**************************************************************************** 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=5vmx.pdb -o=5vmx.out File name: 5vmx.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: 1873 no. of waters: 101 no. of metals: 3 [Zn=3] **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 5CM-c 2 D.5CM8,D.5CM10 **************************************************************************** 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 BBBBBBBBBBBBBBBB. 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.DC28 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.DC26 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 -- n/a cHW cM+W **************************************************************************** List of 38 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5vmx T-gln D.DT4 A.GLN563 9.09 -151.64 -5.29 7.31 1.04 8.70 67.49 -145.62 2 5vmx T-phe D.DT4 A.PHE564 11.38 127.87 9.79 -0.78 5.73 20.91 31.33 124.68 3 5vmx T-asn D.DT5 A.ASN561 11.40 177.33 5.82 -8.71 4.49 -17.55 44.18 177.08 4 5vmx T-gln D.DT5 A.GLN563 7.99 -179.30 -1.89 7.49 -2.03 23.73 53.31 -179.20 5 5vmx C-gln D.DC6 A.GLN563 -8.15 145.14 -1.21 -5.73 -5.66 -37.06 -47.37 139.49 6 5vmx C-glu D.DC7 A.GLU535 10.03 -155.82 -4.34 7.88 4.44 -11.25 34.41 -154.54 7 5vmx C-tyr D.DC7 A.TYR536 10.38 118.30 7.59 -1.24 6.97 24.08 65.36 102.68 8 5vmx C-lys D.DC7 A.LYS539 10.89 -175.99 -1.08 10.54 -2.52 21.58 59.11 -175.30 9 5vmx C-arg D.5CM8 A.ARG511 12.34 -117.94 -7.92 8.64 3.86 -17.83 22.41 -115.71 10 5vmx C-leu D.5CM8 A.LEU533 12.01 -177.16 -6.05 10.19 1.94 35.93 -65.33 -176.43 11 5vmx C-glu D.5CM8 A.GLU535 9.28 -175.00 -1.92 8.88 1.92 0.31 21.66 -174.90 12 5vmx G-ser D.DG9 A.SER508 9.08 -175.52 -5.73 5.48 -4.43 34.43 67.50 -174.32 13 5vmx G-arg D.DG9 A.ARG511 10.94 -155.77 -2.49 10.59 1.10 -5.23 26.63 -155.06 14 5vmx C-cys D.5CM10 A.CYS505 -10.80 -142.30 -5.08 9.44 1.36 14.15 -66.05 -134.25 15 5vmx C-thr D.5CM10 A.THR507 9.42 -171.23 -3.42 7.79 4.04 -32.14 3.40 -170.87 16 5vmx C-ser D.5CM10 A.SER508 -8.65 161.82 3.01 -4.62 -6.66 -55.35 -52.15 156.86 17 5vmx C-arg D.5CM10 A.ARG511 -9.99 173.14 -0.59 -9.79 -1.88 -5.68 -23.06 172.99 18 5vmx G-thr D.DG11 A.THR507 7.85 154.72 0.59 -7.70 1.41 20.61 -0.55 154.29 19 5vmx G-arg D.DG11 A.ARG595 11.97 32.72 -11.13 -2.65 3.53 21.10 5.06 24.64 20 5vmx G-tyr D.DG11 A.TYR597 12.34 68.14 -10.89 1.23 -5.67 10.55 66.53 10.90 21 5vmx A-arg D.DA12 A.ARG595 10.94 -25.60 -10.88 -0.62 0.92 20.14 2.45 -15.70 22 5vmx A-tyr D.DA12 A.TYR597 -11.31 -76.34 -7.99 2.68 -7.54 30.78 63.49 -31.24 23 5vmx T-thr E.DT25 A.THR507 9.89 -118.68 -2.94 9.32 1.51 14.50 17.81 -117.28 24 5vmx T-arg E.DT25 A.ARG595 10.76 33.61 -10.72 0.83 0.42 29.08 10.99 12.93 25 5vmx C-thr E.DC26 A.THR507 -7.48 -154.78 0.41 7.34 -1.38 12.74 -3.34 -154.61 26 5vmx C-arg E.DC26 A.ARG511 9.72 -147.00 -4.84 7.85 3.07 -30.42 7.18 -145.69 27 5vmx C-arg E.DC26 A.ARG595 -12.28 -29.88 -11.66 2.78 -2.67 14.28 0.22 -26.31 28 5vmx G-arg E.DG27 A.ARG511 -10.31 -175.69 -0.61 10.27 0.70 -17.16 21.71 -175.56 29 5vmx G-glu E.DG27 A.GLU535 9.47 -118.44 -5.64 6.90 3.21 -32.49 20.52 -114.37 30 5vmx G-arg E.DG27 A.ARG595 -12.16 -63.92 -9.02 5.12 -6.35 24.49 -9.20 -58.85 31 5vmx G-tyr E.DG27 A.TYR597 -11.89 -79.76 -11.51 1.65 2.48 -3.74 -65.57 -48.05 32 5vmx C-arg E.DC28 A.ARG511 -10.77 154.85 -2.38 -10.23 -2.36 5.14 -27.96 154.04 33 5vmx C-glu E.DC28 A.GLU535 -9.56 -146.47 -3.31 8.96 0.25 -19.75 27.83 -144.87 34 5vmx G-glu E.DG29 A.GLU535 -9.43 176.27 -1.50 -9.05 -2.18 3.20 -23.17 176.20 35 5vmx G-lys E.DG30 A.LYS539 -11.02 171.45 -0.91 -10.78 2.09 23.17 -41.38 170.66 36 5vmx G-tyr E.DG30 A.TYR562 9.19 -145.53 -5.32 7.31 -1.64 23.88 15.13 -144.41 37 5vmx G-gln E.DG30 A.GLN563 9.47 -124.95 -4.58 4.40 7.02 -65.30 22.00 -111.83 38 5vmx G-gln E.DG31 A.GLN563 8.34 -153.18 -1.51 6.86 4.48 -51.89 39.04 -148.09 **************************************************************************** List of 30 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5vmx AT-arg D.DA12 E.DT25 A.ARG595 -10.85 -28.76 -10.82 -0.74 0.25 24.63 -4.25 -14.33 2 5vmx AT-asn E.DA32 D.DT5 A.ASN561 -11.31 -175.99 5.77 8.38 -4.95 -24.55 -43.66 -175.57 3 5vmx AT-gln E.DA33 D.DT4 A.GLN563 -9.05 146.11 -5.54 -7.01 -1.46 14.40 -63.47 139.54 4 5vmx AT-gln E.DA32 D.DT5 A.GLN563 -7.95 175.11 -1.97 -7.54 1.61 29.43 -53.90 174.32 5 5vmx AT-phe E.DA33 D.DT4 A.PHE564 -11.31 -126.15 9.58 0.34 -5.99 12.80 -29.13 -123.82 6 5vmx AT-thr D.DA12 E.DT25 A.THR507 -9.82 116.95 -3.12 -9.15 -1.71 18.78 -11.00 115.66 7 5vmx AT-tyr D.DA12 E.DT25 A.TYR597 -11.22 -71.86 -7.51 2.95 -7.79 35.18 57.73 -25.96 8 5vmx GC-arg E.DG29 D.5CM8 A.ARG511 -12.25 118.36 -7.69 -8.66 -4.00 -16.18 -22.56 116.30 9 5vmx GC-arg D.DG9 E.DC28 A.ARG511 10.85 -155.29 -2.44 10.43 1.74 -0.05 27.35 -154.55 10 5vmx GC-arg E.DG27 D.5CM10 A.ARG511 10.15 -174.41 -0.60 10.05 1.30 -11.42 22.40 -174.27 11 5vmx GC-arg E.DG27 D.5CM10 A.ARG595 -12.11 -65.38 -8.87 5.18 -6.43 28.22 -13.70 -58.10 12 5vmx GC-arg D.DG11 E.DC26 A.ARG511 -9.73 145.60 -4.68 -7.90 -3.23 -26.39 -8.55 144.53 13 5vmx GC-arg D.DG11 E.DC26 A.ARG595 12.12 31.02 -11.41 -2.70 3.10 17.68 2.43 25.48 14 5vmx GC-cys E.DG27 D.5CM10 A.CYS505 -10.84 145.49 -4.88 -9.54 -1.67 18.65 69.29 137.06 15 5vmx GC-gln E.DG31 D.DC6 A.GLN563 8.24 -149.08 -1.37 6.33 5.10 -44.59 43.38 -143.73 16 5vmx GC-gln E.DG30 D.DC7 A.GLN563 9.49 -119.44 -4.20 3.71 7.66 -59.14 27.48 -106.47 17 5vmx GC-glu E.DG30 D.DC7 A.GLU535 -10.11 156.39 -4.60 -7.96 -4.21 -11.45 -25.40 155.66 18 5vmx GC-glu E.DG29 D.5CM8 A.GLU535 -9.36 175.64 -1.71 -8.97 -2.05 1.75 -22.42 175.55 19 5vmx GC-glu D.DG9 E.DC28 A.GLU535 -9.58 146.30 -3.20 -9.00 -0.64 -15.51 -24.80 145.13 20 5vmx GC-glu E.DG27 D.5CM10 A.GLU535 9.36 -116.96 -5.75 6.54 3.44 -27.11 18.18 -113.99 21 5vmx GC-leu E.DG29 D.5CM8 A.LEU533 -12.01 178.77 -5.81 -10.32 -2.02 36.51 64.91 178.46 22 5vmx GC-lys E.DG30 D.DC7 A.LYS539 -10.95 173.70 -0.99 -10.67 2.30 22.44 -50.26 172.89 23 5vmx GC-ser D.DG9 E.DC28 A.SER508 8.99 -173.97 -5.81 5.63 -3.92 39.29 69.05 -172.15 24 5vmx GC-ser E.DG27 D.5CM10 A.SER508 8.75 -164.81 2.99 5.14 6.42 -60.79 52.72 -160.06 25 5vmx GC-thr E.DG27 D.5CM10 A.THR507 -9.54 171.31 -3.38 -7.72 -4.48 -26.45 -1.94 171.07 26 5vmx