**************************************************************************** Note: By default, each nucleotide/amino-acid is identified by chainId.name#. For example, B.DA1689 means adenosine #1689 on chain B, and C.ARG49 denotes arginine #49 on chain C. Use the --idstr=long option to get strictly delineated id strings. Command: x3dna-dssr snap -i=/data/pdb/pdbfiles/4dkj.pdb -o=4dkj.out --type=base File name: 4dkj.pdb no. of peptide chains: 1 [A=389] no. of DNA/RNA chains: 2 [B=14,C=14] no. of amino acids: 389 no. of nucleotides: 29 no. of atoms: 4068 no. of waters: 267 no. of metals: 0 **************************************************************************** List of 3 types of 3 modified nucleotides nt count list 1 5CM-c 1 C.5CM7 2 C37-c 1 B.C37/8 3 SAH-a 1 A.SAH501 **************************************************************************** List of 1 helix Note: a helix is defined by base-stacking interactions, regardless of bp type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[0] bps=12 strand-1 5'-CACATGGCTGAA-3' bp-type |||||||||||| strand-2 3'-GTGTACcGACTT-5' helix-form BB.BBxBB.BB 1 B.DC2 C.DG14 C-G WC 19-XIX cWW cW-W 2 B.DA3 C.DT13 A-T WC 20-XX cWW cW-W 3 B.DC4 C.DG12 C-G WC 19-XIX cWW cW-W 4 B.DA5 C.DT11 A-T WC 20-XX cWW cW-W 5 B.DT6 C.DA10 T-A WC 20-XX cWW cW-W 6 B.DG7 C.DC9 G-C WC 19-XIX cWW cW-W 7 B.DG9 C.5CM7 G-c WC 19-XIX cWW cW-W 8 B.DC10 C.DG6 C-G WC 19-XIX cWW cW-W 9 B.DT11 C.DA5 T-A WC 20-XX cWW cW-W 10 B.DG12 C.DC4 G-C WC 19-XIX cWW cW-W 11 B.DA13 C.DT3 A-T WC 20-XX cWW cW-W 12 B.DA14 C.DT2 A-T WC 20-XX cWW cW-W **************************************************************************** List of 65 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4dkj T-asn B.DT6 A.ASN303 8.56 -169.34 -1.98 7.97 2.42 75.42 -26.58 -166.08 2 4dkj G-val B.DG7 A.VAL140 -7.34 49.71 -5.59 3.61 -3.10 -19.02 41.94 19.25 3 4dkj G-gln B.DG7 A.GLN141 6.30 85.15 -1.77 3.96 4.57 -33.02 -53.08 61.06 4 4dkj G-asn B.DG7 A.ASN303 6.15 161.67 -0.02 -6.14 0.17 -71.42 54.25 154.04 5 4dkj G-ser B.DG7 A.SER304 6.10 166.19 3.63 -3.38 3.54 -7.62 2.67 166.16 6 4dkj G-asn B.DG7 A.ASN324 10.85 174.37 7.96 -3.39 6.55 -62.32 20.93 173.29 7 4dkj C-ser B.C37/8 A.SER132 5.13 -168.23 2.49 3.83 2.34 -38.08 -60.94 -165.45 8 4dkj C-phe B.C37/8 A.PHE133 -6.86 -47.49 5.89 2.84 2.08 0.16 42.43 -21.84 9 4dkj C-pro B.C37/8 A.PRO134 -7.47 57.20 7.06 2.12 -1.19 -15.85 -0.37 55.14 10 4dkj C-cys B.C37/8 A.CYS135 -6.68 176.58 1.34 -3.43 -5.58 28.32 -82.59 175.27 11 4dkj C-glu B.C37/8 A.GLU184 -4.14 125.04 -1.00 -3.73 1.50 26.37 -83.97 100.18 12 4dkj C-asn B.C37/8 A.ASN185 -3.29 49.22 1.88 -0.56 -2.65 -24.55 