**************************************************************************** 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=5mcv.pdb -o=5mcv.out File name: 5mcv.pdb no. of peptide chains: 4 [1.A=200,1.B=200,2.A=200,2.B=200] no. of DNA/RNA chains: 2 [1.C=20,2.C=20] no. of amino acids: 800 no. of nucleotides: 40 no. of atoms: 13266 no. of waters: 1124 no. of metals: 4 [Zn=4] **************************************************************************** List of 2 types of 8 modified nucleotides nt count list 1 DI-g 4 1:C.DI5,1:C.DI15,2:C.DI5,2:C.DI15 2 5CM-c 4 1:C.5CM6,1:C.5CM16,2:C.5CM6,2:C.5CM16 **************************************************************************** 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=20 strand-1 5'-GGGCgcGCCCGGGCgcGCCC-3' bp-type |||||||||||||||||||| strand-2 3'-CCCGcgCGGGCCCGcgCGGG-5' helix-form BBBB.BBBB.BBBB.BBBB 1 1:C.DG1 2:C.DC20 G-C WC 19-XIX cWW cW-W 2 1:C.DG2 2:C.DC19 G-C WC 19-XIX cWW cW-W 3 1:C.DG3 2:C.DC18 G-C WC 19-XIX cWW cW-W 4 1:C.DC4 2:C.DG17 C-G WC 19-XIX cWW cW-W 5 1:C.DI5 2:C.5CM16 g-c WC 19-XIX cWW cW-W 6 1:C.5CM6 2:C.DI15 c-g WC 19-XIX cWW cW-W 7 1:C.DG7 2:C.DC14 G-C WC 19-XIX cWW cW-W 8 1:C.DC8 2:C.DG13 C-G WC 19-XIX cWW cW-W 9 1:C.DC9 2:C.DG12 C-G WC 19-XIX cWW cW-W 10 1:C.DC10 2:C.DG11 C-G WC 19-XIX cWW cW-W 11 1:C.DG11 2:C.DC10 G-C WC 19-XIX cWW cW-W 12 1:C.DG12 2:C.DC9 G-C WC 19-XIX cWW cW-W 13 1:C.DG13 2:C.DC8 G-C WC 19-XIX cWW cW-W 14 1:C.DC14 2:C.DG7 C-G WC 19-XIX cWW cW-W 15 1:C.DI15 2:C.5CM6 g-c WC 19-XIX cWW cW-W 16 1:C.5CM16 2:C.DI5 c-g WC 19-XIX cWW cW-W 17 1:C.DG17 2:C.DC4 G-C WC 19-XIX cWW cW-W 18 1:C.DC18 2:C.DG3 C-G WC 19-XIX cWW cW-W 19 1:C.DC19 2:C.DG2 C-G WC 19-XIX cWW cW-W 20 1:C.DC20 2:C.DG1 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 5mcv G-lys 1:C.DG1 2:B.LYS120 10.01 -137.86 -5.72 7.52 3.30 24.74 -55.42 -130.76 2 5mcv G-lys 1:C.DG2 2:B.LYS120 -10.34 -169.50 -5.03 9.01 0.65 9.54 -59.61 -167.84 3 5mcv G-lys 1:C.DG3 2:B.LYS120 -10.03 160.05 4.01 -8.98 -1.96 6.62 65.08 156.24 4 5mcv G-arg 1:C.DG3 2:B.ARG280 10.15 -173.88 -1.05 10.08 0.63 -8.45 43.07 -173.40 5 5mcv C-arg 1:C.5CM6 1:A.ARG280 12.89 -124.34 -8.56 8.55 4.46 -30.71 40.44 -117.77 6 5mcv G-ala 1:C.DG7 1:A.ALA276 9.69 -147.33 -5.01 6.85 4.67 41.76 -77.30 -134.02 7 5mcv G-arg 1:C.DG7 1:A.ARG280 11.22 -155.79 -3.07 10.58 2.08 -11.44 44.40 -153.67 8 5mcv C-lys 1:C.DC8 1:A.LYS120 9.95 -157.81 3.79 8.95 2.16 3.22 -67.26 -153.26 9 5mcv C-ala 1:C.DC8 1:A.ALA276 -9.19 -163.34 -3.77 