**************************************************************************** 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=3ssd.pdb -o=3ssd.out File name: 3ssd.pdb no. of peptide chains: 2 [A=155,B=148] no. of DNA/RNA chains: 2 [C=12,D=12] no. of amino acids: 303 no. of nucleotides: 24 no. of atoms: 3106 no. of waters: 136 no. of metals: 0 **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 5CM-c 1 C.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 BB.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 44 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 3ssd A-tyr C.DA5 B.TYR41 5.55 81.68 -4.90 0.98 2.41 0.45 65.75 51.47 2 3ssd C-trp C.5CM6 B.TRP49 10.81 -128.41 -5.43 9.35 -0.16 -10.26 36.77 -125.17 3 3ssd C-ala C.5CM6 B.ALA59 -6.78 99.59 0.10 5.45 -4.03 -42.32 -62.06 70.95 4 3ssd C-ser C.5CM6 B.SER60 -6.01 147.63 3.08 3.98 -3.28 7.25 30.60 146.33 5 3ssd C-tyr C.5CM6 B.TYR64 -9.31 122.05 4.47 -5.24 -6.27 1.06 17.89 121.27 6 3ssd C-val C.5CM6 B.VAL66 -10.01 -173.09 -3.07 9.42 -1.46 -25.28 24.03 -172.76 7 3ssd C-leu C.5CM6 B.LEU68 11.23 -125.66 -2.28 9.15 6.11 -39.27 29.47 -119.73 8 3ssd C-ile C.5CM6 B.ILE82 -4.22 -91.56 2.86 0.17 -3.10 -3.43 -37.09 -85.23 9 3ssd C-ser C.5CM6 B.SER83 -2.13 -164.52 1.23 -1.32 -1.12 51.11 56.46 -160.29 10 3ssd C-asp C.5CM6 B.ASP84 2.84 121.95 -2.07 1.92 0.32 74.46 -3.37 104.86 11 3ssd C-thr C.5CM6 B.THR85 5.75 99.11 -3.45 4.58 0.38 -18.62 17.78 96.57 12 3ssd C-tyr C.5CM6 B.TYR117 5.59 64.46 0.91 0.16 5.51 23.95 38.34 47.21 13 3ssd C-tyr C.DC7 B.TYR41 -7.60 -38.45 -1.43 3.94 -6.34 29.83 24.27 -0.16 14 3ssd C-gly C.DC7 B.GLY42 -5.86 -53.73 -5.29 1.59 -1.96 -29.95 -31.09 -32.78 15 3ssd C-asn C.DC7 B.ASN43 -7.07 95.71 -4.68 5.29 -0.39 50.42 -69.19 47.70 16 3ssd G-gly C.DG8 A.GLY42 5.56 66.31 -4.85 -1.21 2.43 -41.96 43.18 29.18 17 3ssd G-asn C.DG8 A.ASN43 6.85 -96.17 -4.81 -4.73 1.22 39.76 67.70 -60.76 18 3ssd G-asn C.DG8 B.ASN43 -7.97 95.23 -5.70 4.07 -3.81 13.81 -85.81 43.54 19 3ssd G-tyr C.DG9 A.TYR41 7.47 -57.25 -5.65 -2.66 4.10 3.75 -20.46 -53.64 20 3ssd G-gly C.DG9 A.GLY42 6.56 -68.27 -5.95 2.13 -1.73 -22.45 59.99 -25.01 21 3ssd T-gln C.DT10 A.GLN21 10.30 -35.25 -9.39 3.92 -1.60 -1.08 30.93 -17.10 22 3ssd T-tyr C.DT10 A.TYR41 -5.25 -67.39 -5.12 -0.90 -0.73 4.69 -40.06 -55.17 23 3ssd T-gly C.DT10 A.GLY42 -6.33 -57.23 -1.90 4.13 -4.40 -23.77 41.37 -32.58 24 3ssd A-tyr D.DA5 A.TYR41 5.57 80.04 -5.00 0.97 2.27 5.38 64.68 49.67 25 3ssd C-trp D.DC6 A.TRP49 10.54 -132.38 -5.26 9.13 0.05 -7.06 35.67 -129.71 26 3ssd C-ala D.DC6 A.ALA59 -6.61 100.31 0.07 5.20 -4.09 -43.87 -63.65 69.75 27 3ssd C-ser D.DC6 A.SER60 -5.90 140.53 2.82 3.71 -3.62 11.78 29.11 138.94 28 3ssd C-tyr D.DC6 A.TYR64 -9.10 118.08 4.14 -5.46 -5.99 -3.61 17.78 117.21 29 3ssd