**************************************************************************** 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=4m9e.pdb -o=4m9e.out --type=either Date and time: Sun Sep 29 22:33:15 2019 File name: 4m9e.pdb no. of peptide chains: 1 [A=85] no. of DNA/RNA chains: 2 [B=10,C=10] no. of amino acids: 85 no. of nucleotides: 20 no. of atoms: 1247 no. of waters: 134 no. of metals: 3 [Zn=3] **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 5CM-c 2 B.5CM5,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'-GAGGcGTGGC-3' bp-type |||||||||| strand-2 3'-CTCCGcACCG-5' helix-form BBBBB.BBB 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.5CM5 C.DG6 c-G WC 19-XIX 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 48 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4m9e G-arg B.DG1 A.ARG467 -17.11 -77.84 -5.64 15.97 -2.37 -22.18 37.36 -66.24 2 4m9e G-phe B.DG1 A.PHE469 13.66 -47.10 -3.99 12.20 4.68 -22.03 9.22 -40.90 3 4m9e G-his B.DG1 A.HIS474 9.60 164.09 4.41 -2.15 8.26 13.84 84.90 158.19 4 4m9e A-arg B.DA2 A.ARG471 11.61 -140.04 -4.17 10.26 3.48 15.26 -37.37 -137.30 5 4m9e A-his B.DA2 A.HIS474 -9.35 140.37 6.20 -3.75 5.91 36.52 80.43 123.59 6 4m9e G-arg B.DG3 A.ARG449 12.45 -140.68 -8.44 9.15 0.27 -27.55 85.63 -123.20 7 4m9e G-lys B.DG3 A.LYS453 -16.40 -175.05 -13.38 6.81 6.58 2.58 -61.01 -174.26 8 4m9e G-arg B.DG3 A.ARG471 11.23 -169.99 -3.05 10.74 1.27 12.95 -43.46 -169.15 9 4m9e G-glu B.DG4 A.GLU446 10.83 154.42 6.21 -2.39 8.54 18.39 59.33 150.04 10 4m9e G-arg B.DG4 A.ARG449 11.98 -161.36 -3.95 11.01 -2.60 1.91 85.55 -154.51 11 4m9e G-arg B.DG4 A.ARG471 -10.64 156.41 1.79 -10.45 -0.89 -4.10 47.96 154.13 12 4m9e C-thr B.5CM5 A.THR423 16.08 -160.75 -12.90 4.34 8.56 35.83 -58.42 -156.66 13 4m9e C-arg B.5CM5 A.ARG443 10.87 -158.08 -5.07 8.81 3.85 39.40 -37.30 -155.33 14 4m9e C-asp B.5CM5 A.ASP445 8.77 -151.12 -2.17 7.57 3.87 -11.52 44.57 -148.56 15 4m9e C-glu B.5CM5 A.GLU446 9.52 123.57 7.19 -2.87 5.55 27.72 55.73 112.95 16 4m9e C-arg B.5CM5 A.ARG449 -10.92 179.05 -0.36 -9.85 -4.70 -28.45 -74.83 178.76 17 4m9e G-lys B.DG6 A.LYS409 17.34 -47.50 -8.10 15.33 -0.31 6.03 28.44 -37.99 18 4m9e G-tyr B.DG6 A.TYR411 13.48 -16.29 -5.10 10.42 6.87 -4.21 -1.90 -15.63 19 4m9e G-arg B.DG6 A.ARG443 10.94 172.50 3.93 -10.16 1.02 -32.83 44.52 171.54 20 4m9e T-tyr B.DT7 A.TYR411 13.14 -53.93 -3.16 12.27 3.46 -5.25 -1.33 -53.68 21 4m9e T-his B.DT7 A.HIS416 8.91 146.01 4.36 -1.61 7.61 8.52 73.99 136.92 22 4m9e T-arg B.DT7 A.ARG443 -9.25 138.99 2.45 -8.82 -1.34 -17.36 