**************************************************************************** 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/5ke8.pdb -o=5ke8.out --type=base File name: 5ke8.pdb no. of peptide chains: 1 [A=85] no. of DNA/RNA chains: 2 [B=10,C=10] no. of amino acids: 85 no. of nucleotides: 20 no. of atoms: 2008 no. of waters: 9 no. of metals: 3 [Zn=3] **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 5CM-c 2 B.5CM5,C.5CM5 **************************************************************************** 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=10 strand-1 5'-GAGGcGTGGC-3' bp-type |||||||||| strand-2 3'-CTCCGcACCG-5' helix-form BBB.BBBBB 1 B.DG1 C.DC10 G-C WC 19-XIX cWW cW-W 2 B.DA2 C.DT9 A-T WC 20-XX cWW cW-W 3 B.DG3 C.DC8 G-C WC 19-XIX cWW cW-W 4 B.DG4 C.DC7 G-C WC 19-XIX cWW cW-W 5 B.5CM5 C.DG6 c-G WC 19-XIX cWW cW-W 6 B.DG6 C.5CM5 G-c WC 19-XIX cWW cW-W 7 B.DT7 C.DA4 T-A WC 20-XX cWW cW-W 8 B.DG8 C.DC3 G-C WC 19-XIX cWW cW-W 9 B.DG9 C.DC2 G-C WC 19-XIX cWW cW-W 10 B.DC10 C.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 33 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5ke8 G-his B.DG1 A.HIS474 10.45 160.73 5.16 -2.23 8.81 12.53 74.23 155.59 2 5ke8 A-arg B.DA2 A.ARG471 11.73 -146.88 -4.74 9.87 4.21 33.57 -39.94 -142.99 3 5ke8 A-his B.DA2 A.HIS474 9.74 131.02 6.50 -3.07 6.57 23.86 68.83 117.98 4 5ke8 G-arg B.DG3 A.ARG449 11.73 -126.85 -6.98 8.51 4.05 -35.15 52.62 -116.59 5 5ke8 G-arg B.DG3 A.ARG471 11.11 -176.90 -2.98 10.64 1.20 21.65 -51.18 -176.49 6 5ke8 G-arg B.DG4 A.ARG449 11.15 -156.04 -3.04 10.69 0.90 -13.05 59.90 -152.07 7 5ke8 G-arg B.DG4 A.ARG471 -10.62 148.23 1.69 -10.42 -1.12 -7.50 54.55 144.04 8 5ke8 C-arg B.5CM5 A.ARG443 11.39 -151.36 -4.06 8.74 6.07 6.86 -49.15 -148.37 9 5ke8 C-asp B.5CM5 A.ASP445 8.72 -156.31 -1.82 7.27 4.47 -21.33 32.07 -154.88 10 5ke8 C-pro B.5CM5 A.PRO446 -8.26 131.06 5.34 -3.61 5.17 20.34 82.06 111.92 11 5ke8 C-arg B.5CM5 A.ARG449 -10.03 176.82 -0.73 -9.80 -2.00 -6.37 -54.73 176.41 12 5ke8 G-arg B.DG6 A.ARG443 11.39 176.65 2.66 -10.35 3.94 -5.39 48.91 176.32 13 5ke8 G-asp B.DG6 A.ASP445 9.08 179.46 -1.31 -8.71 2.19 0.68 -36.92 179.43 14 5ke8 T-his B.DT7 A.HIS416 9.22 149.39 4.12 -2.74 7.78 13.12 72.83 141.40 15 5ke8 T-arg B.DT7 A.ARG443 -10.11 145.71 1.73 -9.92 0.92 10.28 47.23 142.30 16 5ke8 G-lys B.DG8 A.LYS413 9.92 -141.65 -2.28 8.97 3.57 22.97 -52.94 -135.95 17 5ke8 G-his B.DG8 A.HIS416 8.71 122.61 5.65 -3.77 5.46 26.44 70.40 105.39 18 5ke8 G-lys B.DG9 A.LYS413 10.22 -170.74 -0.75 10.18 0.53 8.62 -58.86 -169.33 19 5ke8 C-lys B.DC10 A.LYS413 -9.50 155.51 -0.37 -9.27 -2.06 9.75 57.65 151.86 20 5ke8 G-lys C.DG1 A.LYS413 9.50 -155.34 -0.50 9.40 1.35 4.08 -60.29 -151.38 21 5ke8 G-ser C.DG1 A.SER415 8.67 -139.61 -5.27 6.85 0.73 -12.99 33.25 -137.47 22 5ke8 C-asp C.DC3 A.ASP445 8.64 -127.70 -6.32 4.90 3.26 -30.35 26.30 -124.03 23 5ke8 A-arg C.DA4 A.ARG443 -10.24 -144.75 1.78 9.83 -2.26 -3.67 -50.52 -140.86 24 5ke8 A-asp C.DA4 A.ASP445 7.98 -155.05 -3.68 7.08 0.30 -20.18 33.29 -153.51 25 5ke8 C-asp C.5CM5 A.ASP445 -8.28 168.06 0.51 -7.53 -3.40 11.94 -30.92 167.54 26 5ke8 G-arg C.DG6 A.ARG449 -10.13 168.31 -0.69 -10.05 1.05 11.34 -53.76 166.82 27 5ke8 G-ser C.DG6 A.SER472 9.66 -167.67 -6.60 5.73 -4.11 57.80 22.61 -165.60 28 5ke8 G-asp C.DG6 A.ASP473 8.37 -128.11 -5.63 5.32 3.17 -31.98 37.81 -122.40 29 5ke8 C-arg C.DC7 A.ARG449 -10.57 146.79 -3.46 -9.89 -1.43 -2.43 -48.03 143.53 30 5ke8 C-arg C.DC7 A.ARG471 -10.13 -144.20 1.49 10.02 -0.13 -24.69 -56.48 -138.06 31 5ke8 C-asp C.DC7 A.ASP473 -8.50 -151.55 -3.80 7.60 0.08 -25.02 36.90 -149.20 32 5ke8 C-arg C.DC8 A.ARG471 -11.05 -174.01 1.86 10.63 -2.36 -28.09 -42.75 -173.36 33 5ke8 C-asp C.DC8 A.ASP473 -9.55 -176.23 -1.16 8.97 -3.05 -3.33 47.39 -175.89 **************************************************************************** List of 26 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5ke8 AT-arg B.DA2 C.DT9 A.ARG471 11.66 -148.53 -4.53 9.92 4.14 34.06 -41.15 -144.66 2 5ke8 AT-arg C.DA4 B.DT7 A.ARG443 -10.18 -145.19 1.75 9.90 -1.58 3.35 -49.06 -141.59 3 5ke8 AT-asp C.DA4 B.DT7 A.ASP445 7.92 -150.70 -3.87 6.86 0.88 -14.78 34.86 -148.98 4 5ke8 AT-his B.DA2 C.DT9 A.HIS474 9.74 129.04 6.43 -3.25 6.56 23.67 68.16 115.68 5 5ke8 AT-his C.DA4 B.DT7 A.HIS416 -9.26 -147.45 4.16 2.25 -7.96 6.20 -74.55 -138.68 6 5ke8 GC-arg B.DG3 C.DC8 A.ARG449 11.64 -124.80 -6.79 8.14 4.80 -28.45 54.61 -114.73 7 5ke8 GC-arg B.DG3 C.DC8 A.ARG471 11.08 178.57 2.43 -10.66 1.80 -24.83 46.94 178.40 8 5ke8 GC-arg B.DG4 C.DC7 A.ARG449 10.86 -151.38 -3.26 10.29 1.20 -7.77 53.95 -147.72 9 5ke8 GC-arg B.DG4 C.DC7 A.ARG471 10.37 146.16 1.59 -10.24 -0.48 -16.07 55.73 141.12 10 5ke8 GC-arg C.DG6 B.5CM5 A.ARG443 -11.53 148.78 -4.64 -8.36 -6.44 13.95 51.26 144.98 11 5ke8 GC-arg C.DG6 B.5CM5 A.ARG449 10.08 175.74 0.03 -9.96 1.53 8.83 -54.11 175.20 12 5ke8 GC-arg B.DG6 C.5CM5 A.ARG443 10.99 177.22 2.90 -9.54 4.62 -14.54 51.53 176.88 13 5ke8 GC-asp B.DG3 C.DC8 A.ASP473 9.51 176.35 -0.84 -9.10 2.61 1.63 -42.53 176.08 14 5ke8 GC-asp B.DG4 C.DC7 A.ASP473 -8.63 146.97 -3.79 -7.72 -0.61 -17.29 -37.75 144.60 15 5ke8 GC-asp C.DG6 B.5CM5 A.ASP445 -8.81 149.81 -2.41 -7.03 -4.73 -17.79 -28.74 148.42 16 5ke8 GC-asp C.DG6 B.5CM5 A.ASP473 8.49 -121.16 -6.10 4.92 3.26 -28.74 33.87 -115.91 17 5ke8 GC-asp B.DG6 C.5CM5 A.ASP445 8.68 -174.31 0.89 8.15 2.84 5.54 33.73 -174.04 18 5ke8 GC-asp B.DG8 C.DC3 A.ASP445 -8.63 124.00 -6.20 -4.76 -3.66 -27.40 -27.40 120.31 19 5ke8 GC-his B.DG1 C.DC10 A.HIS474 