: 10.1016/j.jmb.2006.02.028.
|
Structure of e. coli DNA adenine methyltransferase
(dam) . SNAP output
|
2g8f
|
hydrolase-RNA-DNA |
X-ray (1.65 Å) |
Nowotny M, Yang W |
(2006) "Stepwise
analyses of metal ions in RNase H catalysis from
substrate destabilization to product release."
Embo J., 25, 1924-1933. doi:
10.1038/sj.emboj.7601076.
|
B. halodurans rnase h catalytic domain e188a mutant in
complex with mg2+ and RNA-DNA hybrid (non-p nick at the
active site) . SNAP
output
|
2g8h
|
hydrolase-RNA-DNA |
X-ray (1.85 Å) |
Nowotny M, Yang W |
(2006) "Stepwise
analyses of metal ions in RNase H catalysis from
substrate destabilization to product release."
Embo J., 25, 1924-1933. doi:
10.1038/sj.emboj.7601076.
|
B. halodurans rnase h catalytic domain d192n mutant in
complex with mg2+ and RNA-DNA hybrid (non-p nick at the
active site) . SNAP
output
|
2g8i
|
hydrolase-RNA-DNA |
X-ray (1.65 Å) |
Nowotny M, Yang W |
(2006) "Stepwise
analyses of metal ions in RNase H catalysis from
substrate destabilization to product release."
Embo J., 25, 1924-1933. doi:
10.1038/sj.emboj.7601076.
|
B. halodurans rnase h catalytic domain d192n mutant in
complex with mn2+ and RNA-DNA hybrid (non-p nick at the
active site) . SNAP
output
|
2g8k
|
hydrolase-RNA-DNA |
X-ray (1.65 Å) |
Nowotny M, Yang W |
(2006) "Stepwise
analyses of metal ions in RNase H catalysis from
substrate destabilization to product release."
Embo J., 25, 1924-1933. doi:
10.1038/sj.emboj.7601076.
|
B. halodurans rnase h catalytic domain d192n mutant in
complex with ca2+ and RNA-DNA hybrid (non-p nick at the
active site) . SNAP
output
|
2g8u
|
hydrolase-RNA-DNA |
X-ray (2.7 Å) |
Nowotny M, Yang W |
(2006) "Stepwise
analyses of metal ions in RNase H catalysis from
substrate destabilization to product release."
Embo J., 25, 1924-1933. doi:
10.1038/sj.emboj.7601076.
|
B. halodurans rnase h catalytic domain d132n mutant in
complex with mg2+ and RNA-DNA hybrid (non-p nick at the
active site) . SNAP
output
|
2g8v
|
hydrolase-RNA-DNA |
X-ray (1.85 Å) |
Nowotny M, Yang W |
(2006) "Stepwise
analyses of metal ions in RNase H catalysis from
substrate destabilization to product release."
Embo J., 25, 1924-1933. doi:
10.1038/sj.emboj.7601076.
|
B. halodurans rnase h catalytic domain e188a mutant in
complex with mg2+ and RNA-DNA hybrid (reaction product)
. SNAP output
|
2g8w
|
hydrolase-RNA-DNA |
X-ray (2.05 Å) |
Nowotny M, Yang W |
(2006) "Stepwise
analyses of metal ions in RNase H catalysis from
substrate destabilization to product release."
Embo J., 25, 1924-1933. doi:
10.1038/sj.emboj.7601076.
|
B. halodurans rnase h catalytic domain e188a mutant in
complex with ca2+ and RNA-DNA hybrid . SNAP output
|
2gat
|
transcription-DNA |
NMR |
Tjandra N, Omichinski JG, Gronenborn AM, Clore GM,
Bax A |
(1997) "Use of
dipolar 1H-15N and 1H-13C couplings in the structure
determination of magnetically oriented macromolecules
in solution." Nat.Struct.Biol.,
4, 732-738. doi: 10.1038/nsb0997-732.
|
Solution structure of the c-terminal domain of chicken
gata-1 bound to DNA, NMR, regularized mean structure .
SNAP output
|
2gb7
|
hydrolase-DNA |
X-ray (1.7 Å) |
Bochtler M, Szczepanowski RH, Tamulaitis G, Grazulis
S, Czapinska H, Manakova E, Siksnys V |
(2006) "Nucleotide
flips determine the specificity of the Ecl18kI
restriction endonuclease." Embo J.,
25, 2219-2229. doi: 10.1038/sj.emboj.7601096.
|
Metal-depleted ecl18ki in complex with uncleaved,
modified DNA . SNAP
output
|
2ge5
|
hydrolase-DNA |
X-ray (2.4 Å) |
Hiller DA, Perona JJ |
(2006) "Positively
Charged C-Terminal Subdomains of EcoRV Endonuclease:
Contributions to DNA Binding, Bending, and
Cleavage." Biochemistry,
45, 11453-11463. doi: 10.1021/bi0606400.
|
Ecorv restriction endonuclease c-terminal deletion
mutant-gatatc-ca2+ . SNAP output
|
2geq
|
transcription-DNA |
X-ray (2.3 Å) |
Ho WC, Fitzgerald MX, Marmorstein R |
(2006) "Structure
of the p53 Core Domain Dimer Bound to DNA."
J.Biol.Chem., 281,
20494-20502. doi: 10.1074/jbc.M603634200.
|
Crystal structure of a p53 core dimer bound to DNA .
SNAP output
|
2gie
|
hydrolase-DNA |
X-ray (2.6 Å) |
Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton
NC |
(2006) "Alteration
of Sequence Specificity of the Type II Restriction
Endonuclease HincII through an Indirect Readout
Mechanism." J.Biol.Chem.,
281, 23852-23869. doi: 10.1074/jbc.M512339200.
|
Hincii bound to cognate DNA gttaac . SNAP output
|
2gig
|
hydrolase-DNA |
X-ray (1.83 Å) |
Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton
NC |
(2006) "Alteration
of Sequence Specificity of the Type II Restriction
Endonuclease HincII through an Indirect Readout
Mechanism." J.Biol.Chem.,
281, 23852-23869. doi: 10.1074/jbc.M512339200.
|
Alteration of sequence specificity of the type ii
restriction endonuclease hincii through an indirect
readout mechanism . SNAP
output
|
2gih
|
hydrolase-DNA |
X-ray (2.5 Å) |
Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton
NC |
(2006) "Alteration
of Sequence Specificity of the Type II Restriction
Endonuclease HincII through an Indirect Readout
Mechanism." J.Biol.Chem.,
281, 23852-23869. doi: 10.1074/jbc.M512339200.
|
Q138f hincii bound to cognate DNA gtcgac and ca2+ .
SNAP output
|
2gii
|
hydrolase-DNA |
X-ray (2.3 Å) |
Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton
NC |
(2006) "Alteration
of Sequence Specificity of the Type II Restriction
Endonuclease HincII through an Indirect Readout
Mechanism." J.Biol.Chem.,
281, 23852-23869. doi: 10.1074/jbc.M512339200.
|
Q138f hincii bound to cognate DNA gttaac . SNAP output
|
2gij
|
hydrolase-DNA |
X-ray (1.93 Å) |
Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton
NC |
(2006) "Alteration
of Sequence Specificity of the Type II Restriction
Endonuclease HincII through an Indirect Readout
Mechanism." J.Biol.Chem.,
281, 23852-23869. doi: 10.1074/jbc.M512339200.
|
Q138f hincii bound to cognate DNA gttaac and ca2+ .
SNAP output
|
2gkd
|
toxin-DNA |
NMR |
Singh S, Hager MH, Zhang C, Griffith BR, Lee MS,
Hallenga K, Markley JL, Thorson JS |
(2006) "Structural
insight into the self-sacrifice mechanism of enediyne
resistance." Acs Chem.Biol.,
1, 451-460. doi: 10.1021/cb6002898.
|
Structural insight into self-sacrifice mechanism of
enediyne resistance . SNAP output
|
2gli
|
transcription-DNA |
X-ray (2.6 Å) |
Pavletich NP, Pabo CO |
(1993) "Crystal
structure of a five-finger GLI-DNA complex: new
perspectives on zinc fingers." Science,
261, 1701-1707.
|
Five-finger gli-DNA complex . SNAP output
|
2glo
|
transcription-DNA |
NMR |
Cordier F, Hartmann B, Rogowski M, Affolter M,
Grzesiek S |
(2006) "DNA
recognition by the brinker repressor - an extreme case
of coupling between binding and folding."
J.Mol.Biol., 361, 659-672.
doi: 10.1016/j.jmb.2006.06.045.
|
Solution structure of the brinker DNA binding domain in
complex with the omb enhancer . SNAP output
|
2gm4
|
recombination, DNA |
X-ray (3.5 Å) |
Kamtekar S, Ho RS, Cocco MJ, Li W, Wenwieser SV,
Boocock MR, Grindley ND, Steitz TA |
(2006) "Implications
of structures of synaptic tetramers of gamma delta
resolvase for the mechanism of recombination."