53.51 133.19 23 4m9e G-thr B.DG8 A.THR412 11.77 -172.47 -8.13 5.91 -6.12 29.96 66.16 -170.65 24 4m9e G-lys B.DG8 A.LYS413 9.90 -144.84 -3.08 9.03 2.64 33.39 -56.40 -137.89 25 4m9e G-his B.DG8 A.HIS416 8.67 120.38 5.75 -3.69 5.34 17.69 73.86 101.81 26 4m9e G-lys B.DG9 A.LYS413 9.84 -174.86 -1.27 9.75 -0.51 16.54 -63.29 -173.89 27 4m9e C-lys B.DC10 A.LYS413 -9.04 155.30 0.29 -8.41 -3.32 6.72 66.76 150.25 28 4m9e G-lys C.DG1 A.LYS413 9.28 -152.19 0.20 8.95 2.48 -3.14 -65.59 -146.76 29 4m9e G-ser C.DG1 A.SER415 8.39 -138.22 -5.36 6.39 0.96 -9.30 29.78 -136.55 30 4m9e G-lys C.DG1 A.LYS418 13.08 -151.31 -10.03 8.23 -1.69 43.43 13.37 -148.84 31 4m9e C-lys C.DC2 A.LYS413 -9.87 -177.46 0.57 9.84 -0.41 -22.83 -60.18 -177.00 32 4m9e C-ser C.DC2 A.SER415 -9.13 -169.45 -2.71 8.34 -2.55 -2.57 33.46 -168.98 33 4m9e C-tyr C.DC2 A.TYR430 16.95 -103.49 -11.29 10.42 7.15 -27.64 -8.75 -100.49 34 4m9e C-ser C.DC2 A.SER444 12.09 -128.62 -10.22 6.44 -0.54 37.42 41.90 -121.14 35 4m9e C-ser C.DC3 A.SER444 10.42 -157.83 -7.34 6.58 -3.39 48.29 18.33 -155.33 36 4m9e A-arg C.DA4 A.ARG443 -9.04 -140.97 2.51 8.68 0.22 -30.99 -57.79 -133.18 37 4m9e A-asp C.DA4 A.ASP445 7.50 -158.55 -4.04 6.26 0.84 -29.86 37.32 -156.51 38 4m9e C-arg C.5CM5 A.ARG443 -10.65 -168.94 3.65 9.82 -1.90 -44.25 -49.81 -166.75 39 4m9e C-asp C.5CM5 A.ASP445 -8.93 172.90 1.17 -8.62 -2.00 16.57 -41.49 172.33 40 4m9e C-phe C.5CM5 A.PHE460 16.89 -120.35 -10.79 11.77 5.54 -25.68 9.67 -118.41 41 4m9e C-ser C.5CM5 A.SER472 11.48 -149.60 -9.63 5.84 -2.25 45.26 49.11 -143.40 42 4m9e G-arg C.DG6 A.ARG449 11.00 178.56 0.53 -10.15 4.20 32.51 -72.96 178.13 43 4m9e G-asp C.DG6 A.ASP473 8.75 -123.95 -6.49 5.37 2.36 -19.42 38.84 -119.24 44 4m9e C-arg C.DC7 A.ARG449 -11.66 153.88 -3.84 -10.89 1.62 11.09 -76.53 146.36 45 4m9e C-arg C.DC7 A.ARG471 -10.45 -150.61 1.24 10.37 -0.17 -16.11 -51.12 -146.97 46 4m9e C-asp C.DC7 A.ASP473 -8.83 -153.39 -3.66 8.01 -0.71 -9.10 40.38 -151.52 47 4m9e C-arg C.DC8 A.ARG471 -10.93 174.68 -2.50 -10.41 -2.19 20.05 43.75 174.18 48 4m9e C-asp C.DC8 A.ASP473 -9.38 178.42 0.57 -8.70 -3.46 -13.72 -41.41 178.29 **************************************************************************** List of 40 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4m9e AT-arg B.DA2 C.DT9 A.ARG471 11.62 -142.63 -4.01 10.16 3.98 20.84 -39.10 -139.53 2 4m9e AT-arg C.DA4 B.DT7 A.ARG443 9.14 -139.98 2.48 8.77 0.79 -24.11 -55.83 -133.25 3 4m9e AT-asp C.DA4 B.DT7 A.ASP445 7.61 -153.55 -4.26 6.15 1.41 -25.57 39.88 -151.07 4 4m9e AT-his B.DA2 