C-ile D.DC6 A.ILE82 -3.93 -98.57 2.87 -0.06 -2.69 -2.00 -40.13 -92.02 30 3ssd C-ser D.DC6 A.SER83 -1.96 -164.65 1.05 -1.42 -0.87 55.50 54.25 -160.26 31 3ssd C-asp D.DC6 A.ASP84 3.25 119.32 -2.18 2.38 0.35 67.10 -10.55 104.97 32 3ssd C-thr D.DC6 A.THR85 -6.03 94.46 -3.45 4.93 0.45 -23.44 15.90 91.09 33 3ssd C-tyr D.DC6 A.TYR117 5.58 61.24 0.28 0.48 5.55 26.33 37.25 42.00 34 3ssd C-tyr D.DC7 A.TYR41 -8.05 47.88 -1.22 4.18 -6.77 43.03 20.83 2.70 35 3ssd C-gly D.DC7 A.GLY42 -6.45 -50.07 -5.57 2.10 -2.50 -20.19 -29.60 -35.56 36 3ssd C-asn D.DC7 A.ASN43 -7.26 -124.15 -6.94 -1.91 -0.92 -76.81 -29.02 -103.22 37 3ssd G-asn D.DG8 A.ASN43 -7.95 93.77 -5.92 3.74 -3.75 16.16 -83.31 44.36 38 3ssd G-gly D.DG8 B.GLY42 5.50 70.37 -4.77 -1.15 2.51 -43.55 46.29 31.93 39 3ssd G-asn D.DG8 B.ASN43 6.86 -96.01 -4.71 -4.79 1.39 33.26 68.24 -63.89 40 3ssd G-tyr D.DG9 B.TYR41 7.74 -58.34 -5.85 -2.65 4.33 2.54 -20.17 -54.97 41 3ssd G-gly D.DG9 B.GLY42 6.75 -67.11 -6.16 2.26 -1.58 -19.00 59.73 -25.30 42 3ssd T-gln D.DT10 B.GLN21 10.54 -37.58 -9.37 4.58 -1.57 3.45 35.02 -13.41 43 3ssd T-tyr D.DT10 B.TYR41 -5.68 -66.41 -5.56 -0.85 -0.79 2.36 -35.07 -57.27 44 3ssd T-gly D.DT10 B.GLY42 -6.70 -59.01 -2.11 4.23 -4.74 -20.34 45.87 -32.11 **************************************************************************** List of 14 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 3ssd AT-gln C.DA5 D.DT10 B.GLN21 10.42 25.61 -8.97 -4.38 3.01 -4.22 -21.40 13.50 2 3ssd AT-gln D.DA5 C.DT10 A.GLN21 10.34 26.14 -9.15 -3.83 2.93 -5.97 -19.34 16.62 3 3ssd AT-gly C.DA5 D.DT10 B.GLY42 6.72 52.84 -1.28 -4.05 5.20 -25.31 -31.13 35.12 4 3ssd AT-gly D.DA5 C.DT10 A.GLY42 6.56 52.04 -1.34 -4.13 4.92 -26.83 -29.14 34.46 5 3ssd AT-tyr C.DA5 D.DT10 B.TYR41 5.61 72.86 -5.29 0.91 1.63 1.20 50.40 54.44 6 3ssd AT-tyr D.DA5 C.DT10 A.TYR41 5.41 72.94 -5.11 0.93 1.50 4.86 52.37 52.47 7 3ssd GC-asn D.DG8 C.DC7 A.ASN43 -7.82 -160.43 -6.23 1.64 -4.44 -80.63 -29.74 -153.14 8 3ssd GC-asn D.DG8 C.DC7 B.ASN43 6.96 -95.41 -4.70 -5.05 0.93 41.89 68.91 -56.07 9 3ssd GC-asn C.DG8 D.DC7 A.ASN43 7.04 -99.50 -4.99 -4.86 0.99 50.33 72.40 -51.78 10 3ssd GC-asn C.DG8 D.DC7 B.ASN43 -7.67 -158.91 -6.60 1.18 -3.72 -79.99 -25.32 -151.51 11 3ssd GC-gly D.DG8 C.DC7 B.GLY42 5.68 61.78 -5.03 -1.37 2.25 -36.78 38.66 32.35 12 3ssd GC-gly C.DG8 D.DC7 A.GLY42 6.00 57.28 -5.20 -1.63 2.51 -31.11 36.35 32.47 13 3ssd GC-tyr D.DG8 C.DC7 B.TYR41 7.43 28.42 -1.11 -3.44 6.49 21.00 -19.14 0.20 14 3ssd GC-tyr C.DG8 D.DC7 A.TYR41 7.65 -35.44 -1.08 -3.54 6.70 30.08 -18.59 -2.34 **************************************************************************** List of 21 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 3ssd OP1.A@C.5CM6 NZ@B.LYS36 3.65 po4:sidechain:salt-bridge 2 3ssd OP2.A@C.5CM6 