Proc.Natl.Acad.Sci.Usa, 103,
10642-10647. doi: 10.1073/pnas.0604062103.
|
An activated, tetrameric gamma-delta resolvase: hin
chimaera bound to cleaved DNA . SNAP output
|
2gws
|
transferase-DNA |
X-ray (2.4 Å) |
Picher AJ, Garcia-Diaz M, Bebenek K, Pedersen LC,
Kunkel TA, Blanco L |
(2006) "Promiscuous
mismatch extension by human DNA polymerase lambda."
Nucleic Acids Res., 34,
3259-3266. doi: 10.1093/nar/gkl377.
|
Crystal structure of human DNA polymerase lambda with a
g-g mismatch in the primer terminus . SNAP output
|
2gxa
|
replication-DNA |
X-ray (3.15 Å) |
Enemark EJ, Joshua-Tor L |
(2006) "Mechanism
of DNA translocation in a replicative hexameric
helicase." Nature, 442,
270-275. doi: 10.1038/nature04943.
|
Crystal structure of papillomavirus e1 hexameric
helicase with ssDNA and mgadp . SNAP output
|
2gzk
|
DNA-structural protein |
NMR |
Stott K, Tang GS, Lee KB, Thomas JO |
(2006) "Structure
of a Complex of Tandem HMG Boxes and DNA."
J.Mol.Biol., 360, 90-104.
doi: 10.1016/j.jmb.2006.04.059.
|
Structure of a complex of tandem hmg boxes and DNA .
SNAP output
|
2h1k
|
transcription-DNA |
X-ray (2.42 Å) |
Longo A, Guanga GP, Rose RB |
(2007) "Structural
basis for induced fit mechanisms in DNA recognition by
the pdx1 homeodomain." Biochemistry,
46, 2948-2957. doi: 10.1021/bi060969l.
|
Crystal structure of the pdx1 homeodomain in complex
with DNA . SNAP
output
|
2h1o
|
gene regulation-DNA complex |
X-ray (3.0 Å) |
Mattison K, Wilbur JS, So M, Brennan RG |
(2006) "Structure
of FitAB from Neisseria gonorrhoeae bound to DNA
reveals a tetramer of toxin-antitoxin heterodimers
containing pin domains and ribbon-helix-helix
motifs." J.Biol.Chem.,
281, 37942-37951. doi: 10.1074/jbc.M605198200.
|
Structure of fitab bound to ir36 DNA fragment .
SNAP output
|
2h27
|
transferase-DNA |
X-ray (2.3 Å) |
Lane WJ, Darst SA |
(2006) "The
structural basis for promoter -35 element recognition
by the group IV sigma factors." Plos
Biol., 4, e269. doi: 10.1371/journal.pbio.0040269.
|
Crystal structure of escherichia coli sigmae region 4
bound to its-35 element DNA . SNAP output
|
2h3a
|
immune system-DNA |
NMR |
Madl T, Van Melderen L, Mine N, Respondek M, Oberer
M, Keller W, Khatai L, Zangger K |
(2006) "Structural
Basis for Nucleic Acid and Toxin Recognition of the
Bacterial Antitoxin CcdA." J.Mol.Biol.,
364, 170-185. doi: 10.1016/j.jmb.2006.08.082.
|
Structural basis for nucleic acid and toxin recognition
of the bacterial antitoxin ccda . SNAP output
|
2h3c
|
immune system-DNA |
NMR |
Madl T, Van Melderen L, Mine N, Respondek M, Oberer
M, Keller W, Khatai L, Zangger K |
(2006) "Structural
Basis for Nucleic Acid and Toxin Recognition of the
Bacterial Antitoxin CcdA." J.Mol.Biol.,
364, 170-185. doi: 10.1016/j.jmb.2006.08.082.
|
Structural basis for nucleic acid and toxin recognition
of the bacterial antitoxin ccda . SNAP output
|
2h7f
|
isomerase-DNA |
X-ray (2.7 Å) |
Perry K, Hwang Y, Bushman FD, Van Duyne GD |
(2006) "Structural
basis for specificity in the poxvirus
topoisomerase." Mol.Cell,
23, 343-354. doi: 10.1016/j.molcel.2006.06.015.
|
Structure of variola topoisomerase covalently bound to
DNA . SNAP output
|
2h7g
|
isomerase-DNA |
X-ray (1.9 Å) |
Perry K, Hwang Y, Bushman FD, Van Duyne GD |
(2006) "Structural
basis for specificity in the poxvirus
topoisomerase." Mol.Cell,
23, 343-354. doi: 10.1016/j.molcel.2006.06.015.
|
Structure of variola topoisomerase non-covalently bound
to DNA . SNAP output
|
2h7h
|
viral protein-DNA |
X-ray (2.3 Å) |
Kim Y, Borovilos M |
"Crystal structure of the JUN BZIP homodimer
complexed with AP-1 DNA." |
Crystal structure of the jun bzip homodimer complexed
with ap-1 DNA . SNAP
output
|
2h8c
|
hydrolase-DNA |
X-ray (3.1 Å) |
Macmaster R, Sedelnikova S, Baker PJ, Bolt EL, Lloyd
RG, Rafferty JB |
(2006) "RusA
Holliday junction resolvase: DNA complex
structure--insights into selectivity and
specificity." Nucleic Acids Res.,
34, 5577-5584. doi: 10.1093/nar/gkl447.
|
Structure of rusa d70n in complex with DNA . SNAP output
|
2h8r
|
transcription activator-DNA |
X-ray (3.2 Å) |
Lu P, Rha GB, Chi YI |
(2007) "Structural
basis of disease-causing mutations in hepatocyte
nuclear factor 1beta." Biochemistry,
46, 12071-12080. doi: 10.1021/bi7010527.
|
Hepatocyte nuclear factor 1b bound to DNA: mody5 gene
product . SNAP
output
|
2han
|
transcription-DNA |
X-ray (1.95 Å) |
Jakob M, Kolodziejczyk R, Orlowski M, Krzywda S,
Kowalska A, Dutko-Gwozdz J, Gwozdz T, Kochman M,
Jaskolski M, Ozyhar A |
(2007) "Novel
DNA-binding element within the C-terminal extension of
the nuclear receptor DNA-binding domain."
Nucleic Acids Res., 35,
2705-2718. doi: 10.1093/nar/gkm162.
|
Structural basis of heterodimeric ecdysteroid receptor
interaction with natural response element hsp27 gene
promoter . SNAP
output
|
2hap
|
gene regulation-DNA |
X-ray (2.5 Å) |
King DA, Zhang L, Guarente L, Marmorstein R |
(1999) "Structure
of HAP1-18-DNA implicates direct allosteric effect of
protein-DNA interactions on transcriptional
activation." Nat.Struct.Biol.,
6, 22-27. doi: 10.1038/4893.
|
Structure of a hap1-18-DNA complex reveals that
protein-DNA interactions can have direct allosteric
effects on transcriptional activation . SNAP output
|
2hax
|
gene regulation-DNA |
X-ray (1.29 Å) |
Max KE, Zeeb M, Bienert R, Balbach J, Heinemann
U |
(2007) "Common
mode of DNA binding to cold shock domains. Crystal
structure of hexathymidine bound to the domain-swapped
form of a major cold shock protein from Bacillus
caldolyticus." Febs J.,
274, 1265-1279. doi: 10.1111/j.1742-4658.2007.05672.x.
|
Crystal structure of bacillus caldolyticus cold shock
protein in complex with hexathymidine . SNAP output
|
2hdc
|
protein-DNA |
NMR |
Jin C, Marsden I, Chen X, Liao X |
(1999) "Dynamic
DNA contacts observed in the NMR structure of winged
helix protein-DNA complex." J.Mol.Biol.,
289, 683-690. doi: 10.1006/jmbi.1999.2819.
|
Structure of transcription factor genesis-DNA complex .
SNAP output
|
2hdd
|
transcription-DNA |
X-ray (1.9 Å) |
Tucker-Kellogg L, Rould MA, Chambers KA, Ades SE,
Sauer RT, Pabo CO |
(1997) "Engrailed
(Gln50-->Lys) homeodomain-DNA complex at 1.9 A
resolution: structural basis for enhanced affinity and
altered specificity." Structure,
5, 1047-1054. doi: 10.1016/S0969-2126(97)00256-6.
|
Engrailed homeodomain q50k variant DNA complex .
SNAP output
|
2heo
|
immune system-DNA |
X-ray (1.7 Å) |
Magis C, Gasparini D, Lecoq A, Le Du MH, Stura E,
Charbonnier JB, Mourier G, Boulain JC, Pardo L, Caruana
A, Joly A, Lefranc M, Masella M, Menez A, Cuniasse P |
(2006) "Structure-based
secondary structure-independent approach to design
protein ligands: Application to the design of Kv1.2
potassium channel blockers."