38.83 18.18 13 4dkj C-val B.C37/8 A.VAL186 -5.35 101.18 -1.32 2.52 -4.53 -22.86 -10.12 98.87 14 4dkj C-arg B.C37/8 A.ARG228 -9.95 108.07 -8.54 4.71 -1.99 69.13 -38.04 80.97 15 4dkj C-arg B.C37/8 A.ARG230 -6.18 109.11 -6.12 -0.78 -0.38 64.37 -47.06 81.85 16 4dkj C-gly B.C37/8 A.GLY373 9.82 141.13 6.23 4.79 5.89 -69.07 -49.28 126.41 17 4dkj C-asn B.C37/8 A.ASN374 7.38 51.99 0.82 7.10 1.85 32.24 -12.92 39.30 18 4dkj C-ser B.C37/8 A.SER375 6.94 -171.80 -2.26 -4.98 4.26 -65.34 -19.16 -170.10 19 4dkj G-gln B.DG9 A.GLN141 -7.94 46.29 -2.85 6.81 -2.94 -23.24 -39.35 7.59 20 4dkj G-phe B.DG9 A.PHE302 -6.91 170.07 -3.25 -5.50 -2.64 84.93 22.93 166.19 21 4dkj G-ser B.DG9 A.SER321 7.66 -168.68 -4.94 2.63 5.23 -16.76 -10.55 -168.51 22 4dkj G-gly B.DG9 A.GLY322 4.56 -177.31 -2.74 3.63 0.31 42.44 35.36 -176.97 23 4dkj G-ala B.DG9 A.ALA323 -5.62 -125.39 2.31 4.92 -1.44 43.33 54.43 -112.09 24 4dkj G-arg B.DG9 A.ARG326 10.42 -117.36 3.20 9.56 2.64 -6.84 -9.25 -117.00 25 4dkj C-ser B.DC10 A.SER321 7.30 156.32 4.68 -5.41 1.46 27.05 -0.75 155.63 26 4dkj C-gly B.DC10 A.GLY322 -4.93 145.71 1.66 -2.92 -3.61 -43.43 -24.24 142.08 27 4dkj A-arg C.DA5 A.ARG326 12.11 -177.35 -8.09 8.49 3.02 1.90 -6.51 -177.35 28 4dkj G-glu C.DG6 A.GLU305 9.86 155.58 3.44 -5.76 7.23 -29.16 47.42 152.33 29 4dkj G-gly C.DG6 A.GLY322 4.88 -153.74 1.62 3.39 3.12 -51.90 18.31 -150.31 30 4dkj G-arg C.DG6 A.ARG326 10.82 151.88 5.35 -9.39 0.54 -9.97 10.03 151.66 31 4dkj C-thr C.5CM7 A.THR300 10.43 -100.83 -4.30 9.50 0.30 24.15 10.85 -98.22 32 4dkj C-phe C.5CM7 A.PHE302 7.12 -94.28 -3.90 4.61 3.77 -16.80 86.59 -37.39 33 4dkj C-glu C.5CM7 A.GLU305 7.56 124.77 3.21 -4.57 5.09 -20.51 56.17 115.36 34 4dkj C-ala C.5CM7 A.ALA323 5.14 124.06 2.37 -4.18 1.83 36.99 -48.85 113.93 35 4dkj C-arg C.5CM7 A.ARG326 -9.82 118.35 2.92 -9.19 -1.86 -13.44 14.72 117.30 36 4dkj G-val C.DG8 A.VAL140 7.86 -39.53 -3.04 -4.69 5.52 2.94 -39.41 -0.72 37 4dkj G-gln C.DG8 A.GLN141 5.20 -68.52 -2.18 -4.34 -1.86 -33.04 53.59 -28.56 38 4dkj G-thr C.DG8 A.THR301 -9.60 142.83 9.20 0.14 2.72 24.08 77.07 130.55 39 4dkj G-phe C.DG8 A.PHE302 -6.02 -169.33 -5.29 1.41 -2.52 67.37 -44.23 -166.00 40 4dkj G-asn C.DG8 A.ASN303 -5.73 -135.89 0.13 5.06 2.68 -56.52 -54.30 -122.05 41 4dkj G-ser C.DG8 A.SER304 -4.97 -141.89 2.12 4.44 -0.67 -7.92 10.42 -141.63 42 4dkj C-asn C.DC9 A.ASN303 -5.98 -157.19 -0.35 5.97 -0.06 -66.00 -46.06 -149.97 43 4dkj A-val C.DA10 A.VAL140 -7.93 -76.52 -7.83 -1.21 -0.30 -28.17 -34.09 -64.11 44 4dkj A-phe A.SAH501 A.PHE17 -6.90 64.80 -2.15 3.08 -5.79 36.38 47.43 26.27 45 4dkj A-ala A.SAH501 A.ALA18 -9.78 -123.17 -7.93 -5.46 -1.75 -15.79 -21.95 -121.39 46 