**************************************************************************** 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=5vmz.pdb -o=5vmz.out File name: 5vmz.pdb no. of peptide chains: 1 [A=122] no. of DNA/RNA chains: 2 [D=18,E=18] no. of amino acids: 122 no. of nucleotides: 36 no. of atoms: 1868 no. of waters: 84 no. of metals: 3 [Zn=3] **************************************************************************** List of 1 type of 4 modified nucleotides nt count list 1 5CM-c 4 D.5CM8,D.5CM10,E.5CM26,E.5CM28 **************************************************************************** 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=18 strand-1 5'-TGCTTCCcGcGAATAACG-3' bp-type |||||||||||||||||| strand-2 3'-ACGAAGGGcGcTTATTGC-5' helix-form BBBBBBBBBBBBBBBBB 1 D.DT1 E.DA36 T-A WC 20-XX cWW cW-W 2 D.DG2 E.DC35 G-C WC 19-XIX cWW cW-W 3 D.DC3 E.DG34 C-G WC 19-XIX cWW cW-W 4 D.DT4 E.DA33 T-A WC 20-XX cWW cW-W 5 D.DT5 E.DA32 T-A WC 20-XX cWW cW-W 6 D.DC6 E.DG31 C-G WC 19-XIX cWW cW-W 7 D.DC7 E.DG30 C-G WC 19-XIX cWW cW-W 8 D.5CM8 E.DG29 c-G WC 19-XIX cWW cW-W 9 D.DG9 E.5CM28 G-c WC 19-XIX cWW cW-W 10 D.5CM10 E.DG27 c-G WC 19-XIX cWW cW-W 11 D.DG11 E.5CM26 G-c WC 19-XIX cWW cW-W 12 D.DA12 E.DT25 A-T WC 20-XX cWW cW-W 13 D.DA13 E.DT24 A-T WC 20-XX cWW cW-W 14 D.DT14 E.DA23 T-A WC 20-XX cWW cW-W 15 D.DA15 E.DT22 A-T WC 20-XX cWW cW-W 16 D.DA16 E.DT21 A-T WC 20-XX cWW cW-W 17 D.DC17 E.DG20 C-G WC 19-XIX cWW cW-W 18 D.DG18 E.DC19 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 38 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5vmz T-gln D.DT4 A.GLN563 9.07 -153.75 -5.55 7.09 1.12 5.17 69.68 -147.84 2 5vmz T-phe D.DT4 A.PHE564 11.25 128.83 9.51 -0.66 5.98 20.34 34.69 125.24 3 5vmz T-asn D.DT5 A.ASN561 11.46 175.83 5.75 -8.98 4.22 -11.99 40.42 175.53 4 5vmz T-gln D.DT5 A.GLN563 7.98 174.18 1.89 -7.40 -2.32 -18.52 -57.57 173.26 5 5vmz C-gln D.DC6 A.GLN563 -8.29 141.40 -1.27 -5.92 -5.66 -33.92 -50.33 134.97 6 5vmz C-gln D.DC7 A.GLN535 9.83 -151.30 -4.03 7.81 4.41 -7.54 40.00 -149.34 7 5vmz C-tyr D.DC7 A.TYR536 10.40 117.74 7.61 -1.21 6.99 24.34 59.45 104.76 8 5vmz C-arg D.5CM8 A.ARG511 12.16 -120.05 -7.63 8.66 3.84 -16.63 24.93 -117.71 9 5vmz C-leu D.5CM8 A.LEU533 12.04 -179.65 -6.05 10.23 1.86 35.94 -65.66 -179.56 10 5vmz C-gln D.5CM8 A.GLN535 9.31 -173.43 -1.50 9.04 1.63 0.42 24.50 -173.28 11 5vmz G-ser D.DG9 A.SER508 9.02 -173.97 -5.74 5.58 -4.15 37.45 67.95 -172.26 12 5vmz G-arg D.DG9 A.ARG511 10.83 -155.98 -2.57 10.45 1.20 -1.30 26.86 -155.30 13 5vmz C-cys D.5CM10 A.CYS505 -10.88 -144.82 -5.02 