**************************************************************************** File name: 8tdv.pdb no. of peptide chains: 4 [A=439,B=417,E=445,F=439] no. of DNA/RNA chains: 2 [J=6,K=7] no. of amino acids: 1740 no. of nucleotides: 13 no. of atoms: 10957 no. of waters: 0 no. of metals: 2 [Fe=2] **************************************************************************** List of 30 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 8tdv C-lys J.C7 B.LYS377 7.29 89.61 -7.27 0.50 0.03 -81.12 19.67 36.10 2 8tdv C-val J.C7 B.VAL378 8.25 -134.22 -5.61 -4.94 -3.49 -78.91 41.92 -113.68 3 8tdv C-lys J.C7 B.LYS455 4.94 77.95 0.65 3.94 2.90 74.58 19.92 11.73 4 8tdv C-tyr J.C7 B.TYR456 2.86 -68.63 2.04 -1.41 1.44 3.79 -68.53 -0.43 5 8tdv G-lys J.G8 A.LYS116 -8.47 154.22 -0.69 7.53 -3.82 -33.78 -25.08 152.35 6 8tdv G-ile J.G8 A.ILE118 -8.26 140.18 3.63 3.63 -6.47 -6.63 -40.53 137.35 7 8tdv G-ile J.G8 A.ILE136 -6.09 126.96 -3.31 -3.34 -3.87 -34.97 -28.22 122.21 8 8tdv G-asp J.G8 A.ASP137 -5.22 80.71 1.32 -3.96 -3.13 -79.24 15.32 0.72 9 8tdv G-arg J.G8 A.ARG145 10.58 -179.48 -1.59 9.57 4.21 -29.74 17.19 -179.46 10 8tdv G-phe J.G8 A.PHE165 -10.12 -93.57 8.68 4.76 -2.13 62.71 50.48 -52.43 11 8tdv G-tyr J.G8 B.TYR155 8.01 -100.09 3.24 6.54 3.29 12.65 -80.23 -64.45 12 8tdv G-val J.G8 B.VAL156 7.94 -97.37 -3.54 7.02 -1.07 76.23 9.23 -65.23 13 8tdv G-pro J.G8 B.PRO158 -9.21 90.70 7.94 2.22 -4.10 32.34 -43.28 75.84 14 8tdv G-arg J.G8 B.ARG451 6.28 -136.60 2.25 -5.80 0.79 -88.21 -11.77 -117.56 15 8tdv G-lys J.G9 A.LYS116 6.98 -141.71 1.42 -3.62 5.80 -10.38 -38.25 -139.19 16 8tdv C-arg J.C10 B.ARG371 -7.19 125.35 -6.93 -0.00 -1.90 -62.67 13.23 114.44 17 8tdv C-thr K.C6 B.THR114 -7.23 54.78 -6.64 2.83 -0.27 -23.11 -11.89 48.65 18 8tdv C-val K.C7 A.VAL378 -10.61 -89.90 1.56 5.34 -9.04 89.31 6.75 -8.68 19 8tdv C-tyr K.C7 A.TYR456 -5.81 74.50 4.69 -0.82 -3.34 -16.25 -17.28 71.15 20 8tdv C-val K.C7 A.VAL457 6.21 94.12 4.73 -2.85 -2.84 -59.91 -35.71 67.74 21 8tdv G-tyr K.G8 A.TYR155 8.16 -98.02 2.76 6.61 3.90 4.37 -81.99 -59.13 22 8tdv G-val K.G8 A.VAL156 8.31 -92.66 -4.13 7.07 -1.42 71.98 3.50 -62.74 23 8tdv G-arg K.G8 A.ARG451 6.42 -132.35 2.45 -5.77 1.37 -85.07 -26.83 -110.86 24 8tdv G-ile K.G8 B.ILE118 -8.59 145.93 3.97 4.80 -5.92 -16.24 -34.99 143.84 25 8tdv G-val K.G8 B.VAL133 -6.29 161.85 -6.07 0.92 -1.35 -0.81 -77.18 156.72 26 8tdv G-ile K.G8 B.ILE136 -5.74 126.65 -2.49 -3.38 -3.92 -34.52 -22.97 122.63 27 8tdv G-asp K.G8 B.ASP137 4.51 87.59 1.48 -3.41 -2.55 -86.31 13.67 6.79 28 8tdv G-gln K.G8 