**************************************************************************** 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=5kl5.pdb -o=5kl5.out File name: 5kl5.pdb no. of peptide chains: 1 [A=88] no. of DNA/RNA chains: 2 [B=11,C=11] no. of amino acids: 88 no. of nucleotides: 22 no. of atoms: 2277 no. of waters: 86 no. of metals: 3 [Zn=3] **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 1CC-c 1 B.1CC9 2 5CM-c 1 C.5CM3 **************************************************************************** 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'-GCGTGGGcGT-3' bp-type |||||||||| strand-2 3'-CGCACCCGcA-5' helix-form BBBBBBB.. 1 B.DG2 C.DC11 G-C WC 19-XIX cWW cW-W 2 B.DC3 C.DG10 C-G WC 19-XIX cWW cW-W 3 B.DG4 C.DC9 G-C WC 19-XIX cWW cW-W 4 B.DT5 C.DA8 T-A WC 20-XX cWW cW-W 5 B.DG6 C.DC7 G-C WC 19-XIX cWW cW-W 6 B.DG7 C.DC6 G-C WC 19-XIX cWW cW-W 7 B.DG8 C.DC5 G-C WC 19-XIX cWW cW-W 8 B.1CC9 C.DG4 c-G WC 19-XIX cWW cW-W 9 B.DG10 C.5CM3 G-c WC 19-XIX cWW cW-W 10 B.DT11 C.DA2 T-A WC 20-XX cWW cW-W **************************************************************************** List of 45 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5kl5 A-arg B.DA1 A.ARG430 -8.10 74.50 -6.71 1.25 -4.35 -59.89 -35.69 28.09 2 5kl5 G-glu B.DG2 A.GLU427 9.55 151.76 3.68 -1.70 8.65 9.53 75.81 143.83 3 5kl5 G-arg B.DG2 A.ARG430 11.01 -147.49 -2.99 10.49 1.54 -4.52 62.89 -141.65 4 5kl5 C-arg B.DC3 A.ARG424 11.13 -141.41 -3.67 9.02 5.40 13.76 -59.07 -134.98 5 5kl5 C-asp B.DC3 A.ASP426 9.29 -158.74 -3.26 6.83 5.39 -25.22 24.20 -157.70 6 5kl5 C-glu B.DC3 A.GLU427 8.50 125.96 5.51 -1.94 6.18 23.13 80.82 104.59 7 5kl5 C-arg B.DC3 A.ARG430 -10.17 -171.87 0.64 10.09 -1.08 10.91 48.84 -171.03 8 5kl5 G-arg B.DG4 A.ARG424 10.92 -172.88 -1.87 10.33 3.01 6.64 -54.83 -171.96 9 5kl5 T-his B.DT5 A.HIS397 9.26 -178.18 -7.44 4.42 -3.27 20.61 84.42 -177.49 10 5kl5 T-thr B.DT5 A.THR400 10.78 -140.83 -2.75 10.17 2.26 -22.10 51.09 -135.46 11 5kl5 T-arg B.DT5 A.ARG424 9.39 154.92 0.77 -9.29 1.13 4.78 61.53 150.70 12 5kl5 G-arg B.DG6 A.ARG394 11.41 -145.67 -3.35 10.21 3.83 22.98 -44.52 -141.97 13 5kl5 G-his B.DG6 A.HIS397 9.08 137.63 4.55 -4.73 6.27 21.45 83.59 120.62 14 5kl5 G-arg B.DG7 A.ARG372 11.75 -130.64 -7.63 7.60 4.70 -39.74 55.12 -119.53 15 5kl5 G-arg B.DG7 A.ARG394 11.03 -175.90 -2.71 10.52 1.90 16.11 -52.35 -175.38 16 5kl5 G-asp B.DG7 A.ASP396 9.20 172.49 -0.06 -8.56 3.37 14.08 -33.52 172.10 17 5kl5 G-his B.DG7 A.HIS397 -9.34 112.25 5.55 -5.90 4.66 37.18 71.92 85.75 18 5kl5 G-arg B.DG8 A.ARG372 11.36 -155.52 -3.69 10.45 2.51 -13.82 65.84 -150.50 19 5kl5 G-arg B.DG8 A.ARG394 -11.18 148.70 1.41 -11.09 -0.17 -4.64 49.75 145.38 20 5kl5 C-ser B.1CC9 A.SER365 11.62 -175.90 -9.80 5.74 -2.45 12.44 75.02 -174.80 21 5kl5 C-his B.1CC9 A.HIS369 7.94 138.71 2.85 -3.81 6.35 30.54 74.57 124.94 22 5kl5 C-arg B.1CC9 A.ARG372 9.82 176.60 -0.63 -9.79 -0.21 -6.53 -60.11 176.07 23 5kl5 G-arg B.DG10 A.ARG366 10.31 -169.44 -1.27 9.72 3.19 -0.30 -37.12 -168.86 24 5kl5 G-asp B.DG10 A.ASP368 8.97 -179.31 1.28 8.40 2.86 -18.21 55.49 -179.21 25 5kl5 G-his B.DG10 A.HIS369 -9.01 125.73 5.14 -6.28 3.93 53.45 60.28 106.56 26 5kl5 T-arg B.DT11 A.ARG366 -10.58 163.61 0.94 -10.52 0.56 10.29 43.43 162.28 27 5kl5 T-arg C.DT1 A.ARG366 -10.12 -122.09 -0.71 10.09 0.34 -1.75 -29.08 -119.97 28 5kl5 T-ser C.DT1 A.SER367 10.74 175.42 8.45 -4.91 -4.45 -46.80 -32.21 174.79 29 5kl5 T-asp C.DT1 A.ASP368 9.37 -137.56 -6.52 6.27 2.42 -35.15 59.51 -127.86 30 5kl5 A-arg C.DA2 A.ARG366 10.73 -163.10 0.92 10.67 -0.54 7.38 -39.33 -162.01 31 5kl5 A-asp C.DA2 A.ASP368 9.43 -156.79 -3.90 8.58 0.35 2.01 55.00 -153.78 32 5kl5 C-arg C.5CM3 A.ARG366 -9.66 161.25 -2.50 -8.72 -3.32 5.68 42.94 159.81 33 5kl5 C-asp C.5CM3 A.ASP368 -8.15 169.98 0.31 -7.64 -2.81 -19.61 -48.04 168.86 34 5kl5 G-arg C.DG4 A.ARG372 10.05 179.37 0.17 -10.03 0.68 3.81 -67.30 179.25 35 5kl5 G-asp C.DG4 A.ASP396 8.78 -114.29 -6.00 5.69 2.95 -13.30 40.29 -108.82 36 5kl5 C-arg C.DC5 A.ARG372 -10.92 156.98 -3.22 -10.21 -2.18 -12.41 -59.63 153.23 37 5kl5 C-arg C.DC5 A.ARG394 -11.01 -146.43 0.89 10.97 0.27 -7.11 -55.25 -141.88 38 5kl5 C-asp C.DC5 A.ASP396 8.94 -139.78 -3.62 8.17 -0.45 -6.77 36.53 -137.47 39 5kl5 C-arg C.DC6 A.ARG394 -10.67 178.93 -2.21 -10.18 -2.27 18.67 49.04 178.80 40 5kl5 C-asp C.DC6 A.ASP396 -8.96 -172.75 -0.47 8.17 -3.65 10.80 37.50 -172.31 41 5kl5 C-asp C.DC7 A.ASP426 8.73 -115.60 -5.39 6.06 3.24 -18.48 42.11 -109.26 42 5kl5 A-arg C.DA8 A.ARG424 -9.57 -156.05 1.02 9.41 -1.44 -1.45 -55.70 -152.86 43 5kl5 A-asp C.DA8 A.ASP426 -7.66 -150.22 -2.89 7.08 -0.50 -10.62 38.10 -148.31 44 5kl5 C-asp C.DC9 A.ASP426 -8.99 -176.37 -0.34 8.22 -3.63 3.67 39.29 -176.15 45 5kl5 G-arg C.DG10 A.ARG430 -10.57 164.59 0.08 -10.56 0.55 14.59 -55.06 162.45 **************************************************************************** List of 31 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5kl5 AT-arg C.DA8 B.DT5 A.ARG424 -9.48 -155.45 0.89 