9.50 1.73 14.71 -64.22 -137.79 14 5vmz C-thr D.5CM10 A.THR507 9.52 -171.15 -3.35 7.74 4.40 -33.24 4.72 -170.75 15 5vmz C-ser D.5CM10 A.SER508 -8.62 161.44 3.09 -4.68 -6.55 -57.13 -53.70 155.98 16 5vmz C-arg D.5CM10 A.ARG511 -9.95 172.03 -0.51 -9.73 -2.02 -8.26 -24.97 171.82 17 5vmz G-arg D.DG11 A.ARG595 11.98 32.34 -11.09 -2.85 3.53 22.40 3.02 23.29 18 5vmz G-tyr D.DG11 A.TYR597 12.19 68.68 -10.66 1.29 -5.77 14.32 66.27 11.72 19 5vmz A-arg D.DA12 A.ARG595 10.83 -25.98 -10.77 -0.75 0.86 21.59 0.35 -14.53 20 5vmz A-tyr D.DA12 A.TYR597 -11.21 -75.65 -7.74 2.80 -7.62 33.82 62.67 -27.43 21 5vmz A-arg D.DA13 A.ARG595 -11.40 -54.50 -10.93 2.13 -2.46 16.12 -7.03 -51.80 22 5vmz T-thr E.DT25 A.THR507 9.77 -118.20 -2.89 9.25 1.22 17.29 19.30 -116.40 23 5vmz T-arg E.DT25 A.ARG595 10.68 34.50 -10.65 0.81 0.20 29.91 10.70 13.64 24 5vmz C-thr E.5CM26 A.THR507 -7.75 -150.86 -0.09 7.56 -1.71 18.50 0.53 -150.46 25 5vmz C-arg E.5CM26 A.ARG511 9.91 -141.12 -5.17 7.74 3.39 -28.70 8.43 -139.70 26 5vmz C-arg E.5CM26 A.ARG595 -12.23 -28.86 -11.46 2.85 -3.18 18.72 -0.95 -22.05 27 5vmz C-tyr E.5CM26 A.TYR597 -12.41 -65.41 -10.60 -1.04 6.38 12.02 -63.82 -8.27 28 5vmz G-arg E.DG27 A.ARG511 -10.21 -175.61 -0.51 10.18 0.67 -20.17 21.61 -175.45 29 5vmz G-gln E.DG27 A.GLN535 9.55 -122.55 -5.77 6.84 3.34 -35.61 21.48 -118.13 30 5vmz G-arg E.DG27 A.ARG595 -12.17 -64.21 -8.90 5.21 -6.47 23.59 -8.29 -59.63 31 5vmz G-tyr E.DG27 A.TYR597 -11.84 -81.13 -11.44 1.60 2.61 -3.78 -66.24 -49.66 32 5vmz C-arg E.5CM28 A.ARG511 -10.62 152.01 -2.69 -9.95 -2.57 11.85 -26.02 151.10 33 5vmz C-gln E.5CM28 A.GLN535 -9.56 -153.59 -3.29 8.98 0.10 -27.03 29.85 -151.83 34 5vmz C-lys E.5CM28 A.LYS539 13.38 -142.21 -7.57 8.93 6.47 -66.26 35.00 -131.84 35 5vmz G-gln E.DG29 A.GLN535 -9.44 171.76 -1.35 -9.05 -2.31 9.65 -24.34 171.54 36 5vmz G-tyr E.DG30 A.TYR562 9.15 -147.92 -5.40 7.19 -1.68 26.80 17.21 -146.61 37 5vmz G-gln E.DG30 A.GLN563 9.27 -122.59 -4.46 4.36 6.85 -62.22 26.93 -109.29 38 5vmz G-gln E.DG31 A.GLN563 8.44 -150.11 -1.50 7.11 4.30 -49.51 42.42 -144.35 **************************************************************************** List of 31 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5vmz AT-arg D.DA12 E.DT25 A.ARG595 -10.76 -29.78 -10.72 -0.79 0.33 25.80 -5.14 -14.10 2 5vmz AT-arg D.DA13 E.DT24 A.ARG595 -11.27 -57.87 -10.76 2.35 -2.39 24.13 -9.87 -52.12 3 5vmz AT-asn E.DA32 D.DT5 A.ASN561 -11.44 -174.15 5.70 8.70 -4.76 -19.98 -41.71 -173.64 4 5vmz AT-gln E.DA33 D.DT4 A.GLN563 -9.05 147.67 -5.83 -6.76 -1.51 10.50 -64.60 141.35 5 5vmz AT-gln E.DA32 