4dkj A-gly A.SAH501 A.GLY19 10.85 95.87 -2.47 9.42 -4.78 31.96 70.00 62.30 47 4dkj A-ile A.SAH501 A.ILE20 14.32 112.54 -0.97 14.07 -2.49 29.39 -3.07 109.91 48 4dkj A-gly A.SAH501 A.GLY21 -15.03 -131.74 -10.41 -7.69 7.63 11.45 -85.13 -112.10 49 4dkj A-ser A.SAH501 A.SER22 -17.52 67.66 -8.65 15.19 1.18 -40.41 -3.67 55.34 50 4dkj A-gln A.SAH501 A.GLN23 -17.24 -67.06 -16.20 -2.28 -5.45 52.10 -9.44 -42.74 51 4dkj A-val A.SAH501 A.VAL44 -6.32 -87.47 -4.89 -4.01 -0.02 73.24 25.05 -44.41 52 4dkj A-glu A.SAH501 A.GLU45 5.96 149.07 0.02 5.75 1.54 -3.26 -33.42 147.66 53 4dkj A-trp A.SAH501 A.TRP46 5.53 -80.60 -3.85 -1.78 3.55 -79.21 14.77 -2.23 54 4dkj A-ser A.SAH501 A.SER80 9.24 158.39 9.06 0.32 1.79 -52.58 -57.52 152.10 55 4dkj A-phe A.SAH501 A.PHE112 5.71 -76.08 -1.09 -4.14 3.78 -1.31 -66.65 -39.01 56 4dkj A-asp A.SAH501 A.ASP113 3.05 -68.41 0.41 -3.01 -0.29 -51.54 -23.08 -40.32 57 4dkj A-ile A.SAH501 A.ILE114 -3.75 96.07 0.20 -3.22 -1.91 44.63 71.07 51.89 58 4dkj A-ser A.SAH501 A.SER132 -11.66 145.19 4.29 5.22 -9.50 21.72 -12.57 144.31 59 4dkj A-pro A.SAH501 A.PRO134 -9.86 -50.69 -2.51 8.04 -5.11 18.54 -45.00 -14.62 60 4dkj A-arg A.SAH501 A.ARG154 -9.49 128.81 7.98 -3.20 -4.02 41.45 -30.24 122.73 61 4dkj A-leu A.SAH501 A.LEU157 -8.08 161.56 2.69 -6.22 -4.41 50.97 -20.13 159.21 62 4dkj A-ile A.SAH501 A.ILE371 15.63 -160.43 -13.45 -4.58 -6.50 -57.69 59.38 -153.80 63 4dkj A-asn A.SAH501 A.ASN374 -14.82 -126.15 -14.29 3.83 -0.86 -80.67 19.70 -105.57 64 4dkj A-ser A.SAH501 A.SER375 -16.00 164.01 7.73 10.00 -9.81 24.20 -57.42 161.29 65 4dkj A-ile A.SAH501 A.ILE376 -18.32 -134.82 -17.70 -4.72 0.22 78.42 -23.83 -118.83 **************************************************************************** List of 20 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4dkj AT-arg C.DA5 B.DT11 A.ARG326 12.11 -176.96 -8.04 8.24 3.77 8.73 -4.53 -176.95 2 4dkj AT-asn C.DA10 B.DT6 A.ASN303 -8.49 169.35 -2.00 -7.80 -2.69 78.84 24.01 165.83 3 4dkj AT-val C.DA10 B.DT6 A.VAL140 -7.88 -76.88 -7.74 -1.32 -0.60 -27.73 -37.95 -62.68 4 4dkj GC-ala B.DG9 C.5CM7 A.ALA323 -5.38 -124.68 2.34 4.55 -1.64 40.16 51.64 -113.03 5 4dkj GC-arg B.DG9 C.5CM7 A.ARG326 10.12 -117.81 3.05 9.38 2.25 -10.14 -11.99 -117.15 6 4dkj GC-arg C.DG6 B.DC10 A.ARG326 10.81 152.59 5.37 -9.30 1.20 -12.11 4.19 152.41 7 4dkj GC-asn B.DG7 C.DC9 A.ASN303 6.06 159.42 -0.18 -6.06 0.12 -68.73 50.15 151.93 8 4dkj GC-asn B.DG7 C.DC9 A.ASN324 10.83 172.02 7.52 -3.47 6.98 -60.55 16.57 170.65 9 4dkj GC-gln B.DG7 C.DC9 A.GLN141 6.42 82.38 -1.90 3.75 4.84 -28.55 -54.14 58.06 10 4dkj GC-gln B.DG9 C.5CM7 A.GLN141 -8.09 47.32 -3.25 6.67 -3.23 -27.08 -37.78 9.12 11 