**************************************************************************** SNAP: a software tool for the characterization of 3D Structures of Nucleic Acid-Protein complexes v1.0.6-2019sep30, by xiangjun@x3dna.org SNAP has been made possible by the NIH grant R01GM096889 (to X.J.Lu). It is being actively maintained and developed. As always, I greatly appreciate your feedback. Please report all SNAP-related issues on the 3DNA Forum (forum.x3dna.org). I strive to respond promptly to any questions posted there. SNAP is free of charge for NON-COMMERCIAL purposes, and it comes with ABSOLUTELY NO WARRANTY. **************************************************************************** Note: By default, each nucleotide/amino-acid is identified by chainId.name#. So a common case would be B.DA1689, meaning adenosine #1689 on chain B. Use the --idstr=long option to get strictly delineated id strings. Command: x3dna-snap -i=5lty.pdb -o=5lty.out File name: 5lty.pdb no. of peptide chains: 2 [K=71,M=70] no. of DNA/RNA chains: 4 [A=18,B=18,E=18,F=18] no. of amino acids: 141 no. of nucleotides: 72 no. of atoms: 2757 no. of waters: 34 no. of metals: 0 **************************************************************************** List of 1 type of 4 modified nucleotides nt count list 1 5CM-c 4 A.5CM11,B.5CM11,F.5CM25,E.5CM25 **************************************************************************** List of 2 helices Note: a helix is defined by base-stacking interactions, regardless of bp 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=18 strand-1 5'-TTGTGTTTTAcGACCTCC-3' bp-type |||||||||||||||||| strand-2 3'-AACACAAAATGcTGGAGG-5' helix-form B.BBBBBBBBBB.BBB. 1 A.DT1 F.DA36 T-A WC 20-XX cWW cW-W 2 A.DT2 F.DA35 T-A WC 20-XX cWW cW-W 3 A.DG3 F.DC34 G-C WC 19-XIX cWW cW-W 4 A.DT4 F.DA33 T-A WC 20-XX cWW cW-W 5 A.DG5 F.DC32 G-C WC 19-XIX cWW cW-W 6 A.DT6 F.DA31 T-A WC 20-XX cWW cW-W 7 A.DT7 F.DA30 T-A WC 20-XX cWW cW-W 8 A.DT8 F.DA29 T-A WC 20-XX cWW cW-W 9 A.DT9 F.DA28 T-A WC 20-XX cWW cW-W 10 A.DA10 F.DT27 A-T WC 20-XX cWW cW-W 11 A.5CM11 F.DG26 c-G WC 19-XIX cWW cW-W 12 A.DG12 F.5CM25 G-c WC 19-XIX cWW cW-W 13 A.DA13 F.DT24 A-T WC 20-XX cWW cW-W 14 A.DC14 F.DG23 C-G WC 19-XIX cWW cW-W 15 A.DC15 F.DG22 C-G WC 19-XIX cWW cW-W 16 A.DT16 F.DA21 T-A WC 20-XX cWW cW-W 17 A.DC17 F.DG20 C-G WC 19-XIX cWW cW-W 18 A.DC18 F.DG19 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[0] bps=18 strand-1 5'-TTGTGTTTTAcGACCTCC-3' bp-type |||||||||||||||||| strand-2 3'-AACACAAAATGcTGGAGG-5' helix-form .B.BBBBBBBBB.BBB. 1 B.DT1 E.DA36 T-A WC 20-XX cWW cW-W 2 B.DT2 E.DA35 T-A WC 20-XX cWW cW-W 3 B.DG3 E.DC34 G-C WC 19-XIX cWW cW-W 4 B.DT4 E.DA33 T-A WC 20-XX cWW cW-W 5 B.DG5 E.DC32 G-C WC 19-XIX cWW cW-W 6 B.DT6 E.DA31 T-A WC 