J.Am.Chem.Soc., 128,
16190-16205. doi: 10.1021/ja0646491.
|
General structure-based approach to the design of
protein ligands: application to the design of kv1.2
potassium channel blockers. . SNAP output
|
2hhq
|
transferase-DNA |
X-ray (1.8 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
O6-methyl-guanine:t pair in the polymerase-10 basepair
position . SNAP
output
|
2hhs
|
transferase-DNA |
X-ray (1.8 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
O6-methyl:c pair in the polymerase-10 basepair position
. SNAP output
|
2hht
|
transferase-DNA |
X-ray (2.05 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
C:o6-methyl-guanine pair in the polymerase-2 basepair
position . SNAP
output
|
2hhu
|
transferase-DNA |
X-ray (1.8 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
C:o6-methyl-guanine in the polymerase postinsertion
site (-1 basepair position) . SNAP output
|
2hhv
|
transferase-DNA |
X-ray (1.55 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
T:o6-methyl-guanine in the polymerase-2 basepair
position . SNAP
output
|
2hhw
|
transferase-DNA |
X-ray (1.88 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
Ddttp:o6-methyl-guanine pair in the polymerase active
site, in the closed conformation . SNAP output
|
2hhx
|
transferase-DNA |
X-ray (2.26 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
O6-methyl-guanine in the polymerase template
preinsertion site . SNAP
output
|
2hmi
|
immune system-DNA |
X-ray (2.8 Å) |
Ding J, Das K, Hsiou Y, Sarafianos SG, Clark Jr AD,
Jacobo-Molina A, Tantillo C, Hughes SH, Arnold E |
(1998) "Structure
and functional implications of the polymerase active
site region in a complex of HIV-1 RT with a
double-stranded DNA template-primer and an antibody Fab
fragment at 2.8 A resolution."
J.Mol.Biol., 284, 1095-1111.
doi: 10.1006/jmbi.1998.2208.
|
Hiv-1 reverse transcriptase-fragment of fab 28-DNA
complex . SNAP
output
|
2hof
|
recombination-DNA |
X-ray (2.4 Å) |
Ghosh K, Guo F, Van Duyne GD |
(2007) "Synapsis
of loxP sites by Cre recombinase."
J.Biol.Chem., 282,
24004-24016. doi: 10.1074/jbc.M703283200.
|
Crystal structure of the pre-cleavage synaptic complex
in the cre-loxp site-specific recombination . SNAP output
|
2hoi
|
recombination-DNA |
X-ray (2.601 Å) |
Ghosh K, Guo F, Van Duyne GD |
(2007) "Synapsis
of loxP sites by Cre recombinase."
J.Biol.Chem., 282,
24004-24016. doi: 10.1074/jbc.M703283200.
|
Crystal structure of the tetrameric pre-cleavage
synaptic complex in the cre-loxp site-specific
recombination . SNAP
output
|
2hos
|
transcription-DNA |
X-ray (1.9 Å) |
Simon MD, Feldman ME, Rauh D, Maris AE, Wemmer DE,
Shokat KM |
(2006) "Structure
and properties of a re-engineered homeodomain
protein-DNA interface." Acs Chem.Biol.,
1, 755-760. doi: 10.1021/cb6003756.
|
Phage-selected homeodomain bound to unmodified DNA .
SNAP output
|
2hot
|
transcription-DNA |
X-ray (2.19 Å) |
Simon MD, Feldman ME, Rauh D, Maris AE, Wemmer DE,
Shokat KM |
(2006) "Structure
and properties of a re-engineered homeodomain
protein-DNA interface." Acs Chem.Biol.,
1, 755-760. doi: 10.1021/cb6003756.
|
Phage selected homeodomain bound to modified DNA .
SNAP output
|
2hr1
|
transferase-DNA |
X-ray (1.96 Å) |
Shieh FK, Youngblood B, Reich NO |
(2006) "The Role
of Arg165 Towards Base Flipping, Base Stabilization and
Catalysis in M.HhaI." J.Mol.Biol.,
362, 516-527. doi: 10.1016/j.jmb.2006.07.030.
|
Ternary structure of wt m.hhai c5-cytosine DNA
methyltransferase with unmodified DNA and adohcy .
SNAP output
|
2ht0
|
transcription-DNA |
X-ray (2.0 Å) |
Swinger KK, Rice PA |
(2007) "Structure-based
Analysis of HU-DNA Binding." J.Mol.Biol.,
365, 1005-1016. doi: 10.1016/j.jmb.2006.10.024.
|
Ihf bound to doubly nicked DNA . SNAP output
|
2hvh
|
transferase-DNA |
X-ray (2.492 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
Ddctp:o6meg pair in the polymerase active site (0
position) . SNAP
output
|
2hvi
|
transferase-DNA |
X-ray (1.98 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
Ddctp:g pair in the polymerase active site (0 position)
. SNAP output
|
2hvr
|
ligase-RNA-DNA |
X-ray (2.45 Å) |
Nandakumar J, Shuman S, Lima CD |
(2006) "RNA
Ligase Structures Reveal the Basis for RNA Specificity
and Conformational Changes that Drive Ligation
Forward." Cell(Cambridge,Mass.),
127, 71-84. doi: 10.1016/j.cell.2006.08.038.
|
Structure of t4 RNA ligase 2 with nicked 5'-adenylated
nucleic acid duplex containing a 3'-deoxyribonucleotide
at the nick . SNAP
output
|
2hvs
|
ligase-DNA-RNA |
X-ray (2.5 Å) |
Nandakumar J, Shuman S, Lima CD |
(2006) "RNA
Ligase Structures Reveal the Basis for RNA Specificity
and Conformational Changes that Drive Ligation
Forward." Cell(Cambridge,Mass.),
127, 71-84. doi: 10.1016/j.cell.2006.08.038.
|
Structure of t4 RNA ligase 2 with nicked 5'-adenylated
nucleic acid duplex containing a 2'-deoxyribonucleotide
at the nick . SNAP
output
|
2hvy
|
isomerase-biosynthetic protein-RNA |
X-ray (2.3 Å) |
Li L, Ye K |
(2006) "Crystal
structure of an H/ACA box ribonucleoprotein
particle." Nature, 443,
302-307. doi: 10.1038/nature05151.
|
Crystal structure of an h-aca box rnp from pyrococcus
furiosus . SNAP
output
|
2hw3
|
transferase-DNA |
X-ray (1.98 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
T:o6-methyl-guanine pair in the polymerase
postinsertion site (-1 basepair position) . SNAP output
|
2hzv
|
metal binding protein-DNA |
X-ray (3.1 Å) |
Schreiter ER, Wang SC, Zamble DB, Drennan CL |
(2006) "NikR-operator
complex structure and the mechanism of repressor
activation by metal ions."
Proc.Natl.Acad.Sci.Usa, 103,
13676-13681. doi: 10.1073/pnas.0606247103.
|
Nikr-operator DNA complex . SNAP output
|
2i05
|
replication-DNA |
X-ray (2.6 Å) |
Oakley AJ, Mulcair MD, Schaeffer PM, Dixon NE |
"Polarity of Termination of DNA Replication in E.
coli." |
Escherichia coli replication terminator protein (tus)
complexed with tera DNA . SNAP output
|
2i06
|
replication-DNA |
X-ray (2.2 Å) |
Oakley AJ, Mulcair MD, Schaeffer PM, Dixon NE |
"Polarity of Termination of DNA Replication in E.
coli." |
Escherichia coli replication terminator protein (tus)
complexed with DNA- locked form . SNAP output
|
2i0q
|
structural protein-DNA |
X-ray (1.91 Å) |
Buczek P, Horvath MP |
(2006) "Structural
reorganization and the cooperative binding of
single-stranded telomere DNA in Sterkiella nova."
J.Biol.Chem., 281,
40124-40134. doi: 10.1074/jbc.M607749200.
|
Crystal structure of a telomere single-strand
DNA-protein complex from o. nova with full-length alpha
and beta telomere proteins . SNAP output
|
2i13
|
DNA binding protein-DNA |
X-ray (1.96 Å) |
Segal DJ, Crotty JW, Bhakta MS, Barbas CF, Horton
NC |
(2006) "Structure
of Aart, a Designed Six-finger Zinc Finger Peptide,
Bound to DNA." J.Mol.Biol.,
363, 405-421. doi: 10.1016/j.jmb.2006.08.016.
|
Aart, a six finger zinc finger designed to recognize
ann triplets . SNAP
output
|
2i3p
|
hydrolase-DNA |
X-ray (2.3 Å) |
Rosen LE, Morrison HA, Masri S, Brown MJ, Springstubb
B, Sussman D, Stoddard BL, Seligman LM |
(2006) "Homing
endonuclease I-CreI derivatives with novel DNA target
specificities." Nucleic Acids Res.,
34, 4791-4800. doi: 10.1093/nar/gkl645.
|
K28r mutant of homing endonuclease i-crei . SNAP output
|
2i3q
|
hydrolase-DNA |
X-ray (2.3 Å) |
Rosen LE, Morrison HA, Masri S, Brown MJ, Springstubb
B, Sussman D, Stoddard BL, Seligman LM |
(2006) "Homing
endonuclease I-CreI derivatives with novel DNA target
specificities." Nucleic Acids Res.,
34, 4791-4800. doi: 10.1093/nar/gkl645.
|
Q44v mutant of homing endonuclease i-crei . SNAP output
|
2i5s
|
hydrolase-DNA |
X-ray (1.9 Å) |
Lee JE, Bae E, Bingman CA, Phillips Jr GN, Raines
RT |
(2008) "Structural
basis for catalysis by onconase."
