**************************************************************************** File name: 6kup.pdb no. of peptide chains: 3 [A=511,B=701,C=249] no. of DNA/RNA chains: 2 [R=8,V=15] no. of amino acids: 1461 no. of nucleotides: 23 no. of atoms: 12254 no. of waters: 0 no. of metals: 0 **************************************************************************** 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'-CUCCU-3' bp-type ||||| strand-2 3'-GAGGA-5' helix-form AAAA 1 R.C1 V.G15 C-G WC 19-XIX cWW cW-W 2 R.U2 V.A14 U-A WC 20-XX cWW cW-W 3 R.C3 V.G13 C-G WC 19-XIX cWW cW-W 4 R.C4 V.G12 C-G WC 19-XIX cWW cW-W 5 R.U5 V.A11 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#2[0] bps=3 strand-1 5'-AGC-3' bp-type .|| strand-2 3'-ACG-5' helix-form .A 1 V.A1 V.A10 A-A ~Sheared -- tHS tM-m 2 V.G2 V.C9 G-C WC 19-XIX cWW cW-W 3 V.C3 V.G8 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 6kup G-pro R.G6 A.PRO458 -6.78 150.74 2.61 -4.92 -3.86 38.10 -47.46 145.93 2 6kup G-his R.G6 A.HIS490 -8.72 -93.62 -0.30 7.74 4.02 -57.94 -38.97 -66.84 3 6kup C-ser R.C7 C.SER41 5.79 -105.59 1.68 5.51 0.65 68.49 53.08 -67.55 4 6kup C-arg R.C7 C.ARG42 3.68 -28.81 1.38 -0.27 3.40 -20.72 4.04 -19.72 5 6kup C-lys R.C7 C.LYS43 2.67 45.15 0.67 -2.31 1.16 35.80 4.88 27.55 6 6kup C-glu R.C7 C.GLU44 -3.51 -173.35 -1.24 2.22 -2.41 -15.52 -72.68 -171.65 7 6kup C-lys R.C7 C.LYS45 -4.85 -55.80 0.01 -3.76 -3.05 44.97 30.21 -13.91 8 6kup C-arg R.C7 C.ARG50 -11.60 157.76 7.64 4.83 -7.27 -65.94 28.26 152.47 9 6kup U-arg R.U8 B.ARG138 -9.46 168.94 -2.25 9.18 -0.28 -57.29 55.14 165.60 10 6kup U-thr R.U8 C.THR40 -3.91 -153.13 3.30 1.90 -0.91 -60.62 -60.03 -143.17 11 6kup U-ser R.U8 C.SER41 -4.62 -163.73 -0.16 4.09 -2.15 2.13 -41.08 -162.61 12 6kup U-arg R.U8 C.ARG42 -5.80 -72.00 0.22 -0.86 -5.73 43.40 -36.22 -46.58 13 6kup A-leu V.A1 A.LEU342 -6.66 79.50 -4.88 4.31 -1.37 -74.00 -7.80 30.27 14 6kup A-arg V.A1 A.ARG347 -8.01 163.28 1.56 -5.44 -5.67 28.51 -46.35 161.19 15 6kup A-thr V.A1 A.THR499 5.17 -109.58 2.52 -4.04 -2.02 -57.33 -9.20 -97.49 16 6kup A-thr V.A1 A.THR552 7.86 66.54 -7.52 1.98 1.18 -12.32 39.78 53.11 17 6kup G-met V.G2 A.MET497 7.57 -173.04 2.25 -6.97 1.93 13.98 2.36 -172.99 18 6kup C-met V.C3 A.MET497 -8.45 154.60 2.03 8.03 -1.65 -16.66 1.99 154.32 19 6kup G-gly V.G5 A.GLY372 -9.63 -79.53 2.80 8.29 -4.02 45.95 63.93 -12.29 20 6kup G-ala V.G5 A.ALA373 -6.86 53.02 3.83 4.66 -3.26 -8.06 -41.02 33.37 21 6kup G-asp V.G5 A.ASP639 -8.06 -171.68 1.88 -7.17 -3.17 13.00 8.95 -171.60 22 6kup G-ser V.G5 A.SER683 -6.55 83.99 -1.10 -2.32 -6.03 -8.99 -74.71 40.45 23 6kup U-gly V.U6 A.GLY372 -4.73 107.17 1.32 2.98 -3.42 -29.23 0.64 104.32 24 6kup U-tyr V.U6 B.TYR238 10.85 -105.88 1.05 10.79 -0.37 51.81 -32.30 -91.20 25 6kup U-lys V.U6 B.LYS239 9.80 -125.86 -3.13 5.03 7.81 -25.70 -20.13 -123.39 26 6kup A-thr V.A7 A.THR370 -9.64 44.47 4.62 7.73 -3.43 20.58 -38.59 8.26 27 6kup A-his V.A7 B.HIS32 -7.60 169.97 0.60 7.58 -0.01 -32.84 -73.53 166.84 28 6kup G-met V.G8 A.MET497 8.18 27.85 -7.89 -1.95 0.98 -0.15 10.75 25.73 29 6kup C-gly V.C9 A.GLY496 -9.68 -73.17 -7.47 6.09 0.93 -68.38 25.01 -7.79 30 6kup C-met V.C9 A.MET497 -7.78 -9.65 -6.99 2.34 -2.49 3.51 6.49 -6.22 31 6kup A-arg V.A10 A.ARG347 6.20 53.76 -0.46 4.30 4.45 33.58 -22.16 36.42 32 6kup A-ala V.A10 A.ALA348 