B.GLN142 7.87 177.54 -0.75 -6.09 4.93 47.72 -28.38 177.22 29 8tdv G-arg K.G8 B.ARG145 10.84 -176.70 -3.22 9.02 5.08 -38.28 17.01 -176.47 30 8tdv G-phe K.G8 B.PHE165 -10.18 -90.69 8.17 5.53 -2.51 56.36 52.55 -52.11 **************************************************************************** List of 9 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 8tdv OP1@J.G8 NZ@A.LYS116 2.45 po4:sidechain:salt-bridge 2 8tdv OP2@J.G8 NH1@B.ARG451 2.78 po4:sidechain:salt-bridge 3 8tdv OP2@J.G9 NE2@B.HIS376 3.56 po4:sidechain:salt-bridge 4 8tdv OP1@J.C10 ND2@A.ASN119 3.88 po4:sidechain 5 8tdv OP1@J.C10 NE2@A.HIS125 3.63 po4:sidechain:salt-bridge 6 8tdv OP2@K.G8 NE@A.ARG451 3.56 po4:sidechain:salt-bridge 7 8tdv OP1@K.A9 NE2@A.HIS376 3.69 po4:sidechain:salt-bridge 8 8tdv OP1@K.C10 NE2@B.HIS125 3.40 po4:sidechain:salt-bridge 9 8tdv OP2@K.C11 NH2@A.ARG371 3.91 po4:sidechain:salt-bridge **************************************************************************** List of 2 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 8tdv O2'@J.G8 O@A.VAL117 2.11 sugar:backbone 2 8tdv O2'@K.G8 O@B.VAL117 2.52 sugar:backbone **************************************************************************** List of 11 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 8tdv O6@J.G8 NH2@A.ARG145 3.46 base:sidechain 2 8tdv N1@J.G8 OD1@A.ASP137 3.28 base:sidechain 3 8tdv N2@J.G8 OD2@A.ASP137 3.43 base:sidechain 4 8tdv N3@J.G8 NH1@B.ARG451 3.05 base:sidechain 5 8tdv O2@J.C10 NH2@B.ARG371 2.96 base:sidechain 6 8tdv N3@J.C10 NH2@B.ARG371 2.93 base:sidechain 7 8tdv N4@K.C7 O@A.TYR456 2.21 base:backbone 8 8tdv N7@K.G8 NH2@B.ARG145 3.05 base:sidechain 9 8tdv O6@K.G8 NE2@B.GLN142 2.92 base:sidechain 10 8tdv N1@K.G8 OD1@B.ASP137 2.66 base:sidechain 11 8tdv N2@K.G8 OD2@B.ASP137 2.98 base:sidechain **************************************************************************** List of 6 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 8tdv G-asp J.G8 A.ASP137 0.19 12 2 8tdv G-arg J.G8 A.ARG145 0.83 34 3 8tdv C-arg J.C10 B.ARG371 1.46 7 4 8tdv G-asp K.G8 B.ASP137 0.30 20 5 8tdv G-gln K.G8 B.GLN142 1.35 13 6 8tdv G-arg K.G8 B.ARG145 1.29 31 **************************************************************************** List of 2 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 8tdv G-arg J.G8 B.ARG451 3.29 50 2 8tdv G-arg K.G8 A.ARG451 4.06 14 **************************************************************************** List of 3 additional files 1 -- 8tdv-baseAA-pairs.pdb 2 -- 8tdv-baseAA-stacks.pdb 3 -- 8tdv-pairs.pdb