**************************************************************************** File name: 4z31.pdb no. of peptide chains: 2 [A=293,B=295] no. of DNA/RNA chains: 4 [C=14,D=14,E=15,F=15] no. of amino acids: 588 no. of nucleotides: 58 no. of atoms: 5798 no. of waters: 40 no. of metals: 0 **************************************************************************** List of 4 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=6 strand-1 5'-UGUUCU-3' bp-type |||||. strand-2 3'-ACAAGU-5' helix-form AA.A. 1 C.U2 D.A14 U-A WC 20-XX cWW cW-W 2 C.G3 D.C13 G-C WC 19-XIX cWW cW-W 3 C.U4 D.A12 U-A WC 20-XX cWW cW-W 4 C.U5 D.A11 U-A WC 20-XX cWW cW-W 5 C.C6 D.G10 C-G WC 19-XIX cWW cW-W 6 C.U7 D.U9 U-U -- 16-XVI cWW cW-W -------------------------------------------------------------------------- helix#2[0] bps=7 strand-1 5'-UGAACAC-3' bp-type .|||||. strand-2 3'-UCUUGUA-5' helix-form .AAAA. 1 C.U9 D.U7 U-U -- 16-XVI cWW cW-W 2 C.G10 D.C6 G-C WC 19-XIX cWW cW-W 3 C.A11 D.U5 A-U WC 20-XX cWW cW-W 4 C.A12 D.U4 A-U WC 20-XX cWW cW-W 5 C.C13 D.G3 C-G WC 19-XIX cWW cW-W 6 C.A14 D.U2 A-U WC 20-XX cWW cW-W 7 C.C15 D.A1 C-A -- -- cWW cW-W -------------------------------------------------------------------------- helix#3[0] bps=6 strand-1 5'-AUGUUC-3' bp-type .||||| strand-2 3'-CACAAG-5' helix-form .A.A. 1 E.A1 E.C15 A-C -- -- cWW cW-W 2 E.U2 E.A14 U-A WC 20-XX cWW cW-W 3 E.G3 E.C13 G-C WC 19-XIX cWW cW-W 4 E.U4 E.A12 U-A WC 20-XX cWW cW-W 5 E.U5 E.A11 U-A WC 20-XX cWW cW-W 6 E.C6 E.G10 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#4[0] bps=6 strand-1 5'-AUGUUC-3' bp-type .||||| strand-2 3'-CACAAG-5' helix-form .A.A. 1 F.A1 F.C15 A-C -- -- cWW cW-W 2 F.U2 F.A14 U-A WC 20-XX cWW cW-W 3 F.G3 F.C13 G-C WC 19-XIX cWW cW-W 4 F.U4 F.A12 U-A WC 20-XX cWW cW-W 5 F.U5 F.A11 U-A WC 20-XX cWW cW-W 6 F.C6 F.G10 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 39 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4z31 U-gln C.U5 B.GLN315 9.87 41.01 -9.01 3.93 0.94 -15.84 26.91 26.93 2 4z31 C-gln C.C6 B.GLN315 -11.04 -30.06 -6.91 8.21 -2.60 -11.11 27.31 -5.93 3 4z31 C-asp C.C6 B.ASP319 9.70 27.71 -8.83 3.27 2.34 -27.18 5.15 1.71 4 4z31 A-gln C.A12 A.GLN315 10.13 40.57 -9.34 3.81 0.93 -12.21 30.09 24.64 5 4z31 C-gln C.C13 A.GLN315 -11.37 -33.33 -7.37 8.18 -2.85 -10.79 29.06 -12.40 6 4z31 C-asp C.C13 A.ASP319 10.40 -29.78 -9.52 3.50 2.31 -28.46 7.88 -3.86 7 4z31 U-gln D.U5 A.GLN315 -11.14 127.66 0.41 10.69 -3.09 -17.72 17.63 126.29 8 4z31 U-arg D.U7 A.ARG128 10.19 -14.79 8.66 5.11 1.64 12.95 -7.05 -1.22 9 4z31 G-arg D.G8 A.ARG128 10.81 -27.82 9.55 4.84 -1.44 5.07 -15.60 -22.55 10 4z31 A-gln D.A11 B.GLN315 -9.92 152.67 -3.75 9.19 -0.19 -14.61 8.43 152.36 11 4z31 A-gln