J.Mol.Biol., 375, 165-177.
doi: 10.1016/j.jmb.2007.09.089.
|
Crystal structure of onconase with bound nucleic acid .
SNAP output
|
2i5w
|
hydrolase, lyase-DNA |
X-ray (2.6 Å) |
Banerjee A, Verdine GL |
(2006) "A
nucleobase lesion remodels the interaction of its
normal neighbor in a DNA glycosylase complex."
Proc.Natl.Acad.Sci.Usa, 103,
15020-15025. doi: 10.1073/pnas.0603644103.
|
Structure of hogg1 crosslinked to DNA sampling a normal
g adjacent to an oxog . SNAP output
|
2i9g
|
transferase-DNA |
X-ray (2.1 Å) |
Batra VK, Shock DD, Prasad R, Beard WA, Hou EW,
Pedersen LC, Sayer JM, Yagi H, Kumar S, Jerina DM, Wilson
SH |
(2006) "Structure
of DNA polymerase beta with a benzo[c]phenanthrene diol
epoxide-adducted template exhibits mutagenic
features." Proc.Natl.Acad.Sci.Usa,
103, 17231-17236. doi: 10.1073/pnas.0605069103.
|
DNA polymerase beta with a benzo[c]phenanthrene diol
epoxide adducted guanine base . SNAP output
|
2i9k
|
transferase-DNA |
X-ray (2.65 Å) |
Youngblood B, Shieh FK, De Los Rios S, Perona JJ,
Reich NO |
(2006) "Engineered
Extrahelical Base Destabilization Enhances Sequence
Discrimination of DNA Methyltransferase M.HhaI."
J.Mol.Biol., 362, 334-346.
doi: 10.1016/j.jmb.2006.07.031.
|
Engineered extrahelical base destabilization enhances
sequence discrimination of DNA methyltransferase m.hhai
. SNAP output
|
2i9t
|
transcription-DNA |
X-ray (2.8 Å) |
Escalante CR, Shen L, Thanos D, Aggarwal AK |
(2002) "Structure
of NF-kappaB p50/p65 heterodimer bound to the PRDII DNA
element from the interferon-beta promoter."
Structure, 10, 383-391. doi:
10.1016/S0969-2126(02)00723-2.
|
Structure of nf-kb p65-p50 heterodimer bound to prdii
element of b-interferon promoter . SNAP output
|
2ia6
|
transferase-DNA |
X-ray (2.5 Å) |
Bauer J, Xing G, Yagi H, Sayer JM, Jerina DM, Ling
H |
(2007) "A
structural gap in Dpo4 supports mutagenic bypass of a
major benzo[a]pyrene dG adduct in DNA through template
misalignment." Proc.Natl.Acad.Sci.Usa,
104, 14905-14910. doi: 10.1073/pnas.0700717104.
|
Bypass of major benzopyrene-dg adduct by y-family DNA
polymerase with unique structural gap . SNAP output
|
2ibk
|
transferase-DNA |
X-ray (2.25 Å) |
Bauer J, Xing G, Yagi H, Sayer JM, Jerina DM, Ling
H |
(2007) "A
structural gap in Dpo4 supports mutagenic bypass of a
major benzo[a]pyrene dG adduct in DNA through template
misalignment." Proc.Natl.Acad.Sci.Usa,
104, 14905-14910. doi: 10.1073/pnas.0700717104.
|
Bypass of major benzopyrene-dg adduct by y-family DNA
polymerase with unique structural gap . SNAP output
|
2ibs
|
transferase-DNA |
X-ray (2.4 Å) |
Lenz T, Bonnist EYM, Pljevaljcic G, Neely RK, Dryden
DTF, Scheidig AJ, Jones AC, Weinhold E |
(2007) "2-Aminopurine
Flipped into the Active Site of the Adenine-Specific
DNA Methyltransferase M.TaqI: Crystal Structures and
Time-Resolved Fluorescence."
J.Am.Chem.Soc., 129,
6240-6248. doi: 10.1021/ja069366n.
|
Crystal structure of the adenine-specific DNA
methyltransferase m.taqi complexed with the cofactor
analog aeta and a 10 bp DNA containing 2-aminopurine at
the target position . SNAP output
|
2ibt
|
transferase-DNA |
X-ray (1.7 Å) |
Lenz T, Bonnist EYM, Pljevaljcic G, Neely RK, Dryden
DTF, Scheidig AJ, Jones AC, Weinhold E |
(2007) "2-Aminopurine
Flipped into the Active Site of the Adenine-Specific
DNA Methyltransferase M.TaqI: Crystal Structures and
Time-Resolved Fluorescence."
J.Am.Chem.Soc., 129,
6240-6248. doi: 10.1021/ja069366n.
|
Crystal structure of the adenine-specific DNA
methyltransferase m.taqi complexed with the cofactor
analog aeta and a 10 bp DNA containing 2-aminopurine at
the target position and an abasic site analog at the
target base partner position . SNAP output
|
2ief
|
DNA binding protein-DNA |
X-ray (2.601 Å) |
Abbani MA, Papagiannis CV, Sam MD, Cascio D, Johnson
RC, Clubb RT |
(2007) "Structure
of the cooperative Xis-DNA complex reveals a
micronucleoprotein filament that regulates phage lambda
intasome assembly."
Proc.Natl.Acad.Sci.Usa, 104,
2109-2114. doi: 10.1073/pnas.0607820104.
|
Structure of the cooperative excisionase (xis)-DNA
complex reveals a micronucleoprotein filament .
SNAP output
|
2ih2
|
transferase-DNA |
X-ray (1.61 Å) |
Lenz T, Scheidig AJ, Weinhold E |
"Influence of the target base partner on the
methylation rate of the adenine-specific DNA
methyltransferase M.TaqI." |
Crystal structure of the adenine-specific DNA
methyltransferase m.taqi complexed with the cofactor
analog aeta and a 10 bp DNA containing
5-methylpyrimidin-2(1h)-one at the target base partner
position . SNAP
output
|
2ih4
|
transferase-DNA |
X-ray (2.1 Å) |
Lenz T, Scheidig AJ, Weinhold E |
"Influence of the target base partner on the
methylation rate of the adenine-specific DNA
methyltransferase M.TaqI." |
Crystal structure of the adenine-specific DNA
methyltransferase m.taqi complexed with the cofactor
analog aeta and a 10 bp DNA containing pyrrolo-dc at
the target base partner position . SNAP output
|
2ih5
|
transferase-DNA |
X-ray (1.8 Å) |
Lenz T, Scheidig AJ, Weinhold E |
"Influence of the target base partner on the
methylation rate of the adenine-specific DNA
methyltransferase M.TaqI." |
Crystal structure of the adenine-specific DNA
methyltransferase m.taqi complexed with the cofactor
analog aeta and a 10 bp DNA containing an abasic site
analog at the target base partner position . SNAP output
|
2ihm
|
transferase-DNA |
X-ray (2.4 Å) |
Moon AF, Garcia-Diaz M, Bebenek K, Davis BJ, Zhong X,
Ramsden DA, Kunkel TA, Pedersen LC |
(2007) "Structural
insight into the substrate specificity of DNA
Polymerase mu." Nat.Struct.Mol.Biol.,
14, 45-53. doi: 10.1038/nsmb1180.
|
Polymerase mu in ternary complex with gapped 11mer DNA
duplex and bound incoming nucleotide . SNAP output
|
2ihn
|
hydrolase-DNA |
X-ray (3.0 Å) |
Devos JM, Tomanicek SJ, Jones CE, Nossal NG, Mueser
TC |
(2007) "Crystal
structure of bacteriophage T4 5' nuclease in complex
with a branched DNA reveals how FEN-1 family nucleases
bind their substrates." J.Biol.Chem.,
282, 31713-31724. doi: 10.1074/jbc.M703209200.
|
Co-crystal of bacteriophage t4 rnase h with a fork DNA
substrate . SNAP
output
|
2iie
|
recombination-DNA |
X-ray (2.41 Å) |
Bao Q, Chen H, Liu Y, Yan J, Droge P, Davey CA |
(2007) "A
Divalent Metal-mediated Switch Controlling
Protein-induced DNA Bending." J.Mol.Biol.,
367, 731-740. doi: 10.1016/j.jmb.2006.09.082.
|
Single chain integration host factor protein (scihf2)
in complex with DNA . SNAP output
|
2iif
|
recombination-DNA |
X-ray (2.72 Å) |
Bao Q, Chen H, Liu Y, Yan J, Droge P, Davey CA |
(2007) "A
Divalent Metal-mediated Switch Controlling
Protein-induced DNA Bending." J.Mol.Biol.,
367, 731-740. doi: 10.1016/j.jmb.2006.09.082.
|
Single chain integration host factor mutant protein
(scihf2-k45ae) in complex with DNA . SNAP output
|
2imw
|
transferase-DNA |
X-ray (2.05 Å) |
Fiala KA, Brown JA, Ling H, Kshetry AK, Zhang J,
Taylor JS, Yang W, Suo Z |
(2007) "Mechanism
of Template-independent Nucleotide Incorporation
Catalyzed by a Template-dependent DNA Polymerase."