20-XX cWW cW-W 7 B.DT7 E.DA30 T-A WC 20-XX cWW cW-W 8 B.DT8 E.DA29 T-A WC 20-XX cWW cW-W 9 B.DT9 E.DA28 T-A WC 20-XX cWW cW-W 10 B.DA10 E.DT27 A-T WC 20-XX cWW cW-W 11 B.5CM11 E.DG26 c-G WC 19-XIX cWW cW-W 12 B.DG12 E.5CM25 G-c WC 19-XIX cWW cW-W 13 B.DA13 E.DT24 A-T WC 20-XX cWW cW-W 14 B.DC14 E.DG23 C-G WC 19-XIX cWW cW-W 15 B.DC15 E.DG22 C-G WC 19-XIX cWW cW-W 16 B.DT16 E.DA21 T-A WC 20-XX cWW cW-W 17 B.DC17 E.DG20 C-G WC 19-XIX cWW cW-W 18 B.DC18 E.DG19 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 24 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5lty T-arg A.DT8 K.ARG190 8.96 22.06 -8.81 0.84 1.40 10.89 14.46 12.66 2 5lty T-arg A.DT9 K.ARG190 -8.73 -23.05 -7.84 3.10 -2.28 11.41 6.10 -19.12 3 5lty T-asn A.DT9 K.ASN236 9.48 -158.85 -6.07 7.18 -1.21 34.73 61.54 -154.00 4 5lty A-ile A.DA10 K.ILE232 9.51 179.88 8.14 -4.77 1.13 -23.98 -23.54 179.88 5 5lty A-asn A.DA10 K.ASN236 7.89 173.80 3.00 -6.24 -3.78 -53.78 -42.48 172.49 6 5lty C-ile A.5CM11 K.ILE232 -9.71 154.09 7.15 -5.90 -2.89 -21.51 -7.52 153.56 7 5lty T-arg B.DT8 M.ARG190 9.10 20.80 -8.92 0.76 1.60 9.92 13.50 12.38 8 5lty T-arg B.DT9 M.ARG190 -8.88 -23.07 -8.03 3.18 -2.09 10.06 5.52 -20.05 9 5lty T-asn B.DT9 M.ASN236 9.47 -158.95 -6.03 7.19 -1.24 34.88 61.93 -154.06 10 5lty A-ile B.DA10 M.ILE232 9.52 179.96 8.15 -4.80 1.12 -23.86 -23.36 179.96 11 5lty A-asn B.DA10 M.ASN236 7.93 174.02 2.96 -6.28 -3.82 -53.62 -42.96 172.75 12 5lty C-ile B.5CM11 M.ILE232 -9.74 154.11 7.17 -5.92 -2.90 -21.44 -7.71 153.58 13 5lty G-gln F.DG23 K.GLN235 10.92 -69.62 -4.98 7.84 5.74 -0.25 26.93 -64.82 14 5lty T-gln F.DT24 K.GLN235 10.22 -93.84 -2.77 9.61 2.13 6.49 21.55 -91.72 15 5lty A-tyr F.DA28 K.TYR189 10.00 105.59 -7.99 5.66 -2.00 61.98 17.18 88.85 16 5lty A-tyr F.DA29 K.TYR189 -10.68 79.91 -6.91 5.94 -5.58 57.14 -3.14 58.34 17 5lty A-arg F.DA29 K.ARG190 -9.11 -13.85 -9.04 -0.86 -0.72 -1.05 -5.87 -12.51 18 5lty A-arg F.DA30 K.ARG190 -10.21 -51.77 -9.00 2.04 -4.37 -5.01 -9.45 -50.73 19 5lty G-gln E.DG23 M.GLN235 10.96 -69.96 -4.93 7.88 5.80 -0.34 27.24 -65.07 20 5lty T-gln E.DT24 M.GLN235 10.30 -94.19 -2.73 9.69 2.18 6.16 21.67 -92.08 21 5lty A-tyr E.DA28 M.TYR189 10.20 105.38 -8.10 5.87 -1.98 61.82 14.01 89.14 22 5lty A-tyr E.DA29 M.TYR189 -10.87 80.16 -7.04 6.17 -5.53 56.52 -5.53 59.13 23 5lty A-arg E.DA29 M.ARG190 -9.30 -12.92 -9.23 -0.80 -0.88 -1.59 -4.04 -12.17 24 5lty A-arg E.DA30 M.ARG190 -10.37 -50.83 -9.09 2.14 -4.51 -4.74 -7.20 -50.14 **************************************************************************** List of 22 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5lty AT-arg F.DA30 A.DT7 K.ARG190 -10.20 -53.63 -8.81 2.23 -4.63 1.58 -15.03 -51.61 2 5lty AT-arg F.DA29 A.DT8 K.ARG190 -9.04 -16.90 -8.93 -0.86 -1.07 4.90 -10.18 -12.58 3 5lty AT-arg F.DA28 A.DT9 K.ARG190 8.69 20.77 -7.72 -2.98 2.65 7.22 -2.35 19.34 4 5lty AT-arg E.DA30 B.DT7 M.ARG190 -10.33 -52.93 -8.85 2.38 -4.76 1.53 -12.96 -51.41 5 5lty AT-arg E.DA29 B.DT8 M.ARG190 -9.20 -15.64 -9.08 -0.79 -1.24 4.15 -8.78 -12.27 6 5lty AT-arg E.DA28 B.DT9 M.ARG190 8.87 20.69 -7.96 -3.02 2.48 6.02 -1.52 19.75 7 5lty AT-asn F.DA28 A.DT9 K.ASN236 -9.45 156.27 -6.01 -7.17 1.34 36.24 -56.37 151.45 8 5lty AT-asn A.DA10 F.DT27 K.ASN236 7.97 176.54 2.94 -6.48 -3.60 -56.51 -40.11 175.79 9 5lty AT-asn E.DA28 B.DT9 M.ASN236 -9.41 155.83 -6.02 -7.11 1.34 36.37 -56.95 150.82 10 5lty AT-asn B.DA10 E.DT27 M.ASN236 7.97 176.92 2.93 -6.45 -3.64 -56.05 -41.04 176.25 11 5lty AT-gln A.DA13 F.DT24 K.GLN235 -10.20 94.32 -2.74 -9.59 -2.12 6.87 -15.46 93.14 12 5lty AT-gln B.DA13 E.DT24 M.GLN235 -10.25 94.46 -2.74 -9.64 -2.16 6.57 -15.51 93.30 13 5lty AT-ile A.DA10 F.DT27 K.ILE232 9.54 -178.51 -8.17 4.80 1.13 26.82 20.56 -178.45 14 5lty AT-ile B.DA10 E.DT27 M.ILE232 9.54 -178.14 -8.19 4.75 1.13 26.48 20.77 -178.06 15 5lty AT-tyr F.DA29 A.DT8 K.TYR189 -10.60 84.51 -6.58 5.89 -5.87 59.43 -9.42 62.39 16 5lty AT-tyr F.DA28 A.DT9 K.TYR189 10.03 107.96 -7.99 5.58 -2.37 63.17 12.10 92.01 17 5lty AT-tyr E.DA29 B.DT8 M.TYR189 -10.76 84.66 -6.67 6.08 -5.84 58.39 -12.09 63.12 18 5lty AT-tyr E.DA28 B.DT9 M.TYR189 10.19 108.09 -8.09 5.72 -2.36 62.64 9.05 92.79 19 5lty GC-gln F.DG23 A.DC14 K.GLN235 10.88 -67.68 -5.32 7.79 5.43 0.04 19.88 -65.03 20 5lty GC-gln E.DG23 B.DC14 M.GLN235 10.92 -67.89 -5.30 7.81 5.48 -0.06 20.05 -65.20 21 5lty GC-ile F.DG26 A.5CM11 K.ILE232 9.77 -154.21 7.05 6.24 2.61 -28.62 8.01 -153.30 22 5lty GC-ile E.DG26 B.5CM11 M.ILE232 9.79 -154.43 7.09 6.22 2.64 -28.38 8.29 -153.54 **************************************************************************** List of 39 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 5lty OP2@A.DT7 NZ@K.LYS243 3.04 po4:sidechain:salt-bridge 2 5lty OP1@A.DT8 NZ@M.LYS203 3.61 po4:sidechain:salt-bridge 3 5lty OP2@A.DT8 NZ@K.LYS240 3.07 po4:sidechain:salt-bridge 4 5lty OP1@A.DT9 N@K.TYR193 2.88 po4:backbone 5 5lty OP1@A.DT9 NE@K.ARG198 3.06 po4:sidechain:salt-bridge 6 5lty OP1@A.DT9 NH2@K.ARG198 2.74 po4:sidechain:salt-bridge 7 5lty O5'@A.DT9 NH1@K.ARG190 3.21 po4:sidechain 8 5lty OP1@A.DA10 N@K.VAL191 3.13 po4:backbone 9 5lty OP2@A.DA10 OH@K.TYR193 2.53 po4:sidechain 10 5lty OP2@A.DA10 NE2@K.GLN229 2.30 po4:sidechain 11 5lty O3'@A.DT9 N@K.VAL191 3.59 po4:backbone 12 5lty OP1@A.5CM11 N@K.LYS186 2.76 po4:backbone 13 5lty OP2@A.5CM11 NH2@K.ARG228 2.12 po4:sidechain:salt-bridge 14 5lty O3'@A.DA10 O@K.LYS186 2.77 po4:backbone 15 5lty O5'@A.5CM11 NH2@K.ARG228 3.25 po4:sidechain 16 5lty OP2@B.DT7 NZ@M.LYS243 3.29 po4:sidechain:salt-bridge 17 5lty OP2@B.DT8 