D.A12 B.GLN315 -10.34 128.02 0.89 9.81 -3.17 -14.10 14.33 127.15 12 4z31 G-thr E.G3 B.THR237 8.76 89.48 5.99 6.34 0.85 43.36 -59.98 54.38 13 4z31 U-thr E.U4 B.THR237 8.97 79.65 6.49 5.43 -2.97 23.12 -69.24 34.34 14 4z31 U-glu E.U7 B.GLU259 -3.48 141.46 -0.50 -2.35 -2.52 -3.41 -29.11 140.11 15 4z31 U-asp E.U7 B.ASP260 -5.16 174.12 2.90 -3.82 -1.90 83.46 -2.57 172.12 16 4z31 U-ser E.U7 B.SER261 -7.06 -116.09 -5.03 3.64 -3.37 -15.89 7.17 -115.25 17 4z31 U-ser E.U7 B.SER262 -8.40 -94.15 -3.57 -0.07 -7.60 82.24 33.65 -35.02 18 4z31 G-arg E.G8 B.ARG216 6.63 -68.15 4.79 -0.05 4.58 5.18 -54.11 -42.79 19 4z31 G-gln E.G8 B.GLN244 7.39 -159.36 -0.29 -6.98 -2.40 -83.17 -23.58 -151.53 20 4z31 U-tyr E.U9 B.TYR247 -8.63 92.17 0.40 6.91 -5.16 -32.12 -44.11 77.40 21 4z31 U-arg E.U9 B.ARG248 -7.03 -54.43 -4.10 5.26 -2.22 -50.04 13.23 -17.45 22 4z31 U-ser E.U9 B.SER250 -4.96 100.55 2.31 1.49 -4.13 -24.53 39.50 91.85 23 4z31 G-arg E.G10 B.ARG187 10.15 -93.01 -2.53 9.22 3.40 4.25 -56.16 -77.35 24 4z31 G-gly E.G10 B.GLY188 7.34 42.48 5.53 4.81 -0.43 26.08 -10.74 32.09 25 4z31 G-gln E.G10 B.GLN244 -8.55 -135.49 -3.97 7.57 -0.11 -76.32 -22.86 -120.89 26 4z31 G-thr F.G3 A.THR237 8.94 88.71 6.01 6.59 0.62 43.16 -59.41 53.76 27 4z31 U-thr F.U4 A.THR237 9.20 79.33 6.57 5.63 -3.15 23.02 -69.20 33.65 28 4z31 U-glu F.U7 A.GLU259 -3.98 145.96 0.34 -2.96 -2.65 -2.94 -29.06 144.79 29 4z31 U-asp F.U7 A.ASP260 -5.73 177.46 3.60 -4.24 -1.34 82.53 1.33 176.62 30 4z31 U-ser F.U7 A.SER261 -7.45 -109.76 -5.09 4.38 -3.22 -15.19 5.89 -108.93 31 4z31 U-ser F.U7 A.SER262 -8.37 -91.04 -2.99 0.42 -7.81 80.18 33.80 -29.94 32 4z31 G-arg F.G8 A.ARG216 6.72 -69.43 4.95 -0.22 4.54 5.47 -54.57 -44.34 33 4z31 G-gln F.G8 A.GLN244 7.33 -159.96 -0.19 -6.94 -2.37 -82.76 -22.57 -152.53 34 4z31 U-tyr F.U9 A.TYR247 -8.78 90.70 0.43 7.11 -5.12 -30.50 -42.00 77.19 35 4z31 U-arg F.U9 A.ARG248 -7.13 -55.24 -4.14 5.42 -2.09 -50.46 16.23 -16.13 36 4z31 U-ser F.U9 A.SER250 -5.05 101.66 2.39 1.66 -4.13 -22.32 41.32 92.95 37 4z31 G-arg F.G10 A.ARG187 10.03 -92.75 -2.50 9.12 3.35 5.60 -56.77 -76.52 38 4z31 G-gly F.G10 A.GLY188 7.26 43.81 5.51 4.71 -0.42 26.69 -11.36 33.19 39 4z31 G-gln F.G10 A.GLN244 -8.53 -134.36 -3.88 7.60 -0.13 -74.92 -23.78 -119.84 **************************************************************************** List of 19 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4z31 UU-arg C.U9 D.U7 A.ARG128 -10.67 165.31 -5.46 -8.56 -3.31 17.99 -18.99 164.92 2 4z31 AU-gln C.A11 D.U5 A.GLN315 11.21 57.07 -10.73 -0.41 3.22 -11.89 20.98 52.12 3 4z31 AU-gln C.A12 D.U4 A.GLN315 10.10 33.88 -9.37 3.77 0.34 -10.81 21.39 24.13 4 4z31 GC-gln D.G3 C.C13 A.GLN315 11.26 -167.90 8.28 -6.98 3.10 19.45 -6.46 -167.71 