**************************************************************************** File name: 7kti.pdb no. of peptide chains: 1 [A=326] no. of DNA/RNA chains: 3 [D=4,P=5,T=9] no. of amino acids: 326 no. of nucleotides: 18 no. of atoms: 3356 no. of waters: 402 no. of metals: 4 [Na=1,Mn=3] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 8OG-g 1 P.8OG5 **************************************************************************** List of 2 helices Note: A helix is defined by base-stacking interactions, regardless of pair 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=4 strand-1 5'-CGGC-3' bp-type |||| strand-2 3'-GCCG-5' helix-form BBB 1 T.DC1 D.DG4 C-G WC 19-XIX cWW cW-W 2 T.DG2 D.DC3 G-C WC 19-XIX cWW cW-W 3 T.DG3 D.DC2 G-C WC 19-XIX cWW cW-W 4 T.DC4 D.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[0] bps=5 strand-1 5'-CTACG-3' bp-type ||||| strand-2 3'-gATGC-5' helix-form .... 1 T.DC5 P.8OG5 C-g WC 19-XIX cWW cW-W 2 T.DT6 P.DA4 T-A WC 20-XX cWW cW-W 3 T.DA7 P.DT3 A-T WC 20-XX cWW cW-W 4 T.DC8 P.DG2 C-G WC 19-XIX cWW cW-W 5 T.DG9 P.DC1 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 19 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 7kti C-gly T.DC4 A.GLY174 3.69 -74.91 -2.10 2.06 2.23 54.68 30.88 -43.11 2 7kti C-leu T.DC4 A.LEU177 7.78 -114.97 -2.44 -5.01 5.43 -25.00 -47.29 -105.98 3 7kti C-arg T.DC4 A.ARG181 12.03 -129.98 -3.40 -10.94 3.68 -36.11 -74.45 -111.43 4 7kti C-lys T.DC5 A.LYS438 -6.27 176.71 -3.50 1.24 -5.05 -26.03 -44.67 176.35 5 7kti C-arg T.DC5 A.ARG442 -6.71 -177.55 -3.40 -2.15 -5.38 0.01 24.55 -177.49 6 7kti C-arg T.DC5 A.ARG445 -10.08 176.14 4.97 8.63 -1.54 -63.30 -54.50 174.82 7 7kti T-arg T.DT6 A.ARG445 -11.71 165.61 5.29 9.46 -4.44 -70.25 -32.90 161.51 8 7kti A-arg T.DA7 A.ARG387 11.12 43.90 -11.06 -0.53 1.06 30.94 31.05 2.44 9 7kti G-phe P.DG2 A.PHE389 11.43 -154.20 -3.59 -10.81 0.96 -18.85 45.75 -151.54 10 7kti T-phe P.DT3 A.PHE389 12.14 172.74 6.98 9.49 -2.92 4.62 -45.13 172.13 11 7kti A-arg P.DA4 A.ARG387 -12.56 150.45 3.80 11.13 -4.40 -38.78 -24.64 147.84 12 7kti G-lys P.8OG5 A.LYS438 6.25 20.17 -1.49 4.93 3.54 11.33 16.51 2.42 13 7kti G-gln P.8OG5 A.GLN441 7.44 -99.33 -0.67 -1.36 7.28 -6.07 -87.19 -52.90 14 7kti G-arg P.8OG5 A.ARG445 9.84 -56.79 -8.77 -3.89 2.19 22.69 51.63 -6.91 15 7kti G-gly D.DG1 A.GLY174 -3.30 -144.63 1.72 -1.53 -2.37 38.04 66.15 -134.55 16 7kti G-arg D.DG1 A.ARG175 -5.62 -133.27 -4.01 0.65 -3.88 -14.67 -12.68 -132.55 17 7kti G-thr D.DG1 A.THR178 -7.25 -134.31 -3.99 -5.16 -3.15 24.30 37.05 -130.44 18 7kti G-arg D.DG1 A.ARG181 -11.68 -94.25 -10.80 -3.02 -3.29 -61.42 -31.95 -68.46 19 7kti C-thr D.DC2 A.THR178 -8.89 -159.38 -4.21 -5.03 -6.00 26.14 29.99 -158.06 **************************************************************************** List of 15 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 7kti GC-thr T.DG3 D.DC2 A.THR178 8.76 -47.53 -4.69 -4.10 6.16 29.19 30.53 -22.31 2 7kti AT-arg T.DA7 P.DT3 A.ARG387 11.11 42.40 -11.08 -0.74 0.44 34.38 24.20 5.62 3 7kti AT-phe T.DA7 P.DT3 A.PHE389 12.12 41.89 -9.40 -6.74 3.64 41.55 2.22 4.93 4 7kti GC-phe P.DG2 T.DC8 A.PHE389 11.57 -152.73 -3.53 -11.01 0.30 -15.00 38.70 -150.80 5 7kti AT-arg P.DA4 T.DT6 A.ARG387 -12.51 150.34 3.70 11.24 -4.06 -35.09 -24.95 148.05 6 7kti AT-arg P.DA4 T.DT6 A.ARG445 11.70 75.79 -9.65 -5.09 4.22 32.03 66.75 17.46 7 7kti GC-lys P.8OG5 T.DC5 A.LYS438 6.26 35.39 -1.37 4.28 4.36 27.92 21.56 