J.Mol.Biol., 365, 590-602.
doi: 10.1016/j.jmb.2006.10.008.
|
Mechanism of template-independent nucleotide
incorporation catalyzed by a template-dependent DNA
polymerase . SNAP
output
|
2irf
|
gene regulation-DNA |
X-ray (2.2 Å) |
Fujii Y, Shimizu T, Kusumoto M, Kyogoku Y, Taniguchi
T, Hakoshima T |
(1999) "Crystal
structure of an IRF-DNA complex reveals novel DNA
recognition and cooperative binding to a tandem repeat
of core sequences." EMBO J.,
18, 5028-5041. doi: 10.1093/emboj/18.18.5028.
|
Crystal structure of an irf-2-DNA complex. . SNAP output
|
2is1
|
hydrolase-DNA |
X-ray (2.9 Å) |
Lee JY, Yang W |
(2006) "UvrD
helicase unwinds DNA one base pair at a time by a
two-part power stroke."
Cell(Cambridge,Mass.), 127,
1349-1360. doi: 10.1016/j.cell.2006.10.049.
|
Crystal structure of uvrd-DNA-so4 complex . SNAP output
|
2is2
|
hydrolase-DNA |
X-ray (3.0 Å) |
Lee JY, Yang W |
(2006) "UvrD
helicase unwinds DNA one base pair at a time by a
two-part power stroke."
Cell(Cambridge,Mass.), 127,
1349-1360. doi: 10.1016/j.cell.2006.10.049.
|
Crystal structure of uvrd-DNA binary complex . SNAP output
|
2is4
|
hydrolase-DNA |
X-ray (2.6 Å) |
Lee JY, Yang W |
(2006) "UvrD
helicase unwinds DNA one base pair at a time by a
two-part power stroke."
Cell(Cambridge,Mass.), 127,
1349-1360. doi: 10.1016/j.cell.2006.10.049.
|
Crystal structure of uvrd-DNA-adpnp ternary complex .
SNAP output
|
2is6
|
hydrolase-DNA |
X-ray (2.2 Å) |
Lee JY, Yang W |
(2006) "UvrD
helicase unwinds DNA one base pair at a time by a
two-part power stroke."
Cell(Cambridge,Mass.), 127,
1349-1360. doi: 10.1016/j.cell.2006.10.049.
|
Crystal structure of uvrd-DNA-adpmgf3 ternary complex .
SNAP output
|
2iso
|
transferase-DNA |
X-ray (2.1 Å) |
Sucato CA, Upton TG, Kashemirov BA, Batra VK,
Martinek V, Xiang Y, Beard WA, Pedersen LC, Wilson SH,
McKenna CE, Florian J, Warshel A, Goodman MF |
(2007) "Modifying
the beta,gamma Leaving-Group Bridging Oxygen Alters
Nucleotide Incorporation Efficiency, Fidelity, and the
Catalytic Mechanism of DNA Polymerase beta."
Biochemistry, 46, 461-471.
doi: 10.1021/bi061517b.
|
Ternary complex of DNA polymerase beta with a dideoxy
terminated primer and 2'-deoxyguanosine 5'-beta,
gamma-difluoromethylene triphosphate . SNAP output
|
2isp
|
transferase-DNA |
X-ray (2.2 Å) |
Sucato CA, Upton TG, Kashemirov BA, Batra VK,
Martinek V, Xiang Y, Beard WA, Pedersen LC, Wilson SH,
McKenna CE, Florian J, Warshel A, Goodman MF |
(2007) "Modifying
the beta,gamma Leaving-Group Bridging Oxygen Alters
Nucleotide Incorporation Efficiency, Fidelity, and the
Catalytic Mechanism of DNA Polymerase beta."
Biochemistry, 46, 461-471.
doi: 10.1021/bi061517b.
|
Ternary complex of DNA polymerase beta with a dideoxy
terminated primer and 2'-deoxyguanosine 5'-beta,
gamma-methylene triphosphate . SNAP output
|
2isz
|
transcription-DNA |
X-ray (2.403 Å) |
Wisedchaisri G, Chou CJ, Wu M, Roach C, Rice AE,
Holmes RK, Beeson C, Hol WG |
(2007) "Crystal
structures, metal activation, and DNA-binding
properties of two-domain IdeR from Mycobacterium
tuberculosis." Biochemistry,
46, 436-447. doi: 10.1021/bi0609826.
|
Crystal structure of a two-domain ider-DNA complex
crystal form i . SNAP
output
|
2it0
|
transcription-DNA |
X-ray (2.6 Å) |
Wisedchaisri G, Chou CJ, Wu M, Roach C, Rice AE,
Holmes RK, Beeson C, Hol WG |
(2007) "Crystal
structures, metal activation, and DNA-binding
properties of two-domain IdeR from Mycobacterium
tuberculosis." Biochemistry,
46, 436-447. doi: 10.1021/bi0609826.
|
Crystal structure of a two-domain ider-DNA complex
crystal form ii . SNAP
output
|
2itl
|
DNA binding protein-DNA |
X-ray (1.65 Å) |
Bochkareva E, Martynowski D, Seitova A, Bochkarev
A |
(2006) "Structure
of the origin-binding domain of simian virus 40 large T
antigen bound to DNA." Embo J.,
25, 5961-5969. doi: 10.1038/sj.emboj.7601452.
|
The origin binding domain of the sv40 large t antigen
bound to the functional pen palindrome DNA (23 bp) .
SNAP output
|
2ivh
|
hydrolase |
X-ray (2.8 Å) |
Wang YT, Yang WJ, Li CL, Doudeva LG, Yuan HS |
(2007) "Structural
Basis for Sequence-Dependent DNA Cleavage by
Nonspecific Endonucleases." Nucleic Acids
Res., 35, 584. doi: 10.1093/NAR/GKL621.
|
Crystal structure of the nuclease domain of cole7
(h545q mutant) in complex with an 18-bp duplex DNA .
SNAP output
|
2ivk
|
hydrolase |
X-ray (2.9 Å) |
Wang YT, Yang WJ, Li CL, Doudeva LG, Yuan HS |
(2007) "Structural
Basis for Sequence-Dependent DNA Cleavage by
Nonspecific Endonucleases." Nucleic Acids
Res., 35, 584. doi: 10.1093/NAR/GKL621.
|
Crystal structure of the periplasmic endonuclease vvn
complexed with a 16-bp DNA . SNAP output
|
2j6s
|
transferase-DNA |
X-ray (2.5 Å) |
Eoff RL, Irimia A, Egli M, Guengerich FP |
(2007) "Sulfolobus
Solfataricus DNA Polymerase Dpo4 is Partially Inhibited
by "Wobble" Pairing between O6- Methylguanine and
Cytosine, But Accurate Bypass is Preferred."
J.Biol.Chem., 282, 1456. doi:
10.1074/JBC.M609661200.
|
Ternary complex of sulfolobus solfataricus dpo4 DNA
polymerase, o6- methylguanine modified DNA, and datp. .
SNAP output
|
2j6t
|
transferase-DNA |
X-ray (2.6 Å) |
Eoff RL, Irimia A, Egli M, Guengerich FP |
(2007) "Sulfolobus
Solfataricus DNA Polymerase Dpo4 is Partially Inhibited
by "Wobble" Pairing between O6- Methylguanine and
Cytosine, But Accurate Bypass is Preferred."
J.Biol.Chem., 282, 1456. doi:
10.1074/JBC.M609661200.
|
Ternary complex of sulfolobus solfataricus dpo4 DNA
polymerase, o6- methylguanine modified DNA, and datp. .
SNAP output
|
2j6u
|
transferase-DNA |
X-ray (2.5 Å) |
Eoff RL, Irimia A, Egli M, Guengerich FP |
(2007) "Sulfolobus
Solfataricus DNA Polymerase Dpo4 is Partially Inhibited
by "Wobble" Pairing between O6- Methylguanine and
Cytosine, But Accurate Bypass is Preferred."
J.Biol.Chem., 282, 1456. doi:
10.1074/JBC.M609661200.
|
Ternary complex of sulfolobus solfataricus dpo4 DNA
polymerase, o6- methylguanine modified DNA, and dgtp. .