5 4z31 GC-asp D.G3 C.C13 A.ASP319 -10.27 -173.96 3.52 -9.51 -1.59 -1.81 -24.74 -173.81 6 4z31 GC-gln D.G10 C.C6 B.GLN315 10.97 -175.00 8.25 -6.65 2.82 21.27 -7.84 -174.91 7 4z31 GC-asp D.G10 C.C6 B.ASP319 -9.54 179.06 -3.23 8.80 -1.79 1.05 24.13 179.03 8 4z31 AU-gln D.A11 C.U5 B.GLN315 -9.90 153.33 -3.83 9.11 -0.57 -20.75 12.15 152.72 9 4z31 AU-gln D.A12 C.U4 B.GLN315 -10.23 127.27 0.97 9.68 -3.17 -18.73 7.37 126.38 10 4z31 GC-thr E.G3 E.C13 B.THR237 8.84 96.26 5.78 6.55 1.30 42.60 -67.71 58.79 11 4z31 GC-arg E.G10 E.C6 B.ARG187 -10.18 -92.94 -3.69 9.22 2.23 -2.18 -68.06 -67.56 12 4z31 GC-gly E.G10 E.C6 B.GLY188 -7.28 39.94 5.06 5.08 -1.24 11.19 -9.44 37.27 13 4z31 GC-gln E.G10 E.C6 B.GLN244 -8.59 -143.56 -4.09 7.48 -1.07 -79.47 -38.25 -128.38 14 4z31 AU-thr E.A12 E.U4 B.THR237 -8.83 156.66 -5.46 -6.62 2.09 79.95 -25.49 148.44 15 4z31 GC-thr F.G3 F.C13 A.THR237 9.00 95.37 5.83 6.78 1.06 42.24 -67.24 57.91 16 4z31 GC-arg F.G10 F.C6 A.ARG187 -10.06 -92.72 -3.62 9.13 2.20 -0.96 -68.40 -66.88 17 4z31 GC-gly F.G10 F.C6 A.GLY188 -7.19 41.00 5.06 4.96 -1.22 11.96 -9.96 38.05 18 4z31 GC-gln F.G10 F.C6 A.GLN244 -8.57 -142.46 -3.99 7.51 -1.06 -78.26 -38.81 -127.17 19 4z31 AU-thr F.A12 F.U4 A.THR237 -9.07 157.16 -5.63 -6.73 2.30 79.88 -24.75 149.19 **************************************************************************** List of 32 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 4z31 OP1@C.U7 OG@B.SER316 2.48 po4:sidechain 2 4z31 O3'@C.A12 OG@A.SER312 3.01 po4:sidechain 3 4z31 OP1@C.A14 OG@A.SER316 2.74 po4:sidechain 4 4z31 OP1@C.C15 NZ@A.LYS320 3.53 po4:sidechain:salt-bridge 5 4z31 OP1@D.U5 NZ@A.LYS133 2.87 po4:sidechain:salt-bridge 6 4z31 OP2@D.U5 NH2@A.ARG132 2.99 po4:sidechain:salt-bridge 7 4z31 OP2@D.C6 NH2@A.ARG132 3.30 po4:sidechain:salt-bridge 8 4z31 OP1@D.G10 NH1@B.ARG153 2.64 po4:sidechain:salt-bridge 9 4z31 OP1@D.A11 NZ@B.LYS133 2.53 po4:sidechain:salt-bridge 10 4z31 OP1@D.A11 OG@B.SER157 2.16 po4:sidechain 11 4z31 O5'@D.A11 NZ@B.LYS133 3.21 po4:sidechain 12 4z31 OP1@D.A12 NH1@B.ARG161 2.81 po4:sidechain:salt-bridge 13 4z31 OP2@D.A12 NZ@B.LYS133 3.26 po4:sidechain:salt-bridge 14 4z31 OP2@D.C13 NH1@B.ARG161 3.02 po4:sidechain:salt-bridge 15 4z31 OP1@E.A1 NE@B.ARG185 2.80 po4:sidechain:salt-bridge 16 4z31 OP1@E.G3 OG@B.SER235 2.73 po4:sidechain 17 4z31 OP2@E.U4 N@B.THR237 3.03 po4:backbone 18 4z31 OP2@E.U4 OG1@B.THR237 2.68 po4:sidechain 19 4z31 OP1@E.U7 OG@B.SER261 3.27 po4:sidechain 20 4z31 OP1@E.G8 OH@B.TYR247 2.85 po4:sidechain 21 4z31 OP2@E.G8 NE@B.ARG216 3.22 po4:sidechain:salt-bridge 22 4z31 OP2@E.G8 NH1@B.ARG216 3.03 po4:sidechain:salt-bridge 23 4z31 OP2@E.G10 NH2@B.ARG248 2.23 po4:sidechain:salt-bridge 24 4z31 OP1@F.G3 