**************************************************************************** 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=3ssc.pdb -o=3ssc.out File name: 3ssc.pdb no. of peptide chains: 2 [A=154,B=154] no. of DNA/RNA chains: 2 [C=12,D=12] no. of amino acids: 308 no. of nucleotides: 24 no. of atoms: 3261 no. of waters: 251 no. of metals: 0 **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 5CM-c 2 C.5CM6,D.5CM6 **************************************************************************** List of 1 helix 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=10 strand-1 5'-GAGACGTAGC-3' bp-type |||||||||| strand-2 3'-CTCTGCATCG-5' helix-form B..x.x.B. 1 C.DG2 D.DC13 G-C WC 19-XIX cWW cW-W 2 C.DA3 D.DT12 A-T WC 20-XX cWW cW-W 3 C.DG4 D.DC11 G-C WC 19-XIX cWW cW-W 4 C.DA5 D.DT10 A-T WC 20-XX cWW cW-W 5 C.DC7 D.DG8 C-G WC 19-XIX cWW cW-W 6 C.DG8 D.DC7 G-C WC 19-XIX cWW cW-W 7 C.DT10 D.DA5 T-A WC 20-XX cWW cW-W 8 C.DA11 D.DT4 A-T WC 20-XX cWW cW-W 9 C.DG12 D.DC3 G-C WC 19-XIX cWW cW-W 10 C.DC13 D.DG2 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 48 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 3ssc A-tyr C.DA5 B.TYR41 5.38 81.54 -4.82 1.05 2.15 4.02 63.41 54.06 2 3ssc C-trp C.5CM6 B.TRP49 10.89 -128.00 -5.46 9.42 -0.19 -14.01 36.88 -124.49 3 3ssc C-ala C.5CM6 B.ALA59 -6.56 92.51 0.03 5.53 -3.54 -42.26 -59.73 61.12 4 3ssc C-ser C.5CM6 B.SER60 -6.03 146.34 3.13 4.23 -2.94 5.79 31.54 144.93 5 3ssc C-tyr C.5CM6 B.TYR64 -9.21 122.89 4.64 -5.17 -6.05 3.05 19.98 121.90 6 3ssc C-val C.5CM6 B.VAL66 -10.08 -173.18 -3.35 9.39 -1.48 -26.05 21.66 -172.87 7 3ssc C-leu C.5CM6 B.LEU68 11.42 -128.23 -2.83 9.31 5.99 -42.23 26.82 -122.40 8 3ssc C-ile C.5CM6 B.ILE82 -3.98 -89.95 2.77 0.32 -2.85 -4.93 -37.49 -83.21 9 3ssc C-ser C.5CM6 B.SER83 -1.96 -159.96 0.99 -1.22 -1.18 49.91 57.05 -154.52 10 3ssc C-asp C.5CM6 B.ASP84 2.81 124.06 -1.92 2.02 0.31 78.04 -5.46 105.62 11 3ssc C-thr C.5CM6 B.THR85 5.73 102.61 -3.20 4.70 0.69 -19.80 17.03 100.16 12 3ssc C-tyr C.5CM6 B.TYR117 5.74 67.58 0.98 0.59 5.63 23.78 42.88 48.02 13 3ssc C-ser C.5CM6 B.SER120 6.81 91.79 1.51 -5.26 4.06 25.31 39.29 81.39 14 3ssc C-tyr C.DC7 B.TYR41 -8.15 48.44 -0.81 4.44 -6.78 44.75 17.97 4.81 15 3ssc C-gly C.DC7 B.GLY42 -6.41 -51.77 -5.31 2.45 -2.62 -18.15 -31.97 -37.10 16 3ssc C-asn C.DC7 B.ASN43 -7.18 -123.53 -6.94 -1.66 -0.78 -70.91 -32.07 -105.11 17 3ssc G-gly C.DG8 A.GLY42 5.34 64.86 -4.81 -1.06 2.07 -42.15 39.24 31.23 18 3ssc G-asn C.DG8 A.ASN43 6.70 -93.60 -4.52 -4.87 0.79 40.97 65.79 -57.25 19 3ssc G-asn C.DG8 B.ASN43 -7.91 -164.42 -6.28 1.83 -4.44 -81.72 -34.93 -158.12 20 3ssc G-tyr C.DG9 A.TYR41 7.38 -56.31 -5.68 -2.56 3.97 0.93 -19.02 -53.24 21 3ssc G-gly C.DG9 A.GLY42 6.55 -70.27 -5.84 2.33 -1.82 -24.23 62.34 -22.92 22 3ssc T-gln C.DT10 A.GLN21 10.14 -35.38 -9.10 4.10 -1.76 2.76 32.08 -14.86 23 3ssc T-tyr C.DT10 A.TYR41 -5.35 -67.78 -5.22 -0.59 -1.04 6.04 -37.37 -57.30 24 3ssc T-gly C.DT10 A.GLY42 -6.60 -56.60 -1.67 4.58 -4.44 -21.06 44.02 -29.59 25 3ssc A-tyr D.DA5 A.TYR41 5.37 78.66 -4.88 0.99 2.01 5.65 58.98 54.29 26 3ssc C-trp D.5CM6 A.TRP49 10.94 -129.48 -5.69 9.35 0.05 -15.47 37.15 -125.93 27 3ssc C-ala D.5CM6 A.ALA59 -6.73 90.85 0.22 5.56 -3.79 -39.32 -57.83 62.16 28 3ssc C-ser D.5CM6 A.SER60 -5.99 144.95 3.16 3.98 -3.16 10.22 29.77 143.54 29 3ssc C-tyr D.5CM6 A.TYR64 -9.35 123.52 4.74 -5.24 -6.12 4.37 17.87 122.72 30 3ssc C-val D.5CM6 A.VAL66 -10.11 -173.57 -3.41 9.40 -1.53 -27.21 25.48 -173.21 31 3ssc C-leu D.5CM6 A.LEU68 11.26 -127.07 -2.60 9.24 5.88 -40.51 28.96 -121.15 32 3ssc C-ile D.5CM6 A.ILE82 -4.05 -92.42 2.73 0.45 -2.96 -3.09 -34.86 -86.96 33 3ssc C-ser D.5CM6 A.SER83 -1.92 -165.78 0.96 -1.17 -1.18 52.86 59.75 -161.43 34 3ssc C-asp D.5CM6 A.ASP84 2.76 120.32 -1.82 2.03 0.41 74.92 -7.10 102.15 35 3ssc C-thr D.5CM6 A.THR85 5.67 100.54 -3.07 4.74 0.48 -17.32 16.76 98.37 36 3ssc C-tyr D.5CM6 A.TYR117 5.71 69.26 0.96 0.43 5.61 26.26 44.04 48.25 37 3ssc C-ser D.5CM6 A.SER120 6.87 94.96 1.38 -5.46 3.94 28.25 39.13 84.44 38 3ssc C-tyr D.DC7 A.TYR41 -7.41 36.60 -1.42 3.99 -6.08 27.95 23.62 0.94 39 3ssc C-gly D.DC7 A.GLY42 -5.63 -56.79 -5.15 1.61 -1.62 -34.28 -32.39 -32.59 40 3ssc C-asn D.DC7 A.ASN43 -7.02 95.05 -4.41 5.44 -0.48 49.69 -67.73 49.34 41 3ssc G-asn D.DG8 A.ASN43 -7.73 95.68 -5.40 3.96 -3.87 14.73 -85.71 44.63 42 3ssc G-gly D.DG8 B.GLY42 5.39 68.37 -4.66 -1.18 2.42 -45.80 42.03 30.01 43 3ssc G-asn D.DG8 B.ASN43 6.70 -95.76 -4.53 -4.75 1.34 37.99 65.92 -63.23 44 3ssc G-tyr D.DG9 B.TYR41 7.45 -59.07 -5.69 -2.60 4.04 1.86 -21.95 -55.16 45 3ssc G-gly D.DG9 B.GLY42 6.44 -69.44 -5.79 2.15 -1.81 -23.75 59.95 -27.27 46 3ssc T-gln D.DT10 B.GLN21 10.06 -34.59 -8.91 4.28 -1.88 7.17 32.54 -9.43 47 3ssc T-tyr D.DT10 B.TYR41 -5.50 -66.47 -5.32 -0.56 -1.28 10.47 -35.57 -56.19 48 3ssc T-gly D.DT10 B.GLY42 -6.81 -55.23 -1.68 4.79 -4.54 -18.83 44.59 -27.43 **************************************************************************** List of 14 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 3ssc AT-gln C.DA5 D.DT10 B.GLN21 10.06 23.98 -8.71 -4.08 2.95 -0.29 -20.66 12.24 2 3ssc AT-gln D.DA5 C.DT10 A.GLN21 10.11 26.87 -8.94 -3.86 2.71 -1.70 -22.14 15.22 3 3ssc AT-gly C.DA5 D.DT10 B.GLY42 6.62 51.53 -1.08 -4.34 4.88 -23.66 -32.12 33.30 4 3ssc AT-gly D.DA5 C.DT10 A.GLY42 6.53 51.89 -1.20 -4.31 4.76 -23.90 -33.65 32.17 5 3ssc AT-tyr C.DA5 D.DT10 B.TYR41 5.44 73.24 -5.09 0.80 1.75 7.49 49.54 55.25 6 3ssc AT-tyr D.DA5 C.DT10 A.TYR41 5.36 72.67 -5.07 0.79 1.54 5.80 48.18 55.83 7 3ssc GC-asn D.DG8 C.DC7 A.ASN43 -7.32 -156.69 -6.51 1.11 -3.17 -81.47 -23.32 -148.26 8 3ssc GC-asn D.DG8 C.DC7 B.ASN43 6.91 -102.36 -4.71 -4.86 1.40 50.01 73.76 -56.77 9 3ssc GC-asn C.DG8 D.DC7 A.ASN43 6.86 -94.20 -4.47 -5.16 0.65 45.34 66.80 -53.38 10 3ssc GC-asn C.DG8 D.DC7 B.ASN43 -7.77 -161.53 -6.32 1.72 -4.18 -78.41 -31.47 -154.95 11 3ssc GC-gly D.DG8 C.DC7 B.GLY42 5.89 58.88 -4.97 -1.78 2.60 -31.94 37.14 33.73 12 3ssc GC-gly C.DG8 D.DC7 A.GLY42 5.48 60.74 -4.98 -1.34 1.86 -38.23 35.80 31.92 13 3ssc GC-tyr D.DG8 C.DC7 B.TYR41 7.64 -34.87 -0.85 -3.59 6.70 29.91 -17.78 -2.35 14 3ssc GC-tyr C.DG8 D.DC7 A.TYR41 7.21 -31.69 -1.28 -3.54 6.15 23.03 -21.75 -0.86 **************************************************************************** List of 21 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 3ssc OP2.A@C.5CM6 OG@B.SER60 2.55 po4:sidechain 2 3ssc OP1.A@C.DC7 OG@B.SER38 2.65 po4:sidechain 3 3ssc OP2.A@C.DC7 NE1@B.TRP49 2.64 po4:sidechain 4 3ssc OP2.A@C.DC7 OH@B.TYR117 3.89 po4:sidechain 5 3ssc OP1.A@C.DG8 OG1@B.THR45 2.69 po4:sidechain 6 3ssc OP1.A@C.DG8 N@B.SER46 3.75 po4:backbone 7 3ssc OP2.A@C.DG8 NZ@B.LYS116 2.82 po4:sidechain:salt-bridge 8 3ssc OP1.A@C.DA11 OG@A.SER20 3.64 po4:sidechain 9 3ssc OP1.A@C.DA11 N@A.GLN21 2.77 po4:backbone 10 3ssc OP1.A@C.DG12 OG@A.SER22 2.69 po4:sidechain 11 3ssc OP1.A@C.DG12 N@A.THR23 2.80 po4:backbone 12 