10.29 159.06 5.09 -1.63 8.79 9.00 74.66 153.48 20 5ke8 GC-his B.DG8 C.DC3 A.HIS416 8.45 122.13 5.55 -3.36 5.41 21.75 72.11 104.65 21 5ke8 GC-lys B.DG8 C.DC3 A.LYS413 9.73 -139.96 -2.57 8.65 3.63 24.84 -56.39 -133.02 22 5ke8 GC-lys B.DG9 C.DC2 A.LYS413 10.07 -172.55 -0.57 10.01 0.90 11.48 -58.53 -171.42 23 5ke8 GC-lys C.DG1 B.DC10 A.LYS413 9.50 -155.42 -0.44 9.34 1.71 6.93 -59.01 -151.63 24 5ke8 GC-pro C.DG6 B.5CM5 A.PRO446 -8.37 -130.75 5.47 3.07 -5.55 12.12 -80.47 -113.33 25 5ke8 GC-ser C.DG6 B.5CM5 A.SER472 9.77 -162.18 -7.02 5.55 -3.90 62.14 25.34 -158.58 26 5ke8 GC-ser C.DG1 B.DC10 A.SER415 8.67 -137.61 -5.39 6.71 1.08 -10.84 34.00 -135.36 **************************************************************************** List of 6 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 5ke8 OP1@B.DG3 ND1@A.HIS450 2.42 po4:sidechain:salt-bridge 2 5ke8 OP1@B.DG6 OH@A.TYR411 2.96 po4:sidechain 3 5ke8 OP2@C.DC2 OH@A.TYR430 2.98 po4:sidechain 4 5ke8 OP2@C.DC2 OG@A.SER444 2.71 po4:sidechain 5 5ke8 OP2@C.DA4 NH1@A.ARG452 3.69 po4:sidechain:salt-bridge 6 5ke8 OP2@C.5CM5 OG@A.SER472 3.12 po4:sidechain **************************************************************************** List of 12 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 5ke8 N7@B.DA2 NE2@A.HIS474 3.18 base:sidechain 2 5ke8 N7@B.DG3 NH2@A.ARG471 3.10 base:sidechain 3 5ke8 O6@B.DG3 NH1@A.ARG471 2.85 base:sidechain 4 5ke8 N7@B.DG4 NH1@A.ARG449 2.79 base:sidechain 5 5ke8 O6@B.DG4 NH2@A.ARG449 2.88 base:sidechain 6 5ke8 N7@B.DG6 NH2@A.ARG443 3.25 base:sidechain 7 5ke8 O6@B.DG6 NH1@A.ARG443 2.96 base:sidechain 8 5ke8 N7@B.DG8 NE2@A.HIS416 2.90 base:sidechain 9 5ke8 N7@B.DG9 NZ@A.LYS413 3.06 base:sidechain 10 5ke8 N6@C.DA4 NH1@A.ARG443 3.20 base:sidechain 11 5ke8 N4@C.5CM5 OD2@A.ASP445 3.96 base:sidechain 12 5ke8 N4@C.DC7 OD2@A.ASP473 2.96 base:sidechain **************************************************************************** List of 8 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 5ke8 A-his B.DA2 A.HIS474 0.16 11 2 5ke8 G-arg B.DG3 A.ARG471 0.37 29 3 5ke8 G-arg B.DG4 A.ARG449 0.15 5 4 5ke8 G-arg B.DG6 A.ARG443 0.53 19 5 5ke8 G-his B.DG8 A.HIS416 0.07 16 6 5ke8 A-arg C.DA4 A.ARG443 1.29 28 7 5ke8 C-asp C.5CM5 A.ASP445 0.53 61 8 5ke8 C-asp C.DC7 A.ASP473 1.02 26 **************************************************************************** List of 4 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 5ke8 A-arg B.DA2 A.ARG471 3.25 26 2 5ke8 G-arg B.DG3 A.ARG449 3.43 7 3 5ke8 C-arg B.5CM5 A.ARG443 3.65 13 4 5ke8 T-his B.DT7 A.HIS416 3.34 9 **************************************************************************** List of 3 additional files 1 -- 5ke8-baseAA-pairs.pdb 2 -- 5ke8-baseAA-stacks.pdb 3 -- 5ke8-pairs.pdb