SNAP output
|
2ja5
|
transferase |
X-ray (3.8 Å) |
Brueckner F, Hennecke U, Carell T, Cramer P |
(2007) "Cpd
Damage Recognition by Transcribing RNA Polymerase
II." Science, 315, 859.
doi: 10.1126/SCIENCE.1135400.
|
Cpd lesion containing RNA polymerase ii elongation
complex a . SNAP
output
|
2ja6
|
transferase |
X-ray (4.0 Å) |
Brueckner F, Hennecke U, Carell T, Cramer P |
(2007) "CPD
damage recognition by transcribing RNA polymerase
II." Science, 315,
859-862. doi: 10.1126/science.1135400.
|
Cpd lesion containing RNA polymerase ii elongation
complex b . SNAP
output
|
2ja7
|
transferase |
X-ray (3.8 Å) |
Brueckner F, Hennecke U, Carell T, Cramer P |
(2007) "Cpd
Damage Recognition by Transcribing RNA Polymerase
II." Science, 315, 859.
doi: 10.1126/SCIENCE.1135400.
|
Cpd lesion containing RNA polymerase ii elongation
complex c . SNAP
output
|
2ja8
|
transferase |
X-ray (3.8 Å) |
Brueckner F, Hennecke U, Carell T, Cramer P |
(2007) "Cpd
Damage Recognition by Transcribing RNA Polymerase
II." Science, 315, 859.
doi: 10.1126/SCIENCE.1135400.
|
Cpd lesion containing RNA polymerase ii elongation
complex d . SNAP
output
|
2jea
|
hydrolase-RNA |
X-ray (2.33 Å) |
Lorentzen E, Dziembowski A, Lindner D, Seraphin B,
Conti E |
(2007) "RNA
Channelling by the Archaeal Exosome." Embo
Rep., 8, 470. doi: 10.1038/SJ.EMBOR.7400945.
|
Structure of a 9-subunit archaeal exosome bound to RNA
. SNAP output
|
2jef
|
transferase-DNA |
X-ray (2.17 Å) |
Eoff RL, Angel KC, Egli M, Guengerich FP |
(2007) "Molecular
Basis of Selectivity of Nucleoside Triphosphate
Incorporation Opposite O6-Benzylguanine by Sulfolobus
Solfataricus DNA Polymerase Dpo4: Steady-State and
Pre-Steady-State Kinetics and X-Ray Crystallography of
Correct and Incorrect Pairing."
J.Biol.Chem., 282, 13573.
doi: 10.1074/JBC.M700656200.
|
The molecular basis of selectivity of nucleotide
triphosphate incorporation opposite o6-benzylguanine by
sulfolobus solfataricus DNA polymerase iv: steady-state
and pre-steady-state and x-ray crystallography of
correct and incorrect pairing . SNAP output
|
2jeg
|
transferase |
X-ray (2.38 Å) |
Eoff RL, Angel KC, Egli M, Guengerich FP |
(2007) "Molecular
Basis of Selectivity of Nucleoside Triphosphate
Incorporation Opposite O6-Benzylguanine by Sulfolobus
Solfataricus DNA Polymerase Dpo4: Steady-State and
Pre-Steady-State Kinetics and X-Ray Crystallography of
Correct and Incorrect Pairing."
J.Biol.Chem., 282, 13573.
doi: 10.1074/JBC.M700656200.
|
The molecular basis of selectivity of nucleoside
triphosphate incorporation opposite o6-benzylguanine by
sulfolobus solfataricus DNA polymerase iv: steady-state
and pre-steady-state kinetics and x- ray
crystallography of correct and incorrect pairing .
SNAP output
|
2jei
|
transferase |
X-ray (2.39 Å) |
Eoff RL, Angel KC, Egli M, Guengerich FP |
(2007) "Molecular
Basis of Selectivity of Nucleoside Triphosphate
Incorporation Opposite O6-Benzylguanine by Sulfolobus
Solfataricus DNA Polymerase Dpo4: Steady-State and
Pre-Steady-State Kinetics and X-Ray Crystallography of
Correct and Incorrect Pairing."
J.Biol.Chem., 282, 13573.
doi: 10.1074/JBC.M700656200.
|
The molecular basis of selectivity of nucleoside
triphosphate incorporation opposite o6-benzylguanine by
sulfolobus solfataricus DNA polymerase iv: steady-state
and pre-steady-state kinetics and x- ray
crystallography of correct and incorrect pairing .
SNAP output
|
2jej
|
transferase |
X-ray (1.86 Å) |
Eoff RL, Angel KC, Egli M, Guengerich FP |
(2007) "Molecular
Basis of Selectivity of Nucleoside Triphosphate
Incorporation Opposite O6-Benzylguanine by Sulfolobus
Solfataricus DNA Polymerase Dpo4: Steady-State and
Pre-Steady-State Kinetics and X-Ray Crystallography of
Correct and Incorrect Pairing."
J.Biol.Chem., 282, 13573.
doi: 10.1074/JBC.M700656200.
|
The molecular basis of selectivity of nucleoside
triphosphate incorporation opposite o6-benzylguanine by
sulfolobus solfataricus DNA polymerase iv: steady-state
and pre-steady-state kinetics and x- ray
crystallography of correct and incorrect pairing .
SNAP output
|
2jg3
|
transferase-DNA |
X-ray (1.9 Å) |
Pljevaljcic G, Schmidt F, Scheidig AJ, Lurz R,
Weinhold E |
(2007) "Quantitative
Labeling of Long Plasmid DNA with Nanometer
Precision." Chembiochem,
8, 1516. doi: 10.1002/CBIC.200700294.
|
Mtaqi with baz . SNAP
output
|
2jlg
|
transferase |
X-ray (2.8 Å) |
Poranen MM, Salgado PS, Koivunen MRL, Wright S,
Bamford DH, Stuart DI, Grimes JM |
(2008) "Structural
Explanation for the Role of Mn2+ in the Activity of
{Phi}6 RNA-Dependent RNA Polymerase." Nucleic
Acids Res., 36, 6633. doi:
10.1093/NAR/GKN632.
|
Structural explanation for the role of mn in the
activity of phi6 RNA-dependent RNA polymerase .
SNAP output
|
2jp9
|
transcription-DNA |
NMR |
Stoll R, Lee BM, Debler EW, Laity JH, Wilson IA,
Dyson HJ, Wright PE |
(2007) "Structure
of the wilms tumor suppressor protein zinc finger
domain bound to DNA." J.Mol.Biol.,
372, 1227-1245. doi: 10.1016/j.jmb.2007.07.017.
|
Structure of the wilms tumor suppressor protein zinc
finger domain bound to DNA . SNAP output
|
2jpa
|
transcription-DNA |
NMR |
Stoll R, Lee BM, Debler EW, Laity JH, Wilson IA,
Dyson HJ, Wright PE |
(2007) "Structure
of the wilms tumor suppressor protein zinc finger
domain bound to DNA." J.Mol.Biol.,
372, 1227-1245. doi: 10.1016/j.jmb.2007.07.017.
|
Structure of the wilms tumor suppressor protein zinc
finger domain bound to DNA . SNAP output
|
2jx1
|
transcription-DNA |
NMR |
Gamsjaeger R, Swanton MK, Kobus FJ, Lehtomaki E,
Lowry JA, Kwan AH, Matthews JM, Mackay JP |
"Structure of the fifth zinc finger of Myelin
Transcription Factor 1 in complex with RARE DNA." |
Structure of the fifth zinc finger of myelin
transcription factor 1 in complex with rare DNA .
SNAP output
|
2jxi
|
DNA binding protein, DNA |
NMR |
Halouska S, Zhou Y, Becker DF, Powers R |
(2008) "Solution
structure of the Pseudomonas putida protein PpPutA45
and its DNA complex." Proteins,
75, 12-27. doi: 10.1002/prot.22217.
|
Solution structure of the DNA-binding domain of
pseudomonas putida proline utilization a (puta) bound
to gttgca DNA sequence . SNAP output
|
2jzw
|
viral protein-DNA |
NMR |
Bourbigot S, Ramalanjaona N, Boudier C, Salgado GF,
Roques BP, Mely Y, Bouaziz S, Morellet N |
(2008) "How the
HIV-1 nucleocapsid protein binds and destabilises the
(-)primer binding site during reverse
transcription." J.Mol.Biol.,
383, 1112-1128. doi: 10.1016/j.jmb.2008.08.046.
|
How the hiv-1 nucleocapsid protein binds and
destabilises the (-)primer binding site during reverse
transcription . SNAP
output
|
2k1n
|
transcription-DNA |
NMR |
Sullivan DM, Bobay BG, Kojetin DJ, Thompson RJ, Rance
M, Strauch MA, Cavanagh J |
(2008) "Insights
into the Nature of DNA Binding of AbrB-like
Transcription Factors." Structure,
16, 1702-1713. doi: 10.1016/j.str.2008.08.014.
|
DNA bound structure of the n-terminal domain of abrb .