4dkj GC-glu B.DG9 C.5CM7 A.GLU305 -7.68 -124.55 3.28 4.95 -4.86 -17.26 -53.44 -116.35 12 4dkj GC-glu C.DG6 B.DC10 A.GLU305 9.99 154.24 2.96 -5.60 7.72 -31.46 41.52 151.26 13 4dkj GC-gly B.DG9 C.5CM7 A.GLY322 4.26 -176.49 -2.67 3.31 0.12 40.94 31.38 -176.10 14 4dkj GC-gly C.DG6 B.DC10 A.GLY322 4.90 -149.70 1.63 3.16 3.37 -47.66 21.26 -146.16 15 4dkj GC-phe B.DG9 C.5CM7 A.PHE302 -7.01 167.41 -3.51 -5.38 -2.81 85.99 26.18 162.18 16 4dkj GC-ser B.DG7 C.DC9 A.SER304 6.01 165.86 3.40 -3.32 3.68 -5.73 -2.04 165.84 17 4dkj GC-ser B.DG9 C.5CM7 A.SER321 7.42 -169.41 -5.09 2.49 4.79 -18.55 -14.40 -169.18 18 4dkj GC-ser C.DG6 B.DC10 A.SER321 -7.34 -156.54 4.77 5.32 -1.70 22.77 -3.83 -156.05 19 4dkj GC-thr B.DG9 C.5CM7 A.THR300 -10.44 102.39 -3.99 -9.63 -0.40 25.81 -14.71 99.17 20 4dkj GC-val B.DG7 C.DC9 A.VAL140 -7.44 49.14 -5.78 3.67 -2.91 -14.17 42.26 21.23 **************************************************************************** List of 19 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 4dkj OP1@B.DT6 OG@A.SER289 2.44 po4:sidechain 2 4dkj OP2@B.DT6 OG1@A.THR287 2.72 po4:sidechain 3 4dkj OP1@B.DG7 ND2@A.ASN227 3.31 po4:sidechain 4 4dkj OP1@B.DG7 N@A.THR317 2.75 po4:backbone 5 4dkj OP1@B.DG7 OG1@A.THR317 3.19 po4:sidechain 6 4dkj OP2@B.DG7 ND2@A.ASN324 3.06 po4:sidechain 7 4dkj OP1@B.C37/8 NH1@A.ARG230 3.06 po4:sidechain:salt-bridge 8 4dkj OP1@B.C37/8 NH2@A.ARG230 3.36 po4:sidechain:salt-bridge 9 4dkj OP2@B.C37/8 OG@A.SER139 2.50 po4:sidechain 10 4dkj O3'@B.DG7 OG@A.SER139 3.59 po4:sidechain 11 4dkj O5'@B.C37/8 NH2@A.ARG230 3.20 po4:sidechain 12 4dkj OP2@B.DG9 N@A.SER321 2.93 po4:backbone 13 4dkj OP2@B.DG9 OG@A.SER321 2.81 po4:sidechain 14 4dkj O3'@B.C37/8 N@A.ALA320 3.24 po4:backbone 15 4dkj OP2@C.DC4 ND2@A.ASN366 3.19 po4:sidechain 16 4dkj O5'@C.DC4 ND2@A.ASN366 3.38 po4:sidechain 17 4dkj OP2@C.DG8 OG1@A.THR301 2.77 po4:sidechain 18 4dkj O3'@C.DA10 NE2.A@A.GLN144 2.70 po4:sidechain 19 4dkj OP2@C.DG12 N.A@A.HIS192 3.00 po4:backbone **************************************************************************** List of 3 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 4dkj O4'@B.C37/8 NH2@A.ARG230 3.01 sugar:sidechain 2 4dkj O4'@C.DA10 NE2.A@A.GLN144 3.18 sugar:sidechain 3 4dkj O2'@A.SAH501 OE2@A.GLU45 2.76 sugar:sidechain **************************************************************************** List of 30 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 4dkj O6@B.DG7 ND2@A.ASN303 2.75 base:sidechain 2 4dkj N2@B.DG7 O@A.VAL140 2.82 base:backbone 3 4dkj O2@B.C37/8 NH1@A.ARG228 3.03 base:sidechain 4 4dkj O2@B.C37/8 NE@A.ARG230 2.73 base:sidechain 5 4dkj O2@B.C37/8 