GC-thr D.DG11 E.DC26 A.THR507 7.66 154.73 0.50 -7.52 1.40 16.69 1.42 154.45 27 5vmx GC-tyr E.DG30 D.DC7 A.TYR536 -10.41 -115.34 7.86 0.97 -6.76 18.20 -70.75 -96.55 28 5vmx GC-tyr E.DG30 D.DC7 A.TYR562 9.14 -147.44 -5.37 7.35 -0.83 28.19 23.03 -145.68 29 5vmx GC-tyr E.DG27 D.5CM10 A.TYR597 -11.95 -84.63 -11.65 1.53 2.17 -0.80 -70.40 -50.35 30 5vmx GC-tyr D.DG11 E.DC26 A.TYR597 12.53 64.49 -10.78 0.98 -6.30 7.54 63.39 9.74 **************************************************************************** List of 18 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 5vmx OP2@D.DC7 OH@A.TYR536 2.66 po4:sidechain 2 5vmx OP1@D.5CM8 NH1@A.ARG501 2.89 po4:sidechain:salt-bridge 3 5vmx OP2@D.5CM8 OH@A.TYR503 2.69 po4:sidechain 4 5vmx OP1@D.DG9 N@A.VAL504 2.92 po4:backbone 5 5vmx OP2@D.DG9 N@A.CYS505 3.60 po4:backbone 6 5vmx OP2@D.DG9 OG@A.SER508 2.63 po4:sidechain 7 5vmx OP1@D.DA13 N@A.ALA598 2.80 po4:backbone 8 5vmx OP1@E.DT25 NZ@A.LYS520 2.83 po4:sidechain:salt-bridge 9 5vmx OP2@E.DC26 OH@A.TYR522 3.48 po4:sidechain 10 5vmx OP2@E.DG27 OG1@A.THR538 2.65 po4:sidechain 11 5vmx OP1@E.DC28 NH2@A.ARG549 2.78 po4:sidechain:salt-bridge 12 5vmx OP2@E.DC28 NH1@A.ARG549 2.69 po4:sidechain:salt-bridge 13 5vmx OP1@E.DG29 OH@A.TYR584 2.52 po4:sidechain 14 5vmx OP2@E.DG29 OH@A.TYR550 2.56 po4:sidechain 15 5vmx O3'@E.DC28 OH@A.TYR599 3.84 po4:sidechain 16 5vmx OP1@E.DG30 N.A@A.GLY579 2.97 po4:backbone 17 5vmx OP1@E.DG30 O.A@A.GLY579 2.92 po4:backbone 18 5vmx OP2@E.DG30 OH@A.TYR562 2.58 po4:sidechain **************************************************************************** List of 2 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 5vmx O4'@E.DC26 NH2@A.ARG595 2.88 sugar:sidechain 2 5vmx O4'@E.DG27 NH1@A.ARG595 3.15 sugar:sidechain **************************************************************************** List of 13 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 5vmx N4@D.DC7 OE2@A.GLU535 3.59 base:sidechain 2 5vmx N4@D.5CM8 OE1@A.GLU535 3.13 base:sidechain 3 5vmx N4@D.5CM8 OE2@A.GLU535 2.66 base:sidechain 4 5vmx N7@D.DG9 NH2@A.ARG511 3.00 base:sidechain 5 5vmx O6@D.DG9 NH1@A.ARG511 2.88 base:sidechain 6 5vmx O6@D.DG9 NH2@A.ARG511 3.26 base:sidechain 7 5vmx N2@D.DG11 OH@A.TYR597 3.21 base:sidechain 8 5vmx O2@E.DT25 NH2@A.ARG595 2.74 base:sidechain 9 5vmx O2@E.DC26 NH1@A.ARG595 2.95 base:sidechain 10 5vmx O6@E.DG27 NH1@A.ARG511 2.86 base:sidechain 11 5vmx N3@E.DG27 OH@A.TYR597 3.01 base:sidechain 12 5vmx N4@E.DC28 OE1@A.GLU535 2.84 base:sidechain 13 5vmx O6@E.DG31 NE2@A.GLN563 3.05 base:sidechain **************************************************************************** List of 6 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 5vmx G-arg D.DG9 A.ARG511 0.24 27 2 5vmx G-tyr D.DG11 A.TYR597 0.92 44 3 5vmx T-arg E.DT25 A.ARG595 2.42 59 4 5vmx G-arg E.DG27 A.ARG511 0.70 28 5 5vmx G-tyr E.DG27 A.TYR597 1.75 50 6 5vmx G-gln E.DG31 A.GLN563 0.46 60 **************************************************************************** List of 2 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 5vmx C-arg D.5CM8 A.ARG511 3.61 28 2 5vmx C-arg E.DC26 A.ARG511 3.80 36