SNAP output
|
2k7f
|
replication-DNA |
NMR |
Kobayashi M, Ab E, Bonvin AM, Siegal G |
(2010) "Structure
of the DNA-bound BRCA1 C-terminal region from human
replication factor C p140 and model of the protein-DNA
complex." J.Biol.Chem.,
285, 10087-10097. doi: 10.1074/jbc.M109.054106.
|
Haddock calculated model of the complex between the
brct region of rfc p140 and dsDNA . SNAP output
|
2kae
|
transcription-DNA |
NMR |
Lowry JA, Gamsjaeger R, Thong SY, Hung W, Kwan AH,
Broitman-Maduro G, Matthews JM, Maduro M, Mackay JP |
(2009) "Structural
Analysis of MED-1 Reveals Unexpected Diversity in the
Mechanism of DNA Recognition by GATA-type Zinc Finger
Domains." J.Biol.Chem.,
284, 5827-5835. doi: 10.1074/jbc.M808712200.
|
Data-driven model of med1:DNA complex . SNAP output
|
2kdz
|
transcription-DNA |
NMR |
Lou YC, Wei SY, Rajasekaran M, Chou CC, Hsu HM, Tai
JH, Chen C |
(2009) "NMR
structural analysis of DNA recognition by a novel Myb1
DNA-binding domain in the protozoan parasite
Trichomonas vaginalis." Nucleic Acids Res.
doi: 10.1093/nar/gkp097.
|
Structure of the r2r3 DNA binding domain of myb1
protein from protozoan parasite trichomonas vaginalis
in complex with mre-1-mre-2r DNA . SNAP output
|
2kei
|
transcription-DNA |
NMR |
Romanuka J, Folkers GE, Biris N, Tishchenko E, Wienk
H, Bonvin AM, Kaptein R, Boelens R |
(2009) "Specificity
and affinity of Lac repressor for the auxiliary
operators O2 and O3 are explained by the structures of
their protein-DNA complexes." J.Mol.Biol.,
390, 478-489. doi: 10.1016/j.jmb.2009.05.022.
|
Refined solution structure of a dimer of lac repressor
DNA-binding domain complexed to its natural operator o1
. SNAP output
|
2kej
|
transcription-DNA |
NMR |
Romanuka J, Folkers GE, Biris N, Tishchenko E, Wienk
H, Bonvin AM, Kaptein R, Boelens R |
(2009) "Specificity
and affinity of Lac repressor for the auxiliary
operators O2 and O3 are explained by the structures of
their protein-DNA complexes." J.Mol.Biol.,
390, 478-489. doi: 10.1016/j.jmb.2009.05.022.
|
Solution structure of a dimer of lac repressor
DNA-binding domain complexed to its natural operator o2
. SNAP output
|
2kek
|
transcription-DNA |
NMR |
Romanuka J, Folkers GE, Biris N, Tishchenko E, Wienk
H, Bonvin AM, Kaptein R, Boelens R |
(2009) "Specificity
and affinity of Lac repressor for the auxiliary
operators O2 and O3 are explained by the structures of
their protein-DNA complexes." J.Mol.Biol.,
390, 478-489. doi: 10.1016/j.jmb.2009.05.022.
|
Solution structure of a dimer of lac repressor
DNA-binding domain complexed to its natural operator o3
. SNAP output
|
2kfn
|
transferase-DNA |
X-ray (2.03 Å) |
Brautigam CA, Sun S, Piccirilli JA, Steitz TA |
(1999) "Structures
of normal single-stranded DNA and
deoxyribo-3'-S-phosphorothiolates bound to the 3'-5'
exonucleolytic active site of DNA polymerase I from
Escherichia coli." Biochemistry,
38, 696-704. doi: 10.1021/bi981537g.
|
Klenow fragment with bridging-sulfur substrate and
manganese . SNAP
output
|
2kfz
|
transferase-DNA |
X-ray (2.03 Å) |
Brautigam CA, Sun S, Piccirilli JA, Steitz TA |
(1999) "Structures
of normal single-stranded DNA and
deoxyribo-3'-S-phosphorothiolates bound to the 3'-5'
exonucleolytic active site of DNA polymerase I from
Escherichia coli." Biochemistry,
38, 696-704. doi: 10.1021/bi981537g.
|
Klenow fragment with bridging-sulfur substrate and zinc
only . SNAP output
|
2kkf
|
DNA binding protein-DNA |
NMR |
Cierpicki T, Risner LE, Grembecka J, Lukasik SM,
Popovic R, Omonkowska M, Shultis DD, Zeleznik-Le NJ,
Bushweller JH |
(2010) "Structure
of the MLL CXXC domain-DNA complex and its functional
role in MLL-AF9 leukemia."
Nat.Struct.Mol.Biol., 17,
62-68. doi: 10.1038/nsmb.1714.
|
Solution structure of mll cxxc domain in complex with
palindromic cpg DNA . SNAP output
|
2kmk
|
DNA binding protein-DNA |
NMR |
Lee S, Doddapaneni K, Hogue A, McGhee L, Meyers S, Wu
Z |
(2010) "Solution
structure of Gfi-1 zinc domain bound to consensus
DNA." J.Mol.Biol., 397,
1055-1066. doi: 10.1016/j.jmb.2010.02.006.
|
Gfi-1 zinc fingers 3-5 complexed with DNA . SNAP output
|
2kn7
|
hydrolase-DNA |
NMR |
Das D, Folkers GE, van Dijk M, Jaspers NGJ,
Hoeijmakers JHJ, Kaptein R, Boelens R |
(2012) "The
structure of the XPF-ssDNA complex underscores the
distinct roles of the XPF and ERCC1 helix-
hairpin-helix domains in ss/ds DNA recognition."
Structure, 20, 667-675. doi:
10.1016/j.str.2012.02.009.
|
Structure of the xpf-single strand DNA complex .
SNAP output
|
2ko0
|
transcription-DNA |
NMR |
Campagne S, Saurel O, Gervais V, Milon A |
(2010) "Structural
determinants of specific DNA-recognition by the THAP
zinc finger." Nucleic Acids Res. doi:
10.1093/nar/gkq053.
|
Solution structure of the thap zinc finger of thap1 in
complex with its DNA target . SNAP output
|
2ktq
|
transferase-DNA |
X-ray (2.3 Å) |
Li Y, Korolev S, Waksman G |
(1998) "Crystal
structures of open and closed forms of binary and
ternary complexes of the large fragment of Thermus
aquaticus DNA polymerase I: structural basis for
nucleotide incorporation." EMBO J.,
17, 7514-7525. doi: 10.1093/emboj/17.24.7514.
|
Open ternary complex of the large fragment of DNA
polymerase i from thermus aquaticus . SNAP output
|
2kv6
|
DNA binding protein-DNA |
NMR |
Huang H, Kozekov ID, Kozekova A, Rizzo CJ, McCullough
AK, Lloyd RS, Stone MP |
(2010) "Minor
Groove Orientation of the KWKK Peptide Tethered via the
N-Terminal Amine to the Acrolein-Derived
1,N(2)-gamma-Hydroxypropanodeoxyguanosine Lesion with a
Trimethylene Linkage ." Biochemistry,
49, 6155-6164. doi: 10.1021/bi100364f.
|
Tetrapeptide kwkk conjugated to oligonucleotide duplex
by a trimethylene tether . SNAP output
|
2ky8
|
transcription-DNA |
NMR |
Scarsdale JN, Webb HD, Ginder GD, Williams DC |
(2011) "Solution
structure and dynamic analysis of chicken MBD2 methyl
binding domain bound to a target-methylated DNA
sequence." Nucleic Acids Res.,
39, 6741-6752. doi: 10.1093/nar/gkr262.
|
Solution structure and dynamic analysis of chicken mbd2
methyl binding domain bound to a target methylated DNA
sequence . SNAP
output
|
2kzm
|
transferase-DNA |
X-ray (2.6 Å) |
Brautigam CA, Sun S, Piccirilli JA, Steitz TA |
(1999) "Structures
of normal single-stranded DNA and
deoxyribo-3'-S-phosphorothiolates bound to the 3'-5'
exonucleolytic active site of DNA polymerase I from
Escherichia coli." Biochemistry,
38, 696-704. doi: 10.1021/bi981537g.
|
Klenow fragment with normal substrate and zinc and
manganese . SNAP
output
|
2kzz
|
transferase-DNA |
X-ray (2.25 Å) |
Brautigam CA, Sun S, Piccirilli JA, Steitz TA |
(1999) "Structures
of normal single-stranded DNA and
deoxyribo-3'-S-phosphorothiolates bound to the 3'-5'
exonucleolytic active site of DNA polymerase I from
Escherichia coli." Biochemistry,
38, 696-704. doi: 10.1021/bi981537g.
|
Klenow fragment with normal substrate and zinc only .
SNAP output
|
2l1g
|
transcription-DNA |
NMR |
Campagne S, Gervais V, Saurel O, Milon A |
"RDC refined solution structure of the THAP zinc
finger of THAP1 in complex with its 16bp RRM1 DNA
target." |
Rdc refined solution structure of the thap zinc finger
of thap1 in complex with its 16bp rrm1 DNA target .