OG@B.SER60 2.73 po4:sidechain 3 3ssd OP1.A@C.DC7 OG@B.SER38 2.65 po4:sidechain 4 3ssd OP2.A@C.DC7 NE1@B.TRP49 2.73 po4:sidechain 5 3ssd OP1.A@C.DG8 OG1@B.THR45 2.66 po4:sidechain 6 3ssd OP1.A@C.DG8 N@B.SER46 3.50 po4:backbone 7 3ssd OP2.A@C.DG8 NZ@B.LYS116 3.01 po4:sidechain:salt-bridge 8 3ssd OP1.A@C.DA11 N@A.GLN21 2.46 po4:backbone 9 3ssd OP1.A@C.DG12 OG@A.SER22 2.71 po4:sidechain 10 3ssd OP1.A@C.DG12 N@A.THR23 3.00 po4:backbone 11 3ssd OP1.A@C.DG12 N@A.LYS24 2.99 po4:backbone 12 3ssd OP2.A@D.DC6 OG@A.SER60 2.90 po4:sidechain 13 3ssd OP1.A@D.DC7 OG@A.SER38 2.72 po4:sidechain 14 3ssd OP2.A@D.DC7 NE1@A.TRP49 2.68 po4:sidechain 15 3ssd OP1.A@D.DG8 OG1@A.THR45 2.60 po4:sidechain 16 3ssd OP1.A@D.DG8 N@A.SER46 3.54 po4:backbone 17 3ssd OP2.A@D.DG8 NZ@A.LYS116 3.09 po4:sidechain:salt-bridge 18 3ssd OP1.A@D.DC11 N@B.GLN21 2.91 po4:backbone 19 3ssd OP1.A@D.DT12 OG@B.SER22 2.68 po4:sidechain 20 3ssd OP1.A@D.DT12 N@B.THR23 3.40 po4:backbone 21 3ssd OP1.A@D.DT12 N@B.LYS24 3.26 po4:backbone **************************************************************************** List of 6 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 3ssd O4'.A@C.DC7 N@B.TYR41 3.20 sugar:backbone 2 3ssd O4'.A@C.DG8 ND2@B.ASN43 3.06 sugar:sidechain 3 3ssd O4'.A@C.DT10 N@A.GLY42 3.14 sugar:backbone 4 3ssd O4'.A@D.DC7 N@A.TYR41 3.02 sugar:backbone 5 3ssd O4'.A@D.DG8 ND2@A.ASN43 3.42 sugar:sidechain 6 3ssd O4'.A@D.DT10 N@B.GLY42 3.19 sugar:backbone **************************************************************************** List of 14 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 3ssd N3.A@C.5CM6 N@B.ASP84 2.97 base:backbone 2 3ssd O2.A@C.5CM6 N@B.THR85 3.01 base:backbone 3 3ssd O2.A@C.5CM6 OG1@B.THR85 2.74 base:sidechain 4 3ssd N4.A@C.5CM6 O@B.ILE82 2.94 base:backbone 5 3ssd O2.A@C.DC7 N@B.ASN43 2.96 base:backbone 6 3ssd N2.A@C.DG9 O@A.TYR41 3.06 base:backbone 7 3ssd O2.A@D.DC6 N@A.ASP84 3.15 base:backbone 8 3ssd O2.A@D.DC6 N@A.THR85 2.85 base:backbone 9 3ssd O2.A@D.DC6 OG1@A.THR85 2.76 base:sidechain 10 3ssd N3.A@D.DC6 N@A.ASP84 3.05 base:backbone 11 3ssd N4.A@D.DC6 O@A.ILE82 3.21 base:backbone 12 3ssd O2.A@D.DC7 N@A.ASN43 3.27 base:backbone 13 3ssd N2.A@D.DG8 OD1@B.ASN43 3.31 base:sidechain 14 3ssd N2.A@D.DG9 O@B.TYR41 3.34 base:backbone **************************************************************************** List of 6 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 3ssd A-tyr C.DA5 B.TYR41 3.48 18 2 3ssd C-tyr C.5CM6 B.TYR117 3.20 24 3 3ssd C-tyr C.DC7 B.TYR41 4.03 38 4 3ssd A-tyr D.DA5 A.TYR41 3.49 19 5 3ssd C-tyr D.DC6 A.TYR117 3.28 28 6 3ssd C-tyr D.DC7 A.TYR41 3.94 45 **************************************************************************** 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