NZ@M.LYS240 3.22 po4:sidechain:salt-bridge 18 5lty OP1@B.DT9 N@M.TYR193 2.78 po4:backbone 19 5lty OP1@B.DT9 NE@M.ARG198 3.07 po4:sidechain:salt-bridge 20 5lty OP1@B.DT9 NH2@M.ARG198 2.67 po4:sidechain:salt-bridge 21 5lty O5'@B.DT9 NH1@M.ARG190 3.13 po4:sidechain 22 5lty OP1@B.DA10 N@M.VAL191 2.89 po4:backbone 23 5lty OP2@B.DA10 OH@M.TYR193 2.73 po4:sidechain 24 5lty OP2@B.DA10 NE2@M.GLN229 2.35 po4:sidechain 25 5lty OP1@B.5CM11 N@M.LYS186 2.67 po4:backbone 26 5lty OP2@B.5CM11 NH2@M.ARG228 2.00 po4:sidechain:salt-bridge 27 5lty O3'@B.DA10 O@M.LYS186 2.54 po4:backbone 28 5lty O3'@B.DA10 OD1@M.ASP187 2.85 po4:sidechain 29 5lty OP1@F.DG22 NZ@K.LYS216 2.70 po4:sidechain:salt-bridge 30 5lty OP2@F.DG22 NZ@K.LYS231 3.58 po4:sidechain:salt-bridge 31 5lty OP2@F.DG23 NE2@K.GLN235 2.75 po4:sidechain 32 5lty OP1@F.DT24 NE@K.ARG238 3.06 po4:sidechain:salt-bridge 33 5lty OP1@F.DT24 NH1@K.ARG242 3.03 po4:sidechain:salt-bridge 34 5lty OP2@F.DT24 NH2@K.ARG238 3.00 po4:sidechain:salt-bridge 35 5lty OP1@E.DG22 NZ@M.LYS216 2.89 po4:sidechain:salt-bridge 36 5lty OP2@E.DG23 NE2@M.GLN235 2.61 po4:sidechain 37 5lty OP1@E.DT24 NE@M.ARG238 3.24 po4:sidechain:salt-bridge 38 5lty OP1@E.DT24 NH1@M.ARG242 2.90 po4:sidechain:salt-bridge 39 5lty OP2@E.DT24 NH2@M.ARG238 3.09 po4:sidechain:salt-bridge **************************************************************************** List of 3 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 5lty O4'@A.DT9 NH1@K.ARG190 2.78 sugar:sidechain 2 5lty O4'@B.DT9 NH1@M.ARG190 2.64 sugar:sidechain 3 5lty O4'@F.DA31 NH2@K.ARG190 3.35 sugar:sidechain **************************************************************************** List of 10 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 5lty O2@A.DT8 NE@K.ARG190 2.88 base:sidechain 2 5lty N7@A.DA10 ND2@K.ASN236 3.26 base:sidechain 3 5lty N6@A.DA10 OD1@K.ASN236 3.48 base:sidechain 4 5lty O2@B.DT8 NE@M.ARG190 2.96 base:sidechain 5 5lty N7@B.DA10 ND2@M.ASN236 3.31 base:sidechain 6 5lty N6@B.DA10 OD1@M.ASN236 3.65 base:sidechain 7 5lty N3@F.DA28 OH@K.TYR189 2.94 base:sidechain 8 5lty N3@F.DA30 NE@K.ARG190 3.16 base:sidechain 9 5lty N3@E.DA28 OH@M.TYR189 2.97 base:sidechain 10 5lty N3@E.DA30 NE@M.ARG190 3.27 base:sidechain **************************************************************************** List of 4 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 5lty A-asn A.DA10 K.ASN236 0.97 34 2 5lty A-asn B.DA10 M.ASN236 1.19 40 3 5lty A-tyr F.DA28 K.TYR189 1.29 56 4 5lty A-tyr E.DA28 M.TYR189 1.34 54 **************************************************************************** List of 3 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 5lty T-asn A.DT9 K.ASN236 3.87 29 2 5lty T-arg B.DT9 M.ARG190 5.16 65 3 5lty T-asn B.DT9 M.ASN236 3.93 36