SNAP output
|
2l45
|
viral protein-DNA |
NMR |
Quintal S, Viegas A, Erhardt S, Cabrita EJ, Farrell
NP |
(2012) "Platinated
DNA affects zinc finger conformation. Interaction of a
platinated single-stranded oligonucleotide and the
C-terminal zinc finger of nucleocapsid protein
HIVNCp7." Biochemistry,
51, 1752-1761. doi: 10.1021/bi201834g.
|
C-terminal zinc knuckle of the hivncp7 with DNA .
SNAP output
|
2l46
|
viral protein-DNA |
NMR |
Quintal S, Viegas A, Erhardt S, Cabrita EJ, Farrell
NP |
(2012) "Platinated
DNA affects zinc finger conformation. Interaction of a
platinated single-stranded oligonucleotide and the
C-terminal zinc finger of nucleocapsid protein
HIVNCp7." Biochemistry,
51, 1752-1761. doi: 10.1021/bi201834g.
|
C-terminal zinc finger of the hivncp7 with platinated
DNA . SNAP output
|
2l4l
|
viral protein-DNA |
NMR |
Bazzi A, Zargarian L, Chaminade F, Boudier C, De
Rocquigny H, Rene B, Mely Y, Fosse P, Mauffret O |
(2011) "Structural
insights into the cTAR DNA recognition by the HIV-1
nucleocapsid protein: role of sugar deoxyriboses in the
binding polarity of NC." Nucleic Acids
Res., 39, 3903-3916. doi:
10.1093/nar/gkq1290.
|
Structural insights into the ctar DNA recognition by
the hiv-1 nucleocapsid protein: role of sugar
deoxyriboses in the binding polarity of nc . SNAP output
|
2ld5
|
transcription-DNA |
NMR |
Zhang Y, Larsen CA, Stadler HS, Ames JB |
(2011) "Structural
basis for sequence specific DNA binding and protein
dimerization of HOXA13." Plos One,
6, e23069. doi: 10.1371/journal.pone.0023069.
|
Solution NMR-derived complex structure of hoxa13 DNA
binding domain bound to DNA . SNAP output
|
2lef
|
gene regulation-DNA |
NMR |
Love JJ, Li X, Case DA, Giese K, Grosschedl R, Wright
PE |
(1995) "Structural
basis for DNA bending by the architectural
transcription factor LEF-1." Nature,
376, 791-795. doi: 10.1038/376791a0.
|
Lef1 hmg domain (from mouse), complexed with DNA
(15bp), NMR, 12 structures . SNAP output
|
2lev
|
transcription regulator-DNA |
multiple methods: solution nmr, solution
scattering |
Cordeiro TN, Schmidt H, Madrid C, Juarez A, Bernado
P, Griesinger C, Garcia J, Pons M |
(2011) "Indirect
DNA Readout by an H-NS Related Protein: Structure of
the DNA Complex of the C-Terminal Domain of Ler."
Plos Pathog., 7, e1002380.
doi: 10.1371/journal.ppat.1002380.
|
Structure of the DNA complex of the c-terminal domain
of ler . SNAP output
|
2lex
|
transcription-DNA |
NMR |
Yamasaki K, Kigawa T, Watanabe S, Inoue M, Yamasaki
T, Seki M, Shinozaki K, Yokoyama S |
(2012) "Structural
basis for sequence-spscific DNA recognition by an
Arabidopsis WRKY transcription factor."
J.Biol.Chem. doi: 10.1074/jbc.M111.279844.
|
Complex of the c-terminal wrky domain of atwrky4 and a
w-box DNA . SNAP
output
|
2lkx
|
transcription-DNA |
NMR |
Chaney BA, Clark-Baldwin K, Dave V, Ma J, Rance
M |
(2005) "Solution
structure of the K50 class homeodomain PITX2 bound to
DNA and implications for mutations that cause Rieger
syndrome." Biochemistry,
44, 7497-7511. doi: 10.1021/bi0473253.
|
NMR structure of the homeodomain of pitx2 in complex
with a taatcc DNA binding site . SNAP output
|
2lt7
|
metal binding protein-DNA |
NMR |
Buck-Koehntop BA, Stanfield RL, Ekiert DC,
Martinez-Yamout MA, Dyson HJ, Wilson IA, Wright PE |
(2012) "Molecular
basis for recognition of methylated and specific DNA
sequences by the zinc finger protein Kaiso."
Proc.Natl.Acad.Sci.USA, 109,
15229-15234. doi: 10.1073/pnas.1213726109.
|
Solution NMR structure of kaiso zinc finger DNA binding
domain in complex with kaiso binding site DNA .
SNAP output
|
2ltt
|
transcription, DNA binding protein-DNA |
NMR |
Rossi P, Barbieri CM, Aramini JM, Bini E, Lee HW,
Janjua H, Xiao R, Acton TB, Montelione GT |
(2013) "Structures
of apo- and ssDNA-bound YdbC from Lactococcus lactis
uncover the function of protein domain family DUF2128
and expand the single-stranded DNA-binding domain
proteome." Nucleic Acids Res.,
41, 2756-2768. doi: 10.1093/nar/gks1348.
|
Solution NMR structure of ydbc:dt19g1 complex.
northeast structural genomics consortium (nesg) target
kr150 . SNAP output
|
2m2w
|
transferase-DNA |
NMR |
Wu WJ, Su MI, Wu JL, Kumar S, Lim LH, Wang CW,
Nelissen FH, Chen MC, Doreleijers JF, Wijmenga SS, Tsai
MD |
(2014) "How a
low-fidelity DNA polymerase chooses non-Watson-Crick
from Watson-Crick incorporation."
J.Am.Chem.Soc., 136,
4927-4937. doi: 10.1021/ja4102375.
|
Ternary complex of asfv pol x with DNA and mgdgtp .
SNAP output
|
2map
|
transcription-DNA |
NMR |
Campagne S, Marsh ME, Capitani G, Vorholt JA, Allain
FH |
(2014) "Structural
basis for -10 promoter element melting by
environmentally induced sigma factors."
Nat.Struct.Mol.Biol., 21,
269-276. doi: 10.1038/nsmb.2777.
|
Solution structure of the complex formed by the region
2 of e. coli sigmae and its cognate -10 promoter
element non template strand tgtcaaa. . SNAP output
|
2me6
|
transcription-DNA |
NMR |
Proudfoot A, Wuthrich K, Serrano P, Geralt M |
"NMR Structure of the homeodomain transcription
factor Gbx1 from Homo sapiens in complex with the DNA
sequence CGACTAATTAGTCG." |
NMR structure of the homeodomain transcription factor
gbx1 from homo sapiens in complex with the DNA sequence
cgactaattagtcg . SNAP
output
|
2mf8
|
metal binding protein-DNA |
NMR |
Gamsjaeger R, O'Connell MR, Cubeddu L, Shepherd NE,
Lowry JA, Kwan AH, Vandevenne M, Swanton MK, Matthews JM,
Mackay JP |
(2013) "A
structural analysis of DNA binding by myelin
transcription factor 1 double zinc fingers."
J.Biol.Chem., 288,
35180-35191. doi: 10.1074/jbc.M113.482075.
|
Haddock model of myt1 f4f5 - DNA complex . SNAP output
|
2mna
|
DNA binding protein-DNA |
NMR |
Gamsjaeger R, Kariawasam R, Gimenez AX, Touma C,
McIlwain E, Bernardo RE, Shepherd NE, Ataide SF, Dong Q,
Richard DJ, White MF, Cubeddu L |
(2015) "The
structural basis of DNA binding by the single-stranded
DNA-binding protein from Sulfolobus solfataricus."
Biochem.J., 465, 337-346.
doi: 10.1042/BJ20141140.
|
The structural basis of DNA binding by the
single-stranded DNA-binding protein from sulfolobus
solfataricus . SNAP
output
|
2moe
|
hydrolase-DNA |
NMR |
Walavalkar NM, Cramer JM, Buchwald WA, Scarsdale JN,
Williams DC |
(2015) "Solution
structure and intramolecular exchange of
methyl-cytosine binding domain protein 4 (MBD4) on DNA
suggests a mechanism to scan for mCpG/TpG
mismatches." Nucleic Acids Res.,
42, 11218-11232. doi: 10.1093/nar/gku782.
|
Solution structure of mbd4 methyl-cytosine binding
domain bound to methylated DNA . SNAP output
|
2mru
|
DNA binding protein-DNA |
NMR |
Zorzini V, Buts L, Schrank E, Sterckx YG, Respondek
M, Engelberg-Kulka H, Loris R, Zangger K, van Nuland
NA |
(2015) "Escherichia
coli antitoxin MazE as transcription factor: insights
into MazE-DNA binding." Nucleic Acids
Res., 43, 1241-1256. doi:
10.1093/nar/gku1352.
|
Structure of truncated ecmaze-DNA complex . |