D.DT5 A.GLN563 -7.99 -179.04 1.97 7.55 1.75 -25.29 56.62 -178.88 6 5vmz AT-phe E.DA33 D.DT4 A.PHE564 -11.19 -126.98 9.32 0.17 -6.18 11.46 -33.47 -124.13 7 5vmz AT-thr D.DA12 E.DT25 A.THR507 -9.70 117.16 -2.98 -9.13 -1.37 20.53 -13.21 115.53 8 5vmz AT-tyr D.DA12 E.DT25 A.TYR597 -11.13 -72.70 -7.33 3.10 -7.78 38.13 57.91 -23.39 9 5vmz GC-arg E.DG29 D.5CM8 A.ARG511 -12.10 119.05 -7.58 -8.55 -3.98 -12.55 -22.70 117.28 10 5vmz GC-arg D.DG9 E.5CM28 A.ARG511 10.72 -153.95 -2.63 10.22 1.89 5.28 26.45 -153.20 11 5vmz GC-arg E.DG27 D.5CM10 A.ARG511 10.08 -173.81 -0.52 9.97 1.35 -14.22 23.30 -173.63 12 5vmz GC-arg E.DG27 D.5CM10 A.ARG595 -12.07 -65.80 -8.73 5.32 -6.42 28.43 -12.38 -58.78 13 5vmz GC-arg D.DG11 E.5CM26 A.ARG511 -9.86 141.32 -4.93 -7.82 -3.44 -26.92 -9.70 140.03 14 5vmz GC-arg D.DG11 E.5CM26 A.ARG595 12.10 30.58 -11.27 -2.85 3.36 20.57 1.97 22.67 15 5vmz GC-cys E.DG27 D.5CM10 A.CYS505 -10.88 147.67 -4.83 -9.53 -2.03 19.34 68.40 139.98 16 5vmz GC-gln E.DG31 D.DC6 A.GLN563 8.36 -145.67 -1.39 6.55 5.01 -41.82 46.56 -139.59 17 5vmz GC-gln E.DG30 D.DC7 A.GLN535 -9.93 151.68 -4.32 -7.91 -4.18 -8.61 -30.95 150.50 18 5vmz GC-gln E.DG30 D.DC7 A.GLN563 9.33 -117.22 -4.09 3.68 7.54 -56.27 32.67 -103.68 19 5vmz GC-gln E.DG29 D.5CM8 A.GLN535 -9.37 172.59 -1.43 -9.05 -1.97 5.04 -24.44 172.41 20 5vmz GC-gln D.DG9 E.5CM28 A.GLN535 9.58 151.70 -3.27 -8.98 -0.60 -21.00 -26.89 150.37 21 5vmz GC-gln E.DG27 D.5CM10 A.GLN535 9.45 -120.36 -5.84 6.43 3.72 -29.47 19.99 -117.02 22 5vmz GC-leu E.DG29 D.5CM8 A.LEU533 -12.06 -177.69 5.86 10.28 -2.29 -39.96 -65.74 -177.05 23 5vmz GC-lys D.DG9 E.5CM28 A.LYS539 -13.36 140.54 -7.71 -8.59 -6.73 -60.68 -31.04 131.90 24 5vmz GC-ser D.DG9 E.5CM28 A.SER508 8.91 -170.24 -5.82 5.67 -3.64 43.17 69.08 -167.11 25 5vmz GC-ser E.DG27 D.5CM10 A.SER508 8.68 -165.34 3.02 5.22 6.24 -62.73 53.53 -160.46 26 5vmz GC-thr E.DG27 D.5CM10 A.THR507 -9.62 171.22 -3.35 -7.60 -4.85 -27.42 -2.08 170.96 27 5vmz GC-thr D.DG11 E.5CM26 A.THR507 7.85 151.87 0.10 -7.65 1.76 20.12 -1.68 151.42 28 5vmz GC-tyr E.DG30 D.DC7 A.TYR536 -10.43 -115.04 7.89 0.93 -6.76 18.66 -65.43 -99.24 29 5vmz GC-tyr E.DG30 D.DC7 A.TYR562 9.13 -150.13 -5.47 7.27 -0.86 30.58 25.45 -148.18 30 5vmz GC-tyr E.DG27 D.5CM10 A.TYR597 -11.84 -86.00 -11.51 1.45 2.36 0.34 -70.75 -52.47 31 5vmz GC-tyr D.DG11 E.5CM26 A.TYR597 12.30 67.02 -10.63 1.17 -6.08 13.17 65.04 9.99 **************************************************************************** List of 18 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 5vmz OP2@D.DC7 OH@A.TYR536 2.73 po4:sidechain 