7.30 -4.12 -7.56 85.19 -157.24 10 5mcv C-cys 1:C.DC8 1:A.CYS277 8.64 -129.96 -0.17 8.56 -1.13 19.07 -31.71 -127.03 11 5mcv C-arg 1:C.DC8 1:A.ARG280 -9.88 173.32 -0.72 -9.83 -0.61 -5.39 -39.92 172.88 12 5mcv G-lys 1:C.DG11 2:A.LYS120 10.02 -137.61 -5.76 7.52 3.26 25.75 -54.83 -130.50 13 5mcv G-lys 1:C.DG12 2:A.LYS120 -10.33 -169.49 -5.04 9.00 0.63 10.48 -59.00 -167.86 14 5mcv G-lys 1:C.DG13 2:A.LYS120 -10.02 159.84 4.01 -8.97 -1.95 5.54 65.03 156.00 15 5mcv G-arg 1:C.DG13 2:A.ARG280 10.13 -173.43 -1.04 10.06 0.65 -7.85 42.94 -172.93 16 5mcv C-arg 1:C.5CM16 1:B.ARG280 12.88 -124.04 -8.51 8.56 4.47 -29.90 40.95 -117.45 17 5mcv G-ala 1:C.DG17 1:B.ALA276 9.69 -146.94 -5.02 6.81 4.72 40.43 -76.57 -133.98 18 5mcv G-arg 1:C.DG17 1:B.ARG280 11.23 -155.56 -3.04 10.63 1.98 -12.11 44.98 -153.36 19 5mcv C-lys 1:C.DC18 1:B.LYS120 9.97 -156.82 3.73 9.03 1.97 3.28 -66.68 -152.16 20 5mcv C-ala 1:C.DC18 1:B.ALA276 -9.22 -164.49 -3.80 7.22 -4.28 -8.27 86.16 -158.64 21 5mcv C-cys 1:C.DC18 1:B.CYS277 8.65 -128.66 -0.17 8.56 -1.25 18.31 -30.82 -125.83 22 5mcv C-arg 1:C.DC18 1:B.ARG280 -9.93 173.63 -0.74 -9.87 -0.76 -4.38 -40.24 173.21 23 5mcv G-lys 2:C.DG1 1:B.LYS120 10.01 -137.86 -5.72 7.52 3.30 24.74 -55.42 -130.76 24 5mcv G-lys 2:C.DG2 1:B.LYS120 -10.34 -169.50 -5.03 9.01 0.65 9.54 -59.61 -167.84 25 5mcv G-lys 2:C.DG3 1:B.LYS120 -10.03 160.05 4.01 -8.98 -1.96 6.62 65.08 156.24 26 5mcv G-arg 2:C.DG3 1:B.ARG280 10.15 -173.88 -1.05 10.08 0.63 -8.45 43.07 -173.40 27 5mcv C-arg 2:C.5CM6 2:A.ARG280 12.89 -124.34 -8.56 8.55 4.46 -30.71 40.44 -117.77 28 5mcv G-ala 2:C.DG7 2:A.ALA276 9.69 -147.33 -5.01 6.85 4.67 41.76 -77.30 -134.02 29 5mcv G-arg 2:C.DG7 2:A.ARG280 11.22 -155.79 -3.07 10.58 2.08 -11.44 44.40 -153.67 30 5mcv C-lys 2:C.DC8 2:A.LYS120 9.95 -157.81 3.79 8.95 2.16 3.22 -67.26 -153.26 31 5mcv C-ala 2:C.DC8 2:A.ALA276 -9.19 -163.34 -3.77 7.30 -4.12 -7.56 85.19 -157.24 32 5mcv C-cys 2:C.DC8 2:A.CYS277 8.64 -129.96 -0.17 8.56 -1.13 19.07 -31.71 -127.03 33 5mcv C-arg 2:C.DC8 2:A.ARG280 -9.88 173.32 -0.72 -9.83 -0.61 -5.39 -39.92 172.88 34 5mcv G-lys 2:C.DG11 1:A.LYS120 10.02 -137.61 -5.76 7.52 3.26 25.75 -54.83 -130.50 35 5mcv G-lys 2:C.DG12 1:A.LYS120 -10.33 -169.49 -5.04 9.00 0.63 10.48 -59.00 -167.86 36 5mcv G-lys 2:C.DG13 1:A.LYS120 -10.02 159.84 4.01 -8.97 -1.95 5.54 65.03 156.00 37 5mcv G-arg 2:C.DG13 1:A.ARG280 10.13 -173.43 -1.04 10.06 0.65 -7.85 42.94 -172.93 38 5mcv C-arg 2:C.5CM16 2:B.ARG280 12.88 -124.04 -8.51 8.56 4.47 -29.90 40.95 -117.45 39 5mcv G-ala 2:C.DG17 2:B.ALA276 9.69 -146.94 -5.02 6.81 4.72 40.43 -76.57 -133.98 40 5mcv G-arg 2:C.DG17 2:B.ARG280 11.23 -155.56 -3.04 10.63 1.98 -12.11 44.98 -153.36 41 5mcv C-lys 2:C.DC18 2:B.LYS120 9.97 -156.82 3.73 9.03 1.97 3.28 -66.68 -152.16 42 5mcv C-ala 2:C.DC18 2:B.ALA276 -9.22 -164.49 -3.80 7.22 -4.28 -8.27 86.16 -158.64 43 5mcv C-cys 2:C.DC18 2:B.CYS277 8.65 -128.66 -0.17 8.56 -1.25 18.31 -30.82 -125.83 44 5mcv C-arg 2:C.DC18 2:B.ARG280 -9.93 173.63 -0.74 -9.87 -0.76 -4.38 -40.24 173.21 **************************************************************************** List of 36 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5mcv GC-ala 1:C.DG3 2:C.DC18 2:B.ALA276 9.20 163.43 -3.68 -7.39 4.07 -6.10 -87.09 157.03 2 5mcv GC-ala 2:C.DG17 1:C.DC4 2:B.ALA276 9.63 -149.97 -4.77 6.57 5.17 43.95 -76.56 -137.68 3 5mcv GC-ala 1:C.DG7 2:C.DC14 1:A.ALA276 9.63 -150.07 -4.76 6.64 5.09 44.86 -76.88 -137.54 4 5mcv GC-ala 2:C.DG13 1:C.DC8 1:A.ALA276 9.18 162.64 -3.63 -7.45 3.96 -6.12 -86.35 156.07 5 5mcv GC-ala 1:C.DG13 2:C.DC8 2:A.ALA276 9.18 162.64 -3.63 -7.45 3.96 -6.12 -86.35 156.07 6 5mcv GC-ala 2:C.DG7 1:C.DC14 2:A.ALA276 9.63 -150.07 -4.76 6.64 5.09 44.86 -76.88 -137.54 7 5mcv GC-ala 1:C.DG17 2:C.DC4 1:B.ALA276 9.63 -149.97 -4.77 6.57 5.17 43.95 -76.56 -137.68 8 5mcv GC-ala 2:C.DG3 1:C.DC18 1:B.ALA276 9.20 163.43 -3.68 -7.39 4.07 -6.10 -87.09 157.03 9 5mcv GC-arg 1:C.DG3 2:C.DC18 2:B.ARG280 10.04 -173.75 -0.90 9.98 0.69 -6.40 41.67 -173.30 10 5mcv GC-arg 2:C.DG17 1:C.DC4 2:B.ARG280 11.15 -153.91 -3.08 10.41 2.52 -8.23 45.92 -151.54 11 5mcv GC-arg 1:C.DI5 2:C.5CM16 2:B.ARG280 -12.86 117.47 -8.81 -8.03 -4.82 -26.36 -37.40 111.43 12 5mcv GC-arg 2:C.DI15 1:C.5CM6 1:A.ARG280 -12.86 117.50 -8.86 -7.97 -4.83 -26.68 -36.92 111.52 13 5mcv GC-arg 1:C.DG7 2:C.DC14 1:A.ARG280 11.15 -154.34 -3.09 10.39 2.58 -8.07 45.68 -152.04 14 5mcv GC-arg 2:C.DG13 1:C.DC8 1:A.ARG280 10.00 -173.37 -0.88 9.94 0.63 -6.61 41.44 -172.90 15 5mcv GC-arg 1:C.DG13 2:C.DC8 2:A.ARG280 10.00 -173.37 -0.88 9.94 0.63 -6.61 41.44 -172.90 16 5mcv GC-arg 2:C.DG7 1:C.DC14 2:A.ARG280 11.15 -154.34 -3.09 10.39 2.58 -8.07 45.68 -152.04 17 5mcv GC-arg 1:C.DI15 2:C.5CM6 2:A.ARG280 -12.86 117.50 -8.86 -7.97 -4.83 -26.68 -36.92 111.52 18 5mcv GC-arg 2:C.DI5 1:C.5CM16 1:B.ARG280 -12.86 117.47 -8.81 -8.03 -4.82 -26.36 -37.40 111.43 19 5mcv GC-arg 1:C.DG17 2:C.DC4 1:B.ARG280 11.15 -153.91 -3.08 10.41 2.52 -8.23 45.92 -151.54 20 5mcv GC-arg 2:C.DG3 1:C.DC18 1:B.ARG280 