**************************************************************************** File name: 5tbb.pdb no. of peptide chains: 1 [A=296] no. of DNA/RNA chains: 3 [D=5,P=11,T=16] no. of amino acids: 296 no. of nucleotides: 32 no. of atoms: 3076 no. of waters: 35 no. of metals: 5 [Na=4,Mn=1] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 43X-c 1 P.43X101 **************************************************************************** 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=5 strand-1 5'-GTCGG-3' bp-type ||||| strand-2 3'-CAGCC-5' helix-form BBBB 1 D.DG1 T.DC5 G-C WC 19-XIX cWW cW-W 2 D.DT2 T.DA4 T-A WC 20-XX cWW cW-W 3 D.DC3 T.DG3 C-G WC 19-XIX cWW cW-W 4 D.DG4 T.DC2 G-C WC 19-XIX cWW cW-W 5 D.DG5 T.DC1 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[0] bps=11 strand-1 5'-GCTGATGCGCc-3' bp-type ||||||||||| strand-2 3'-CGACTACGCGG-5' helix-form BBBBBBBBBx 1 P.DG1 T.DC16 G-C WC 19-XIX cWW cW-W 2 P.DC2 T.DG15 C-G WC 19-XIX cWW cW-W 3 P.DT3 T.DA14 T-A WC 20-XX cWW cW-W 4 P.DG4 T.DC13 G-C WC 19-XIX cWW cW-W 5 P.DA5 T.DT12 A-T WC 20-XX cWW cW-W 6 P.DT6 T.DA11 T-A WC 20-XX cWW cW-W 7 P.DG7 T.DC10 G-C WC 19-XIX cWW cW-W 8 P.DC8 T.DG9 C-G WC 19-XIX cWW cW-W 9 P.DG9 T.DC8 G-C WC 19-XIX cWW cW-W 10 P.DC10 T.DG7 C-G WC 19-XIX cWW cW-W 11 P.43X101 T.DG6 c-G WC 19-XIX cWW cW-W **************************************************************************** List of 10 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5tbb G-his D.DG1 A.HIS34 -4.78 -101.72 -1.49 2.11 -4.02 -72.58 -27.24 -71.91 2 5tbb G-lys D.DG1 A.LYS35 -5.95 -133.15 -3.51 0.31 -4.79 -4.27 2.63 -133.10 3 5tbb G-ala D.DG1 A.ALA38 -7.39 -144.90 -3.06 -5.32 -4.12 20.36 47.87 -140.80 4 5tbb G-lys P.DG9 A.LYS234 -12.64 179.51 -1.92 12.45 -1.11 -12.47 -24.49 179.50 5 5tbb C-his T.DC5 A.HIS34 5.24 -95.57 -3.29 3.55 2.03 69.03 53.78 -43.07 6 5tbb G-tyr T.DG6 A.TYR271 -12.52 124.16 -11.86 2.27 -3.30 46.01 -25.69 117.00 7 5tbb G-lys T.DG9 A.LYS234 -11.55 -43.27 -10.44 4.27 -2.49 24.58 -0.84 -35.88 8 5tbb C-asp P.43X101 A.ASP190 -16.63 -117.78 -12.80 8.32 -6.61 54.93 -27.27 -106.17 9 5tbb C-asp P.43X101 A.ASP192 -15.59 -85.24 -12.13 9.65 1.65 -6.54 -56.72 -66.20 10 5tbb C-tyr P.43X101 A.TYR271 12.70 77.82 -2.45 12.19 2.60 17.41 -31.93 70.03 **************************************************************************** List of 8 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5tbb GC-his D.DG1 T.DC5 A.HIS34 -5.01 -107.75 -1.33 1.94 -4.43 -79.30 -30.62 -73.80 2 5tbb GC-lys D.DG1 T.DC5 A.LYS35 -6.07 -134.21 -3.12 0.12 -5.21 -7.82 -4.08 -134.06 3 5tbb GC-ala D.DG1 T.DC5 A.ALA38 -7.48 -144.43 -2.67 -5.52 -4.29 17.52 40.79 -141.47 4 5tbb GC-lys P.DG9 T.DC8 A.LYS234 -12.69 -178.26 2.13 -12.37 -1.83 17.77 19.64 -178.21 5 5tbb GC-asp T.DG6 P.43X101 A.ASP190 16.56 -90.29 9.14 -12.69 5.45 -24.28 60.44 -66.37 6 5tbb GC-asp T.DG6 P.43X101 A.ASP192 15.53 -115.84 9.92 -11.67 -2.55 -53.96 -0.70 -106.83 7 5tbb GC-tyr T.DG6 P.43X101 A.TYR271 -12.61 118.98 -12.03 2.35 -2.96 38.86 -21.71 113.47 8 5tbb GC-lys T.DG9 P.DC8 A.LYS234 -11.58 -44.49 -10.43 4.21 -2.76 27.94 -4.14 -34.74 **************************************************************************** List of 16 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 5tbb OP1@D.DT2 N@A.GLY66 2.84 po4:backbone 2 5tbb OP1@D.DT2 N@A.ILE69 3.01 po4:backbone 3 5tbb OP2@D.DT2 N@A.LYS68 3.00 po4:backbone 4 5tbb OP1@D.DC3 N@A.GLY64 2.86 po4:backbone 5 5tbb OP1@P.DC8 N@A.GLY107 3.06 po4:backbone 6 5tbb OP1@P.DC8 N@A.ALA110 2.83 po4:backbone 7 5tbb OP2@P.DC8 N@A.SER109 3.14 po4:backbone 8 5tbb OP1@P.DG9 N@A.GLY105 2.75 po4:backbone 9 5tbb OP1@P.DC10 NE@A.ARG254 3.15 po4:sidechain:salt-bridge 10 5tbb OP1@P.DC10 NH2@A.ARG254 2.79 po4:sidechain:salt-bridge 11 5tbb O3'@T.DC8 OH@A.TYR296 3.86 po4:sidechain 12 5tbb OP1@T.DC10 N@A.GLU232 3.02 po4:backbone 13 5tbb OP1@T.DC10 N@A.THR233 3.05 po4:backbone 14 5tbb OP1@T.DC10 N@A.LYS234 3.13 po4:backbone 15 5tbb OP1@T.DA11 N@A.LYS230 3.11 po4:backbone 16 5tbb O3'@T.DC10 N@A.LYS230 3.38 po4:backbone **************************************************************************** List of 2 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 5tbb N3@T.DG9 NZ@A.LYS234 3.37 base:sidechain 2 5tbb O2@P.43X101 OH@A.TYR271 3.09 base:sidechain **************************************************************************** List of 1 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 5tbb C-his T.DC5 A.HIS34 3.31 4 **************************************************************************** List of 2 additional files 1 -- 5tbb-baseAA-stacks.pdb 2 -- 5tbb-pairs.pdb