2 5vmz OP1@D.5CM8 NH1@A.ARG501 3.39 po4:sidechain:salt-bridge 3 5vmz OP2@D.5CM8 OH@A.TYR503 2.58 po4:sidechain 4 5vmz OP1@D.DG9 N@A.VAL504 2.89 po4:backbone 5 5vmz OP2@D.DG9 N@A.CYS505 3.83 po4:backbone 6 5vmz OP2@D.DG9 OG@A.SER508 2.65 po4:sidechain 7 5vmz OP1@D.DA13 N@A.ALA598 2.74 po4:backbone 8 5vmz OP1@E.DT25 NZ@A.LYS520 2.55 po4:sidechain:salt-bridge 9 5vmz OP2@E.5CM26 OH@A.TYR522 3.03 po4:sidechain 10 5vmz OP2@E.DG27 OG1@A.THR538 2.59 po4:sidechain 11 5vmz OP1@E.5CM28 NH2@A.ARG549 2.71 po4:sidechain:salt-bridge 12 5vmz OP2@E.5CM28 NH1@A.ARG549 2.79 po4:sidechain:salt-bridge 13 5vmz OP1@E.DG29 OH@A.TYR584 2.60 po4:sidechain 14 5vmz OP2@E.DG29 OH@A.TYR550 2.65 po4:sidechain 15 5vmz O3'@E.5CM28 OH@A.TYR599 3.75 po4:sidechain 16 5vmz OP1@E.DG30 N.A@A.GLY579 2.69 po4:backbone 17 5vmz OP2@E.DG30 OH@A.TYR562 2.61 po4:sidechain 18 5vmz OP1@E.DG31 OG.A@A.SER578 3.60 po4:sidechain **************************************************************************** List of 2 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 5vmz O4'@E.5CM26 NH2@A.ARG595 2.80 sugar:sidechain 2 5vmz O4'@E.DG27 NH1@A.ARG595 2.93 sugar:sidechain **************************************************************************** List of 14 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 5vmz N4@D.DC6 NE2@A.GLN563 3.34 base:sidechain 2 5vmz N4@D.5CM8 OE1@A.GLN535 2.87 base:sidechain 3 5vmz N7@D.DG9 NH2@A.ARG511 2.90 base:sidechain 4 5vmz O6@D.DG9 NH1@A.ARG511 2.88 base:sidechain 5 5vmz O6@D.DG9 NH2@A.ARG511 3.06 base:sidechain 6 5vmz N2@D.DG11 OH@A.TYR597 3.24 base:sidechain 7 5vmz O2@E.DT25 NH2@A.ARG595 2.65 base:sidechain 8 5vmz O2@E.5CM26 NH1@A.ARG595 2.97 base:sidechain 9 5vmz O2@E.5CM26 NH2@A.ARG595 3.29 base:sidechain 10 5vmz N4@E.5CM26 OG1@A.THR507 3.97 base:sidechain 11 5vmz O6@E.DG27 NH1@A.ARG511 2.71 base:sidechain 12 5vmz N3@E.DG27 OH@A.TYR597 2.83 base:sidechain 13 5vmz N4@E.5CM28 OE1@A.GLN535 2.78 base:sidechain 14 5vmz O6@E.DG31 NE2@A.GLN563 2.81 base:sidechain **************************************************************************** List of 6 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 5vmz C-gln D.5CM8 A.GLN535 2.12 63 2 5vmz G-arg D.DG9 A.ARG511 0.43 27 3 5vmz G-tyr D.DG11 A.TYR597 0.86 49 4 5vmz G-arg E.DG27 A.ARG511 0.58 28 5 5vmz G-tyr E.DG27 A.TYR597 1.50 52 6 5vmz G-gln E.DG31 A.GLN563 0.41 53 **************************************************************************** List of 2 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 5vmz C-arg D.5CM8 A.ARG511 3.66 27 2 5vmz C-arg E.5CM26 A.ARG511 3.96 33