5.44 86.99 1.96 1.95 4.69 10.15 28.09 82.69 33 6kup A-his V.A11 A.HIS490 -6.30 -86.05 -5.04 3.11 -2.14 -21.41 -79.66 -27.08 **************************************************************************** List of 9 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6kup AA-leu V.A1 V.A10 A.LEU342 -9.24 85.08 -8.31 3.54 -1.95 -81.80 -0.61 25.80 2 6kup AA-arg V.A1 V.A10 A.ARG347 -6.10 154.69 -1.61 -2.68 -5.24 24.93 -40.09 152.34 3 6kup AA-ala V.A1 V.A10 A.ALA348 -7.00 105.46 1.80 -3.20 -5.96 -23.70 -18.85 102.29 4 6kup AA-thr V.A1 V.A10 A.THR499 8.49 -119.95 1.73 -7.60 -3.38 -63.79 -10.65 -107.37 5 6kup AA-thr V.A1 V.A10 A.THR552 11.06 63.98 -10.83 2.24 0.05 -16.36 44.92 43.84 6 6kup GC-gly V.G2 V.C9 A.GLY496 9.58 -175.56 5.96 -7.40 -1.23 28.48 -69.11 -174.41 7 6kup GC-met V.G2 V.C9 A.MET497 7.67 -173.41 2.30 -6.98 2.21 10.24 2.93 -173.39 8 6kup GC-met V.G8 V.C3 A.MET497 8.32 29.09 -7.97 -1.99 1.31 -1.07 13.70 25.70 9 6kup AU-his V.A11 R.U5 A.HIS490 -6.41 -80.75 -5.25 2.91 -2.24 -29.03 -72.58 -22.11 **************************************************************************** List of 16 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 6kup OP1@R.U5 NH1@B.ARG668 3.61 po4:sidechain:salt-bridge 2 6kup OP1@R.G6 N@B.ARG668 3.12 po4:backbone 3 6kup OP1@R.G6 N@B.THR669 2.53 po4:backbone 4 6kup OP1@R.G6 OG1@B.THR669 2.65 po4:sidechain 5 6kup O5'@R.C7 NH2@C.ARG50 2.85 po4:sidechain 6 6kup OP1@V.G2 NZ@A.LYS310 3.47 po4:sidechain:salt-bridge 7 6kup OP2@V.A4 NZ@A.LYS264 2.95 po4:sidechain:salt-bridge 8 6kup O3'@V.C3 NZ@A.LYS264 3.29 po4:sidechain 9 6kup OP2@V.U6 OH@B.TYR38 4.00 po4:sidechain 10 6kup OP2@V.A7 NE1@B.TRP386 3.15 po4:sidechain 11 6kup OP1@V.G8 OG1@B.THR34 3.35 po4:sidechain 12 6kup O3'@V.A7 N@B.THR34 3.88 po4:backbone 13 6kup O5'@V.G8 NE@B.ARG358 3.47 po4:sidechain 14 6kup OP1@V.C9 NZ@A.LYS351 3.18 po4:sidechain:salt-bridge 15 6kup OP2@V.A11 N@A.GLY346 2.34 po4:backbone 16 6kup OP2@V.A11 N@A.ARG347 3.13 po4:backbone **************************************************************************** List of 5 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 6kup O4'@R.C7 NH2@C.ARG50 3.34 sugar:sidechain 2 6kup O4'@V.A1 NH1@A.ARG347 3.19 sugar:sidechain 3 6kup O2'@V.U6 NZ@B.LYS37 3.07 sugar:sidechain 4 6kup O2'@V.C9 O@A.GLY496 2.39 sugar:backbone 5 6kup O2'@V.A10 O@A.GLY344 3.17 sugar:backbone **************************************************************************** List of 6 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 6kup N4@R.C7 N@C.GLU44 3.17 base:backbone 2 6kup O2@R.U8 NH1@B.ARG138 2.50 base:sidechain 3 6kup O4@R.U8 O@C.THR40 3.08 base:backbone 4 6kup N1@V.A1 OG1@A.THR499 3.63 base:sidechain 5 6kup N2@V.G2 O@A.MET497 3.90 base:backbone 6 6kup O4@V.U6 OH@B.TYR238 3.30 base:sidechain **************************************************************************** List of 1 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 6kup U-arg R.U8 B.ARG138 1.31 19 **************************************************************************** List of 1 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 6kup A-his V.A11 A.HIS490 3.32 15 **************************************************************************** List of 3 additional files 1 -- 6kup-baseAA-pairs.pdb 2 -- 6kup-baseAA-stacks.pdb 3 -- 6kup-pairs.pdb