3ssc OP1.A@C.DG12 N@A.LYS24 2.81 po4:backbone 13 3ssc OP2.A@D.5CM6 OG@A.SER60 2.68 po4:sidechain 14 3ssc OP1.A@D.DC7 OG@A.SER38 2.65 po4:sidechain 15 3ssc OP2.A@D.DC7 NE1@A.TRP49 2.58 po4:sidechain 16 3ssc OP1.A@D.DG8 OG1@A.THR45 2.71 po4:sidechain 17 3ssc OP1.A@D.DG8 N@A.SER46 3.52 po4:backbone 18 3ssc OP1.A@D.DC11 N@B.GLN21 2.95 po4:backbone 19 3ssc OP1.A@D.DT12 OG@B.SER22 2.68 po4:sidechain 20 3ssc OP1.A@D.DT12 N@B.THR23 2.95 po4:backbone 21 3ssc OP1.A@D.DT12 N@B.LYS24 2.86 po4:backbone **************************************************************************** List of 6 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 3ssc O4'.A@C.DC7 N@B.TYR41 3.02 sugar:backbone 2 3ssc O4'.A@C.DG8 ND2@B.ASN43 3.03 sugar:sidechain 3 3ssc O4'.A@C.DT10 N@A.GLY42 3.13 sugar:backbone 4 3ssc O4'.A@D.DC7 N@A.TYR41 3.01 sugar:backbone 5 3ssc O4'.A@D.DG8 ND2@A.ASN43 3.04 sugar:sidechain 6 3ssc O4'.A@D.DT10 N@B.GLY42 3.21 sugar:backbone **************************************************************************** List of 13 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 3ssc N3.A@C.5CM6 N@B.ASP84 2.81 base:backbone 2 3ssc O2.A@C.5CM6 N@B.THR85 2.83 base:backbone 3 3ssc O2.A@C.5CM6 OG1@B.THR85 2.60 base:sidechain 4 3ssc N4.A@C.5CM6 O@B.ILE82 2.80 base:backbone 5 3ssc O2.A@C.DC7 N@B.ASN43 3.17 base:backbone 6 3ssc N2.A@C.DG8 OD1@A.ASN43 3.29 base:sidechain 7 3ssc N2.A@C.DG9 O@A.TYR41 3.03 base:backbone 8 3ssc N3.A@D.5CM6 N@A.ASP84 2.72 base:backbone 9 3ssc O2.A@D.5CM6 N@A.THR85 2.68 base:backbone 10 3ssc O2.A@D.5CM6 OG1@A.THR85 2.62 base:sidechain 11 3ssc N4.A@D.5CM6 O@A.ILE82 2.69 base:backbone 12 3ssc O2.A@D.DC7 N@A.ASN43 2.77 base:backbone 13 3ssc N2.A@D.DG9 O@B.TYR41 3.05 base:backbone **************************************************************************** List of 6 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 3ssc A-tyr C.DA5 B.TYR41 3.45 19 2 3ssc C-tyr C.5CM6 B.TYR117 3.15 22 3 3ssc C-tyr C.DC7 B.TYR41 3.81 50 4 3ssc A-tyr D.DA5 A.TYR41 3.49 18 5 3ssc C-tyr D.5CM6 A.TYR117 3.19 21 6 3ssc C-tyr D.DC7 A.TYR41 3.88 35 **************************************************************************** List of 2 interface stack(s) 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 AYC C.DA5,B.TYR41,C.DC7 2 size=3 AYC D.DA5,A.TYR41,D.DC7