2.94 8 7kti GC-gln P.8OG5 T.DC5 A.GLN441 7.52 -94.90 0.10 -2.40 7.13 2.55 -74.29 -63.88 9 7kti GC-arg P.8OG5 T.DC5 A.ARG442 6.59 -9.63 -2.32 -2.54 5.63 8.18 -5.09 -0.00 10 7kti GC-arg P.8OG5 T.DC5 A.ARG445 9.96 -69.60 -8.69 -4.43 2.01 38.47 57.98 -1.48 11 7kti GC-gly D.DG1 T.DC4 A.GLY174 -3.49 -143.95 1.89 -1.81 -2.31 34.49 60.40 -135.74 12 7kti GC-arg D.DG1 T.DC4 A.ARG175 -5.75 -134.71 -3.84 0.41 -4.27 -18.87 -17.99 -133.44 13 7kti GC-leu D.DG1 T.DC4 A.LEU177 -7.57 -85.45 -5.02 -2.09 -5.27 -40.90 -22.60 -73.69 14 7kti GC-thr D.DG1 T.DC4 A.THR178 -7.40 -134.05 -3.84 -5.42 -3.26 20.32 31.57 -131.31 15 7kti GC-arg D.DG1 T.DC4 A.ARG181 -11.86 -98.73 -10.87 -3.20 -3.49 -67.92 -34.08 -68.54 **************************************************************************** List of 26 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 7kti OP1@T.DC4 NZ@A.LYS450 2.87 po4:sidechain:salt-bridge 2 7kti O3'@T.DG3 NZ@A.LYS450 3.28 po4:sidechain 3 7kti OP1@T.DC5 NH2@A.ARG442 2.86 po4:sidechain:salt-bridge 4 7kti OP2@T.DC5 NE@A.ARG442 2.96 po4:sidechain:salt-bridge 5 7kti OP1@T.DT6 NE@A.ARG449 2.74 po4:sidechain:salt-bridge 6 7kti OP1@T.DT6 NH2@A.ARG449 3.22 po4:sidechain:salt-bridge 7 7kti O5'@T.DA7 ND2@A.ASN457 3.31 po4:sidechain 8 7kti OP1@T.DC8 NE2@A.HIS459 3.34 po4:sidechain:salt-bridge 9 7kti O3'@T.DA7 NE2@A.HIS459 3.60 po4:sidechain 10 7kti OP1@T.DG9 N@A.GLU386 2.67 po4:backbone 11 7kti OP1@T.DG9 N@A.ARG387 2.98 po4:backbone 12 7kti OP1@P.DG2 N@A.GLY247 2.90 po4:backbone 13 7kti OP1@P.DG2 N@A.THR250 3.06 po4:backbone 14 7kti OP1@P.DG2 OG1@A.THR250 2.69 po4:sidechain 15 7kti OP1@P.DT3 N@A.GLY245 2.87 po4:backbone 16 7kti OP1@P.DA4 NH2@A.ARG416 2.92 po4:sidechain:salt-bridge 17 7kti OP1@P.8OG5 OD1@A.ASP330 3.12 po4:sidechain 18 7kti OP1@P.8OG5 OD1@A.ASP332 3.08 po4:sidechain 19 7kti O3'@P.DA4 OD2@A.ASP418 3.35 po4:sidechain 20 7kti OP1@D.DG1 NE.A@A.ARG175 2.71 po4:sidechain:salt-bridge 21 7kti OP1@D.DG1 NH2.A@A.ARG175 2.77 po4:sidechain:salt-bridge 22 7kti OP1@D.DC2 N@A.GLY206 2.98 po4:backbone 23 7kti OP1@D.DC2 N@A.SER209 2.85 po4:backbone 24 7kti OP1@D.DC2 OG.A@A.SER209 3.12 po4:sidechain 25 7kti OP2@D.DC2 N@A.HIS208 3.13 po4:backbone 26 7kti OP1.A@D.DC3 N@A.HIS204 2.89 po4:backbone **************************************************************************** List of 2 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 7kti O4'@T.DT6 NH1@A.ARG445 3.11 sugar:sidechain 2 7kti O4'@D.DC2 OG1@A.THR178 3.62 sugar:sidechain **************************************************************************** List of 4 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 7kti O2@T.DC5 NH1@A.ARG445 3.10 base:sidechain 2 7kti O2@T.DT6 NH1@A.ARG445 3.17 base:sidechain 3 7kti N3@T.DA7 NH1@A.ARG387 3.21 base:sidechain 4 7kti N3@D.DG1 OG1@A.THR178 2.66 base:sidechain **************************************************************************** List of 3 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 7kti C-arg T.DC5 A.ARG445 1.95 59 2 7kti T-arg T.DT6 A.ARG445 1.32 64 3 7kti A-arg T.DA7 A.ARG387 0.62 32 **************************************************************************** List of 1 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 7kti C-arg T.DC5 A.ARG442 3.59 32 **************************************************************************** List of 3 additional files 1 -- 7kti-baseAA-pairs.pdb 2 -- 7kti-baseAA-stacks.pdb 3 -- 7kti-pairs.pdb