9.35 -1.28 1.60 -58.67 -151.76 2 5kl5 AT-arg C.DA2 B.DT11 A.ARG366 10.65 -163.35 0.92 10.60 -0.55 8.83 -41.38 -162.14 3 5kl5 AT-asp C.DA8 B.DT5 A.ASP426 -7.57 -147.43 -3.00 6.93 -0.52 -9.40 34.83 -145.69 4 5kl5 AT-asp C.DA2 B.DT11 A.ASP368 9.30 -155.75 -3.83 8.47 0.26 3.05 52.85 -152.86 5 5kl5 AT-his C.DA8 B.DT5 A.HIS397 -9.23 175.02 -7.53 -4.40 3.03 21.40 -87.10 172.98 6 5kl5 AT-thr C.DA8 B.DT5 A.THR400 -10.82 137.15 -2.91 -10.09 -2.62 -19.85 -51.53 131.31 7 5kl5 GC-arg B.DG2 C.DC11 A.ARG430 10.84 -143.46 -3.37 10.13 1.93 -1.89 58.20 -137.94 8 5kl5 GC-arg C.DG10 B.DC3 A.ARG424 -11.19 140.93 -3.68 -8.90 -5.70 18.91 57.16 134.53 9 5kl5 GC-arg C.DG10 B.DC3 A.ARG430 -10.37 168.18 0.37 -10.33 0.82 12.81 -51.90 166.76 10 5kl5 GC-arg B.DG4 C.DC9 A.ARG424 10.81 -174.42 -1.66 10.12 3.42 9.04 -54.14 -173.71 11 5kl5 GC-arg B.DG6 C.DC7 A.ARG394 11.43 -147.38 -3.11 10.10 4.37 25.74 -42.60 -143.93 12 5kl5 GC-arg B.DG7 C.DC6 A.ARG372 11.59 -129.64 -7.56 7.30 4.90 -37.33 55.93 -118.55 13 5kl5 GC-arg B.DG7 C.DC6 A.ARG394 10.85 -177.41 -2.46 10.35 2.09 17.39 -50.69 -177.10 14 5kl5 GC-arg B.DG8 C.DC5 A.ARG372 11.14 -156.23 -3.46 10.33 2.34 -13.09 62.74 -151.87 15 5kl5 GC-arg B.DG8 C.DC5 A.ARG394 -11.09 147.54 1.15 -11.03 -0.22 -5.90 52.49 143.64 16 5kl5 GC-arg C.DG4 B.1CC9 A.ARG372 9.93 -178.65 -0.41 9.91 0.45 -5.25 63.72 -178.41 17 5kl5 GC-arg B.DG10 C.5CM3 A.ARG366 9.99 -165.29 -1.90 9.24 3.27 2.56 -40.12 -164.33 18 5kl5 GC-asp C.DG10 B.DC3 A.ASP426 -9.41 154.60 -3.28 -6.74 -5.68 -22.28 -25.80 153.41 19 5kl5 GC-asp B.DG4 C.DC9 A.ASP426 9.08 175.70 -0.31 -8.46 3.29 6.32 -38.29 175.44 20 5kl5 GC-asp B.DG6 C.DC7 A.ASP426 -8.81 115.44 -5.47 -6.09 -3.25 -18.18 -38.47 110.06 21 5kl5 GC-asp B.DG7 C.DC6 A.ASP396 9.08 172.62 -0.27 -8.37 3.51 12.46 -35.52 172.20 22 5kl5 GC-asp B.DG8 C.DC5 A.ASP396 -8.91 140.28 -3.34 -8.25 0.27 -4.60 -39.17 137.69 23 5kl5 GC-asp C.DG4 B.1CC9 A.ASP396 8.79 -112.54 -6.27 5.64 2.46 -16.08 37.21 -107.41 24 5kl5 GC-asp B.DG10 C.5CM3 A.ASP368 8.56 -174.71 0.78 8.03 2.84 -19.05 51.75 -174.03 25 5kl5 GC-glu B.DG2 C.DC11 A.GLU427 9.47 149.53 3.57 -0.97 8.72 3.48 77.01 140.73 26 5kl5 GC-glu C.DG10 B.DC3 A.GLU427 -8.65 -126.35 5.44 1.94 -6.44 20.32 -77.11 -107.98 27 5kl5 GC-his B.DG6 C.DC7 A.HIS397 9.04 136.44 4.19 -4.65 6.53 21.05 79.89 120.79 28 5kl5 GC-his B.DG7 C.DC6 A.HIS397 -9.20 111.41 5.28 -5.94 4.64 37.58 69.37 86.29 29 5kl5 GC-his C.DG4 B.1CC9 A.HIS369 -8.03 -141.37 3.00 3.93 -6.33 29.96 -72.22 -129.55 30 5kl5 