OG@A.SER235 2.63 po4:sidechain 25 4z31 OP2@F.U4 N@A.THR237 3.03 po4:backbone 26 4z31 OP2@F.U4 OG1@A.THR237 2.53 po4:sidechain 27 4z31 OP1@F.U7 OG@A.SER261 2.49 po4:sidechain 28 4z31 OP1@F.G8 OH@A.TYR247 2.64 po4:sidechain 29 4z31 OP2@F.G8 NE@A.ARG216 3.28 po4:sidechain:salt-bridge 30 4z31 OP2@F.G8 NH1@A.ARG216 2.91 po4:sidechain:salt-bridge 31 4z31 OP2@F.G10 NE@A.ARG248 2.91 po4:sidechain:salt-bridge 32 4z31 OP2@F.G10 NH2@A.ARG248 3.11 po4:sidechain:salt-bridge **************************************************************************** List of 11 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 4z31 O2'@C.U5 OG@B.SER312 2.80 sugar:sidechain 2 4z31 O2'@C.U5 OE1@B.GLN315 2.64 sugar:sidechain 3 4z31 O2'@C.C6 OD2@B.ASP319 2.47 sugar:sidechain 4 4z31 O2'@C.A12 OG@A.SER312 2.65 sugar:sidechain 5 4z31 O2'@C.A12 OE1@A.GLN315 2.73 sugar:sidechain 6 4z31 O2'@C.C13 OD2@A.ASP319 2.67 sugar:sidechain 7 4z31 O4'@E.U7 N@B.SER262 3.02 sugar:backbone 8 4z31 O2'@E.G8 OE1@B.GLN244 3.18 sugar:sidechain 9 4z31 O2'@E.G8 NE2@B.GLN244 3.13 sugar:sidechain 10 4z31 O4'@F.U7 N@A.SER262 2.98 sugar:backbone 11 4z31 O2'@F.G8 NE2@A.GLN244 3.03 sugar:sidechain **************************************************************************** List of 7 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 4z31 O2@C.U5 NE2@B.GLN315 2.69 base:sidechain 2 4z31 N3@C.A12 NE2@A.GLN315 3.17 base:sidechain 3 4z31 N7@D.G8 NH1@A.ARG128 3.11 base:sidechain 4 4z31 O6@D.G8 NH2@A.ARG128 2.75 base:sidechain 5 4z31 N2@E.G8 OE1@B.GLN244 2.84 base:sidechain 6 4z31 N2@F.G8 OE1@A.GLN244 2.74 base:sidechain 7 4z31 O2@F.U9 O@A.ARG248 3.09 base:backbone **************************************************************************** List of 5 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 4z31 U-gln C.U5 B.GLN315 1.03 34 2 4z31 A-gln C.A12 A.GLN315 0.79 37 3 4z31 G-arg D.G8 A.ARG128 0.16 9 4 4z31 G-gln E.G8 B.GLN244 2.07 21 5 4z31 G-gln F.G8 A.GLN244 2.07 21 **************************************************************************** List of 7 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 4z31 C-gln C.C6 B.GLN315 4.12 31 2 4z31 C-gln C.C13 A.GLN315 4.27 32 3 4z31 U-arg D.U7 A.ARG128 3.49 11 4 4z31 G-arg E.G8 B.ARG216 3.52 15 5 4z31 G-gln E.G10 B.GLN244 4.20 31 6 4z31 G-arg F.G8 A.ARG216 3.57 15 7 4z31 G-gln F.G10 A.GLN244 4.20 32 **************************************************************************** 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 RGG A.ARG216,F.G8,F.G10 2 size=3 RGG B.ARG216,E.G8,E.G10 **************************************************************************** List of 3 additional files 1 -- 4z31-baseAA-pairs.pdb 2 -- 4z31-baseAA-stacks.pdb 3 -- 4z31-pairs.pdb