10.04 -173.75 -0.90 9.98 0.69 -6.40 41.67 -173.30 21 5mcv GC-cys 1:C.DG3 2:C.DC18 2:B.CYS277 -8.68 130.00 -0.01 -8.59 1.24 20.47 30.65 127.09 22 5mcv GC-cys 2:C.DG13 1:C.DC8 1:A.CYS277 -8.68 130.91 -0.03 -8.60 1.19 20.68 31.05 127.99 23 5mcv GC-cys 1:C.DG13 2:C.DC8 2:A.CYS277 -8.68 130.91 -0.03 -8.60 1.19 20.68 31.05 127.99 24 5mcv GC-cys 2:C.DG3 1:C.DC18 1:B.CYS277 -8.68 130.00 -0.01 -8.59 1.24 20.47 30.65 127.09 25 5mcv GC-lys 1:C.DG1 2:C.DC20 2:B.LYS120 9.96 -139.92 -5.53 7.27 3.96 30.42 -53.47 -133.00 26 5mcv GC-lys 1:C.DG2 2:C.DC19 2:B.LYS120 -10.20 -173.25 -4.67 9.00 1.18 13.87 -60.11 -172.14 27 5mcv GC-lys 1:C.DG3 2:C.DC18 2:B.LYS120 -10.00 158.43 3.87 -9.00 -1.97 4.95 65.88 154.21 28 5mcv GC-lys 2:C.DG13 1:C.DC8 1:A.LYS120 -9.98 158.82 3.90 -8.96 -2.06 4.38 66.14 154.64 29 5mcv GC-lys 2:C.DG12 1:C.DC9 1:A.LYS120 -10.22 -173.06 -4.73 8.99 1.06 14.56 -60.37 -171.90 30 5mcv GC-lys 2:C.DG11 1:C.DC10 1:A.LYS120 9.95 -139.58 -5.63 7.29 3.79 30.88 -53.89 -132.44 31 5mcv GC-lys 1:C.DG11 2:C.DC10 2:A.LYS120 9.95 -139.58 -5.63 7.29 3.79 30.88 -53.89 -132.44 32 5mcv GC-lys 1:C.DG12 2:C.DC9 2:A.LYS120 -10.22 -173.06 -4.73 8.99 1.06 14.56 -60.37 -171.90 33 5mcv GC-lys 1:C.DG13 2:C.DC8 2:A.LYS120 -9.98 158.82 3.90 -8.96 -2.06 4.38 66.14 154.64 34 5mcv GC-lys 2:C.DG3 1:C.DC18 1:B.LYS120 -10.00 158.43 3.87 -9.00 -1.97 4.95 65.88 154.21 35 5mcv GC-lys 2:C.DG2 1:C.DC19 1:B.LYS120 -10.20 -173.25 -4.67 9.00 1.18 13.87 -60.11 -172.14 36 5mcv GC-lys 2:C.DG1 1:C.DC20 1:B.LYS120 9.96 -139.92 -5.53 7.27 3.96 30.42 -53.47 -133.00 **************************************************************************** List of 24 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 5mcv OP2@1:C.5CM6 NH1@1:A.ARG273 2.86 po4:sidechain:salt-bridge 2 5mcv OP2@1:C.5CM6 NH2@1:A.ARG273 3.12 po4:sidechain:salt-bridge 3 5mcv O5'@1:C.5CM6 NH2@1:A.ARG273 3.22 po4:sidechain 4 5mcv OP1@1:C.DG7 OG@1:A.SER241 2.65 po4:sidechain 5 5mcv OP2@1:C.DG7 N@1:A.ALA276 2.88 po4:backbone 6 5mcv OP1@1:C.DC9 NH2.A@2:B.ARG248 3.21 po4:sidechain:salt-bridge 7 5mcv OP2@1:C.5CM16 NH1@1:B.ARG273 2.87 po4:sidechain:salt-bridge 8 5mcv OP2@1:C.5CM16 NH2@1:B.ARG273 3.12 po4:sidechain:salt-bridge 9 5mcv O5'@1:C.5CM16 NH2@1:B.ARG273 3.25 po4:sidechain 10 5mcv OP1@1:C.DG17 OG@1:B.SER241 2.59 po4:sidechain 11 5mcv OP2@1:C.DG17 N@1:B.ALA276 2.91 po4:backbone 12 5mcv OP1@1:C.DC19 NH2.A@2:A.ARG248 3.21 po4:sidechain:salt-bridge 13 5mcv OP2@2:C.5CM6 NH1@2:A.ARG273 2.86 po4:sidechain:salt-bridge 14 