GC-his B.DG10 C.5CM3 A.HIS369 -8.66 126.94 5.34 -5.67 3.77 48.22 63.52 108.81 31 5kl5 GC-ser C.DG4 B.1CC9 A.SER365 -11.68 174.19 -9.95 -5.64 2.35 11.11 -78.73 172.44 **************************************************************************** List of 7 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 5kl5 OP1@B.DG4 ND1@A.HIS401 2.74 po4:sidechain:salt-bridge 2 5kl5 OP1@B.DG7 NE@A.ARG362 2.98 po4:sidechain:salt-bridge 3 5kl5 OP1@B.DG7 NH1@A.ARG376 3.56 po4:sidechain:salt-bridge 4 5kl5 OP2@B.DG7 ND1@A.HIS373 2.84 po4:sidechain:salt-bridge 5 5kl5 OP1@C.DC5 NZ@A.LYS399 3.37 po4:sidechain:salt-bridge 6 5kl5 OP2@C.DC5 NZ@A.LYS399 2.94 po4:sidechain:salt-bridge 7 5kl5 OP2@C.DC6 OG@A.SER425 3.61 po4:sidechain **************************************************************************** List of 15 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 5kl5 N7@B.DG2 NH2@A.ARG430 2.88 base:sidechain 2 5kl5 O6@B.DG2 NH1@A.ARG430 2.91 base:sidechain 3 5kl5 N7@B.DG4 NH1@A.ARG424 2.91 base:sidechain 4 5kl5 O6@B.DG4 NH2@A.ARG424 2.82 base:sidechain 5 5kl5 O4@B.DT5 NH1@A.ARG424 2.75 base:sidechain 6 5kl5 N7@B.DG6 NE2@A.HIS397 2.84 base:sidechain 7 5kl5 N7@B.DG7 NH1@A.ARG394 2.93 base:sidechain 8 5kl5 O6@B.DG7 NH2@A.ARG394 2.84 base:sidechain 9 5kl5 N7@B.DG8 NH2@A.ARG372 2.98 base:sidechain 10 5kl5 O6@B.DG8 NH1@A.ARG372 3.05 base:sidechain 11 5kl5 O6@B.DG10 NH2@A.ARG366 2.65 base:sidechain 12 5kl5 O6@B.DG10 NE2@A.HIS369 3.69 base:sidechain 13 5kl5 O4@B.DT11 NH1@A.ARG366 2.80 base:sidechain 14 5kl5 N4@C.5CM3 OD2@A.ASP368 3.46 base:sidechain 15 5kl5 N4@C.DC5 OD2@A.ASP396 2.98 base:sidechain **************************************************************************** List of 10 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 5kl5 G-arg B.DG2 A.ARG430 0.53 16 2 5kl5 G-arg B.DG4 A.ARG424 0.58 28 3 5kl5 T-arg B.DT5 A.ARG424 2.46 29 4 5kl5 G-his B.DG6 A.HIS397 0.59 3 5 5kl5 G-arg B.DG7 A.ARG394 0.03 27 6 5kl5 G-arg B.DG8 A.ARG372 0.46 15 7 5kl5 G-his B.DG10 A.HIS369 0.05 28 8 5kl5 T-arg B.DT11 A.ARG366 0.77 45 9 5kl5 C-asp C.5CM3 A.ASP368 0.19 21 10 5kl5 C-asp C.DC5 A.ASP396 0.54 19 **************************************************************************** List of 6 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 5kl5 A-arg B.DA1 A.ARG430 3.38 12 2 5kl5 C-arg B.DC3 A.ARG424 3.54 19 3 5kl5 T-his B.DT5 A.HIS397 3.53 10 4 5kl5 G-arg B.DG7 A.ARG372 3.54 12 5 5kl5 C-his B.1CC9 A.HIS369 3.43 19 6 5kl5 T-asp C.DT1 A.ASP368 4.70 45