**************************************************************************** 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=5ke7.pdb -o=5ke7.out File name: 5ke7.pdb no. of peptide chains: 1 [A=87] no. of DNA/RNA chains: 2 [B=10,C=10] no. of amino acids: 87 no. of nucleotides: 20 no. of atoms: 2133 no. of waters: 71 no. of metals: 3 [Zn=3] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 5CM-c 1 C.5CM5 **************************************************************************** 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'-GAGGTGTGGC-3' bp-type |||||||||| strand-2 3'-CTCCAcACCG-5' helix-form BBBBBBB.B 1 B.DG1 C.DC10 G-C WC 19-XIX cWW cW-W 2 B.DA2 C.DT9 A-T WC 20-XX cWW cW-W 3 B.DG3 C.DC8 G-C WC 19-XIX cWW cW-W 4 B.DG4 C.DC7 G-C WC 19-XIX cWW cW-W 5 B.DT5 C.DA6 T-A WC 20-XX cWW cW-W 6 B.DG6 C.5CM5 G-c WC 19-XIX cWW cW-W 7 B.DT7 C.DA4 T-A WC 20-XX cWW cW-W 8 B.DG8 C.DC3 G-C WC 19-XIX cWW cW-W 9 B.DG9 C.DC2 G-C WC 19-XIX cWW cW-W 10 B.DC10 C.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 30 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5ke7 G-his B.DG1 A.HIS474 9.77 165.38 4.67 -2.54 8.20 11.98 85.23 159.95 2 5ke7 A-arg B.DA2 A.ARG471 11.71 -139.02 -4.30 10.29 3.55 13.08 -36.32 -136.46 3 5ke7 A-his B.DA2 A.HIS474 -9.45 141.04 6.41 -3.80 5.82 34.78 82.16 124.14 4 5ke7 G-arg B.DG3 A.ARG449 12.45 -157.11 -5.03 9.97 5.49 43.11 -78.08 -147.65 5 5ke7 G-arg B.DG3 A.ARG471 11.19 -171.88 -3.01 10.67 1.55 12.00 -42.47 -171.24 6 5ke7 G-arg B.DG4 A.ARG449 11.94 -160.16 -3.99 10.98 -2.51 2.42 86.58 -152.61 7 5ke7 G-arg B.DG4 A.ARG471 -10.62 156.33 1.90 -10.43 -0.71 -3.33 46.88 154.16 8 5ke7 T-arg B.DT5 A.ARG443 11.36 -156.66 -5.51 8.99 4.25 37.60 -39.82 -153.66 9 5ke7 T-asp B.DT5 A.ASP445 9.14 -149.23 -2.67 7.65 4.23 -15.41 40.76 -146.80 10 5ke7 T-glu B.DT5 A.GLU446 9.72 123.45 7.41 -2.52 5.76 25.06 58.21 112.35 11 5ke7 T-arg B.DT5 A.ARG449 -11.13 -177.01 0.12 10.20 -4.46 28.01 72.45 -176.16 12 5ke7 G-arg B.DG6 A.ARG443 10.82 168.36 3.44 -10.16 1.40 -29.64 40.60 167.14 13 5ke7 G-asp B.DG6 A.ASP445 9.09 -178.37 1.63 8.83 1.38 3.82 51.80 -178.18 14 5ke7 T-his B.DT7 A.HIS416 9.40 148.47 4.33 -2.69 7.89 8.83 71.04 140.86 15 5ke7 T-arg B.DT7 A.ARG443 -10.14 138.68 3.09 -9.57 -1.33 -13.82 47.32 134.32 16 5ke7 G-lys B.DG8 A.LYS413 10.07 -143.42 -2.88 9.12 3.16 27.13 -56.78 -136.83 17 5ke7 G-his B.DG8 A.HIS416 8.72 120.68 5.60 -3.59 5.63 18.62 75.31 101.18 18 5ke7 G-lys B.DG9 A.LYS413 -10.30 -170.44 -1.24 10.22 -0.31 10.03 -60.66 -168.87 19 5ke7 C-lys B.DC10 A.LYS413 -9.31 157.00 -0.26 -8.89 -2.75 11.29 65.87 152.37 20 5ke7 G-lys C.DG1 A.LYS413 9.58 -151.81 -0.35 9.41 1.78 0.41 -60.11 -147.32 21 5ke7 G-ser C.DG1 A.SER415 8.66 -137.46 -5.25 6.87 0.44 -8.60 33.45 -135.35 22 5ke7 C-lys C.DC2 A.LYS413 -10.22 -179.54 0.22 10.16 -1.11 -18.07 -55.73 -179.47 23 5ke7 C-ser C.DC3 A.SER444 10.08 -161.53 -7.19 6.24 -3.31 48.39 20.77 -159.37 24 5ke7 A-arg C.DA4 A.ARG443 -9.87 -137.93 2.50 9.55 -0.19 -29.18 -59.10 -129.34 25 5ke7 A-asp C.DA4 A.ASP445 8.13 -157.43 -4.06 7.02 0.55 -28.69 35.41 -155.49 26 5ke7 C-asp C.5CM5 A.ASP445 -8.86 168.52 0.95 -8.35 -2.81 18.02 -38.56 167.68 27 5ke7 A-arg C.DA6 A.ARG449 -11.30 165.03 -0.78 -10.85 3.06 34.32 -77.10 159.75 28 5ke7 A-asp C.DA6 A.ASP473 8.65 -134.27 -5.33 6.36 2.44 -24.93 45.00 -128.90 29 5ke7 C-arg C.DC7 A.ARG471 -10.25 -152.74 1.57 10.12 -0.54 -18.73 -51.84 -149.17 30 5ke7 C-asp C.DC7 A.ASP473 -8.58 -155.49 -3.22 7.92 -0.65 -12.31 38.20 -153.88 **************************************************************************** List of 24 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5ke7 AT-arg B.DA2 C.DT9 A.ARG471 11.72 -141.41 -4.14 10.07 4.32 20.52 -37.59 -138.42 2 5ke7 AT-arg C.DA6 B.DT5 A.ARG443 -11.35 156.19 -5.64 -8.66 -4.70 44.98 38.84 152.52 3 5ke7 AT-arg C.DA6 B.DT5 A.ARG449 11.22 170.94 -0.32 -10.55 3.78 31.22 -74.73 168.07 4 5ke7 AT-arg C.DA4 B.DT7 A.ARG443 10.00 -138.16 2.77 9.59 0.59 -21.44 -53.30 -131.94 5 5ke7 AT-asp C.DA6 B.DT5 A.ASP445 -9.17 143.55 -2.91 -7.35 -4.65 -10.52 -39.73 140.97 6 5ke7 AT-asp C.DA6 B.DT5 A.ASP473 8.56 -129.09 -5.63 5.98 2.43 -21.68 39.82 -124.48 7 5ke7 AT-asp C.DA4 B.DT7 A.ASP445 8.24 -153.55 -4.15 6.96 1.52 -22.52 42.18 -151.02 8 5ke7 AT-glu C.DA6 B.DT5 A.GLU446 -9.76 -123.34 7.26 2.19 -6.13 19.12 -54.16 -114.48 9 5ke7 AT-his B.DA2 C.DT9 A.HIS474 9.43 136.71 6.00 -3.52 6.37 29.35 77.02 121.27 10 5ke7 AT-his C.DA4 B.DT7 A.HIS416 -9.37 -145.31 4.52 2.00 -7.96 2.17 -77.20 -135.13 11 5ke7 GC-arg B.DG3 C.DC8 A.ARG449 12.42 -137.21 -8.58 8.93 0.93 -21.65 85.65 -118.86 12 5ke7 GC-arg B.DG3 C.DC8 A.ARG471 11.13 -173.82 -2.75 10.57 2.16 16.06 -42.03 -173.31 13 5ke7 GC-arg B.DG4 C.DC7 A.ARG449 11.73 -154.68 -4.10 10.80 -2.02 6.24 80.66 -146.52 14 5ke7 GC-arg B.DG4 C.DC7 A.ARG471 10.44 154.49 1.73 -10.29 -0.09 -10.99 49.50 151.72 15 5ke7 GC-arg B.DG6 C.5CM5 A.ARG443 10.70 168.18 3.53 -9.89 2.07 -38.95 45.85 166.34 16 5ke7 