5mcv OP2@2:C.5CM6 NH2@2:A.ARG273 3.12 po4:sidechain:salt-bridge 15 5mcv O5'@2:C.5CM6 NH2@2:A.ARG273 3.22 po4:sidechain 16 5mcv OP1@2:C.DG7 OG@2:A.SER241 2.65 po4:sidechain 17 5mcv OP2@2:C.DG7 N@2:A.ALA276 2.88 po4:backbone 18 5mcv OP1@2:C.DC9 NH2.A@1:B.ARG248 3.21 po4:sidechain:salt-bridge 19 5mcv OP2@2:C.5CM16 NH1@2:B.ARG273 2.87 po4:sidechain:salt-bridge 20 5mcv OP2@2:C.5CM16 NH2@2:B.ARG273 3.12 po4:sidechain:salt-bridge 21 5mcv O5'@2:C.5CM16 NH2@2:B.ARG273 3.25 po4:sidechain 22 5mcv OP1@2:C.DG17 OG@2:B.SER241 2.59 po4:sidechain 23 5mcv OP2@2:C.DG17 N@2:B.ALA276 2.91 po4:backbone 24 5mcv OP1@2:C.DC19 NH2.A@1:A.ARG248 3.21 po4:sidechain:salt-bridge **************************************************************************** List of 20 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 5mcv N7@1:C.DG2 NZ@2:B.LYS120 2.77 base:sidechain 2 5mcv O6@1:C.DG2 NZ@2:B.LYS120 3.32 base:sidechain 3 5mcv O6@1:C.DG3 NZ@2:B.LYS120 2.67 base:sidechain 4 5mcv N7@1:C.DG7 NH2@1:A.ARG280 3.02 base:sidechain 5 5mcv O6@1:C.DG7 NH1@1:A.ARG280 2.95 base:sidechain 6 5mcv N7@1:C.DG12 NZ@2:A.LYS120 2.80 base:sidechain 7 5mcv O6@1:C.DG12 NZ@2:A.LYS120 3.31 base:sidechain 8 5mcv O6@1:C.DG13 NZ@2:A.LYS120 2.64 base:sidechain 9 5mcv N7@1:C.DG17 NH2@1:B.ARG280 3.01 base:sidechain 10 5mcv O6@1:C.DG17 NH1@1:B.ARG280 2.96 base:sidechain 11 5mcv N7@2:C.DG2 NZ@1:B.LYS120 2.77 base:sidechain 12 5mcv O6@2:C.DG2 NZ@1:B.LYS120 3.32 base:sidechain 13 5mcv O6@2:C.DG3 NZ@1:B.LYS120 2.67 base:sidechain 14 5mcv N7@2:C.DG7 NH2@2:A.ARG280 3.02 base:sidechain 15 5mcv O6@2:C.DG7 NH1@2:A.ARG280 2.95 base:sidechain 16 5mcv N7@2:C.DG12 NZ@1:A.LYS120 2.80 base:sidechain 17 5mcv O6@2:C.DG12 NZ@1:A.LYS120 3.31 base:sidechain 18 5mcv O6@2:C.DG13 NZ@1:A.LYS120 2.64 base:sidechain 19 5mcv N7@2:C.DG17 NH2@2:B.ARG280 3.01 base:sidechain 20 5mcv O6@2:C.DG17 NH1@2:B.ARG280 2.96 base:sidechain **************************************************************************** List of 4 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 5mcv G-arg 1:C.DG7 1:A.ARG280 0.11 20 2 5mcv G-arg 1:C.DG17 1:B.ARG280 0.09 17 3 5mcv G-arg 2:C.DG7 2:A.ARG280 0.11 20 4 5mcv G-arg 2:C.DG17 2:B.ARG280 0.09 17 **************************************************************************** List of 4 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 5mcv C-arg 1:C.5CM6 1:A.ARG280 3.59 16 2 5mcv C-arg 1:C.5CM16 1:B.ARG280 3.63 14 3 5mcv C-arg 2:C.5CM6 2:A.ARG280 3.59 16 4 5mcv C-arg 2:C.5CM16 2:B.ARG280 3.63 14