C.DT9 A.HIS474 9.38 136.21 5.94 -3.60 6.31 32.35 76.55 120.22 5 4m9e AT-his C.DA4 B.DT7 A.HIS416 -8.93 -145.02 4.49 0.99 -7.65 1.89 -76.83 -134.88 6 4m9e AT-tyr C.DA4 B.DT7 A.TYR411 -13.17 52.33 -3.69 -12.25 -3.13 -7.51 7.47 51.32 7 4m9e GC-arg B.DG1 C.DC10 A.ARG467 -17.02 -74.64 -5.72 15.85 -2.34 -20.03 32.62 -65.35 8 4m9e GC-arg B.DG3 C.DC8 A.ARG449 12.33 -138.27 -8.49 8.92 0.60 -23.79 84.01 -121.03 9 4m9e GC-arg B.DG3 C.DC8 A.ARG471 11.08 -172.33 -2.78 10.58 1.73 16.50 -43.60 -171.65 10 4m9e GC-arg B.DG4 C.DC7 A.ARG449 11.82 -157.58 -3.89 10.97 -2.08 6.57 81.15 -150.29 11 4m9e GC-arg B.DG4 C.DC7 A.ARG471 -10.54 153.46 1.51 -10.43 -0.36 -10.10 49.56 150.59 12 4m9e GC-arg C.DG6 B.5CM5 A.ARG443 -10.83 158.80 -5.03 -8.77 -3.87 41.14 38.85 155.89 13 4m9e GC-arg C.DG6 B.5CM5 A.ARG449 10.96 179.76 0.44 -10.00 4.45 30.49 -73.92 179.68 14 4m9e GC-arg B.DG6 C.5CM5 A.ARG443 10.79 170.69 3.79 -10.00 1.46 -38.54 47.17 169.20 15 4m9e GC-asp B.DG3 C.DC8 A.ASP473 9.50 -179.09 0.48 8.98 3.05 -17.92 41.09 -179.01 16 4m9e GC-asp B.DG4 C.DC7 A.ASP473 -8.84 151.61 -3.56 -8.09 0.19 -2.51 -41.85 149.55 17 4m9e GC-asp C.DG6 B.5CM5 A.ASP445 -8.77 150.75 -2.13 -7.53 -3.96 -9.64 -43.09 148.38 18 4m9e GC-asp C.DG6 B.5CM5 A.ASP473 8.66 -123.35 -6.44 5.26 2.43 -17.03 38.63 -118.86 19 4m9e GC-asp B.DG6 C.5CM5 A.ASP445 9.04 -174.99 1.20 8.83 1.54 11.01 44.66 -174.56 20 4m9e GC-glu B.DG4 C.DC7 A.GLU446 10.66 150.36 6.21 -1.89 8.46 12.64 60.31 145.34 21 4m9e GC-glu C.DG6 B.5CM5 A.GLU446 -9.52 -121.87 7.14 2.88 -5.60 25.78 -55.15 -111.41 22 4m9e GC-his B.DG1 C.DC10 A.HIS474 9.47 161.27 4.32 -1.58 8.27 8.91 84.23 154.55 23 4m9e GC-his B.DG8 C.DC3 A.HIS416 8.56 119.30 5.61 -3.58 5.39 16.06 72.28 101.48 24 4m9e GC-lys B.DG3 C.DC8 A.LYS453 -16.24 -177.87 -13.13 6.62 6.91 5.80 -60.84 -177.53 25 4m9e GC-lys B.DG6 C.5CM5 A.LYS409 17.28 -44.21 -8.09 15.25 -0.96 5.36 21.91 -38.27 26 4m9e GC-lys B.DG8 C.DC3 A.LYS413 9.79 -145.59 -3.07 8.86 2.82 35.61 -56.82 -138.43 27 4m9e GC-lys B.DG9 C.DC2 A.LYS413 9.85 -178.69 -0.92 9.81 -0.05 19.68 -61.73 -178.45 28 4m9e GC-lys C.DG1 B.DC10 A.LYS413 9.16 -153.72 0.25 8.69 2.91 1.78 -66.27 -148.50 29 4m9e GC-lys C.DG1 B.DC10 A.LYS418 12.98 -149.83 -10.10 8.04 -1.35 47.94 13.33 -146.66 30 4m9e GC-phe B.DG1 C.DC10 A.PHE469 13.57 -45.68 -4.34 12.02 4.57 -20.67 4.10 -40.77 31 4m9e GC-phe B.DG6 C.5CM5 A.PHE460 -16.85 119.58 -10.67 -11.53 -6.09 -19.12 -9.19 118.42 32 4m9e GC-ser B.DG6 C.5CM5 A.SER472 -11.41 148.67 -9.54 -5.95 1.93 51.58 -50.10 141.02 33 4m9e GC-ser B.DG8 C.DC3 A.SER444 -10.41 156.91 -7.27 -6.65 3.38 50.21 -17.84 154.12 34 4m9e GC-ser B.DG9 C.DC2 A.SER415 9.07 169.64 -2.53 -8.43 2.21 1.97 -31.08 169.24 35 4m9e GC-ser B.DG9 C.DC2 A.SER444 -12.02 127.52 -10.13 -6.45 0.65 40.54 -37.75 120.08 36 4m9e GC-ser C.DG1 B.DC10 A.SER415 8.28 -135.65 -5.45 6.12 1.19 -5.13 28.50 -134.11 37 4m9e GC-thr C.DG6 B.5CM5 A.THR423 -16.01 161.84 -12.93 -4.27 -8.43 37.43 59.97 157.69 38 4m9e GC-thr B.DG8 C.DC3 A.THR412 11.67 -170.98 -8.14 5.87 -5.96 31.62 66.53 -168.72 39 4m9e GC-tyr B.DG6 C.5CM5 A.TYR411 13.43 -19.20 -5.51 10.49 6.32 -6.22 -8.12 -16.27 40 4m9e GC-tyr B.DG9 C.DC2 A.TYR430 -16.87 105.99 -11.31 -10.41 -6.93 -25.61 12.65 103.21 **************************************************************************** List of 4 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 4m9e OP2@B.DG6 OH@A.TYR411 3.26 po4:sidechain 2 4m9e OP2@B.DG8 OG1@A.THR412 3.65 po4:sidechain 3 4m9e OP2@C.DC2 OH@A.TYR430 2.47 po4:sidechain 4 4m9e OP2.A@C.5CM5 OG@A.SER472 3.32 po4:sidechain **************************************************************************** List of 13 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 4m9e N7@B.DA2 NE2@A.HIS474 2.94 base:sidechain 2 4m9e N7@B.DG3 NH1@A.ARG471 2.94 base:sidechain 3 4m9e O6@B.DG3 NH2@A.ARG471 2.92 base:sidechain 4 4m9e N7@B.DG4 NH2@A.ARG449 2.88 base:sidechain 5 4m9e O6@B.DG4 NH1@A.ARG449 2.93 base:sidechain 6 4m9e N4@B.5CM5 OD2@A.ASP445 3.25 base:sidechain 7 4m9e N7@B.DG6 NH2@A.ARG443 3.01 base:sidechain 8 4m9e O6@B.DG6 NH1@A.ARG443 2.86 base:sidechain 9 4m9e N7@B.DG8 NE2@A.HIS416 2.84 base:sidechain 10 4m9e O6@B.DG9 NZ@A.LYS413 3.14 base:sidechain 11 4m9e O6@C.DG1 NZ@A.LYS413 2.60 base:sidechain 12 4m9e O6@C.DG6 NH1@A.ARG449 3.26 base:sidechain 13 4m9e N4@C.DC7 OD2@A.ASP473 2.84 base:sidechain **************************************************************************** List of 8 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 4m9e A-his B.DA2 A.HIS474 0.33 13 2 4m9e G-arg B.DG3 A.ARG471 0.22 17 3 4m9e G-arg B.DG4 A.ARG449 0.18 17 4 4m9e C-asp B.5CM5 A.ASP445 1.87 41 5 4m9e G-arg B.DG6 A.ARG443 0.24 6 6 4m9e G-his B.DG8 A.HIS416 0.19 19 7 4m9e G-arg C.DG6 A.ARG449 2.04 29 8 4m9e C-asp C.DC7 A.ASP473 1.25 25 **************************************************************************** List of 2 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 4m9e C-arg B.5CM5 A.ARG443 3.40 5 2 4m9e T-his B.DT7 A.HIS416 3.33 11 **************************************************************************** Time used: 00:00:00:00