GC-asp B.DG4 C.DC7 A.ASP473 -8.67 151.95 -3.24 -8.04 0.01 -5.14 -40.48 150.03 17 5ke7 GC-asp B.DG6 C.5CM5 A.ASP445 8.97 -173.44 1.31 8.62 2.13 10.93 45.21 -172.86 18 5ke7 GC-his B.DG1 C.DC10 A.HIS474 9.62 161.42 4.44 -1.83 8.33 6.36 83.66 154.93 19 5ke7 GC-his B.DG8 C.DC3 A.HIS416 8.50 120.85 5.34 -3.35 5.70 16.55 73.08 103.09 20 5ke7 GC-lys B.DG8 C.DC3 A.LYS413 9.90 -143.18 -2.90 8.79 3.52 30.49 -55.82 -136.37 21 5ke7 GC-lys B.DG9 C.DC2 A.LYS413 10.26 -175.43 -0.74 10.23 0.42 14.03 -58.17 -174.72 22 5ke7 GC-lys C.DG1 B.DC10 A.LYS413 9.45 -154.37 -0.30 9.17 2.27 5.81 -63.08 -149.78 23 5ke7 GC-ser B.DG8 C.DC3 A.SER444 -10.11 158.69 -7.13 -6.33 3.34 49.76 -19.87 156.09 24 5ke7 GC-ser C.DG1 B.DC10 A.SER415 8.54 -135.03 -5.32 6.65 0.59 -3.80 29.76 -133.35 **************************************************************************** List of 5 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 5ke7 OP2@B.DG3 NZ@A.LYS453 2.81 po4:sidechain:salt-bridge 2 5ke7 OP1@B.DG6 NZ@A.LYS409 2.95 po4:sidechain:salt-bridge 3 5ke7 OP2@B.DG6 OH@A.TYR411 2.81 po4:sidechain 4 5ke7 OP2@C.DC2 OH@A.TYR430 2.40 po4:sidechain 5 5ke7 OP2@C.5CM5 OG@A.SER472 2.92 po4:sidechain **************************************************************************** List of 11 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 5ke7 N7@B.DA2 NE2@A.HIS474 2.95 base:sidechain 2 5ke7 N7@B.DG3 NH1@A.ARG471 2.95 base:sidechain 3 5ke7 O6@B.DG3 NH2@A.ARG471 2.95 base:sidechain 4 5ke7 N7@B.DG4 NH2@A.ARG449 2.76 base:sidechain 5 5ke7 O6@B.DG4 NH1@A.ARG449 2.91 base:sidechain 6 5ke7 N7@B.DG6 NH2@A.ARG443 3.04 base:sidechain 7 5ke7 O6@B.DG6 NH1@A.ARG443 2.69 base:sidechain 8 5ke7 N7@B.DG8 NE2@A.HIS416 2.86 base:sidechain 9 5ke7 O6@B.DG9 NZ@A.LYS413 2.74 base:sidechain 10 5ke7 O6@C.DG1 NZ@A.LYS413 2.70 base:sidechain 11 5ke7 N4@C.DC7 OD2@A.ASP473 2.73 base:sidechain **************************************************************************** List of 6 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 5ke7 A-his B.DA2 A.HIS474 0.13 15 2 5ke7 G-arg B.DG3 A.ARG471 0.03 14 3 5ke7 G-arg B.DG4 A.ARG449 0.00 14 4 5ke7 G-arg B.DG6 A.ARG443 0.10 15 5 5ke7 G-his B.DG8 A.HIS416 0.13 23 6 5ke7 C-asp C.DC7 A.ASP473 0.43 19 **************************************************************************** List of 3 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 5ke7 G-his B.DG1 A.HIS474 3.51 16 2 5ke7 T-arg B.DT5 A.ARG443 3.42 8 3 5ke7 T-his B.DT7 A.HIS416 3.38 9