NH2@A.ARG230 2.95 base:sidechain 6 4dkj N3@B.C37/8 OE2@A.GLU184 2.85 base:sidechain 7 4dkj N4@B.C37/8 O@A.PHE133 2.88 base:backbone 8 4dkj N4@B.C37/8 OE1@A.GLU184 2.73 base:sidechain 9 4dkj O6@B.DG9 N@A.ALA323 2.87 base:backbone 10 4dkj N4@B.DC10 OG@A.SER321 3.86 base:sidechain 11 4dkj N7@C.DA5 NH1@A.ARG326 2.99 base:sidechain 12 4dkj O6@C.DG6 NH2@A.ARG326 3.08 base:sidechain 13 4dkj N4@C.5CM7 OE1@A.GLU305 2.79 base:sidechain 14 4dkj N7@C.DG8 N@A.ASN303 2.97 base:backbone 15 4dkj O6@C.DG8 N@A.SER304 2.95 base:backbone 16 4dkj O6@C.DG8 OG@A.SER304 2.76 base:sidechain 17 4dkj N1@C.DG8 OE1@A.GLN141 2.85 base:sidechain 18 4dkj N2@C.DG8 O@A.GLN141 3.03 base:backbone 19 4dkj N2@C.DG8 OE1@A.GLN141 2.99 base:sidechain 20 4dkj N@A.SAH501 OE1.A@A.GLN23 2.77 base:sidechain 21 4dkj N@A.SAH501 OG@A.SER132 2.70 base:sidechain 22 4dkj O@A.SAH501 O@A.ALA18 3.34 base:backbone 23 4dkj O@A.SAH501 N@A.SER22 3.00 base:backbone 24 4dkj O@A.SAH501 OG@A.SER22 2.76 base:sidechain 25 4dkj O@A.SAH501 OG@A.SER375 3.06 base:sidechain 26 4dkj OXT@A.SAH501 N@A.ILE20 3.06 base:backbone 27 4dkj OXT@A.SAH501 OG@A.SER375 3.11 base:sidechain 28 4dkj N7@A.SAH501 NH2.A@A.ARG154 3.28 base:sidechain 29 4dkj N6@A.SAH501 OD1@A.ASP113 3.17 base:sidechain 30 4dkj N1@A.SAH501 N@A.ILE114 3.10 base:backbone **************************************************************************** List of 7 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 4dkj G-asn B.DG7 A.ASN303 1.52 46 2 4dkj C-glu B.C37/8 A.GLU184 0.52 11 3 4dkj C-arg B.C37/8 A.ARG228 1.45 8 4 4dkj C-arg B.C37/8 A.ARG230 0.32 50 5 4dkj C-glu C.5CM7 A.GLU305 1.22 42 6 4dkj G-gln C.DG8 A.GLN141 0.69 41 7 4dkj A-arg A.SAH501 A.ARG154 0.89 4 **************************************************************************** List of 6 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 4dkj G-gln B.DG7 A.GLN141 3.46 26 2 4dkj G-gln B.DG9 A.GLN141 4.43 50 3 4dkj G-phe B.DG9 A.PHE302 3.07 7 4 4dkj C-phe C.5CM7 A.PHE302 3.41 3 5 4dkj G-phe C.DG8 A.PHE302 3.44 15 6 4dkj A-trp A.SAH501 A.TRP46 3.92 22 **************************************************************************** List of 2 interface stacks with 3+ planar moieties Note: an interface stack is an ordered list of three and more nucleobases and planar moieties of amino acids, assembled together via stacking interactions (nucleobases within to a stem are excluded by default). 1 size=3 GQG B.DG7,A.GLN141,B.DG9 2 size=4 CFGC C.5CM7,A.PHE302,C.DG8,C.DC9 **************************************************************************** List of 3 additional files 1 -- 4dkj-baseAA-pairs.pdb 2 -- 4dkj-baseAA-stacks.pdb 3 -- 4dkj-pairs.pdb