**************************************************************************** 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=6d1t.pdb -o=6d1t.out File name: 6d1t.pdb no. of peptide chains: 1 [A=69] no. of DNA/RNA chains: 2 [B=12,C=12] no. of amino acids: 69 no. of nucleotides: 24 no. of atoms: 1027 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 5CM-c 2 B.5CM6,C.5CM6 **************************************************************************** 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=12 strand-1 5'-GCCAAcGTTGGC-3' bp-type |||||||||||| strand-2 3'-CGGTTGcAACCG-5' helix-form BBBBBBBBBBB 1 B.DG1 C.DC12 G-C WC 19-XIX cWW cW-W 2 B.DC2 C.DG11 C-G WC 19-XIX cWW cW-W 3 B.DC3 C.DG10 C-G WC 19-XIX cWW cW-W 4 B.DA4 C.DT9 A-T WC 20-XX cWW cW-W 5 B.DA5 C.DT8 A-T WC 20-XX cWW cW-W 6 B.5CM6 C.DG7 c-G WC 19-XIX cWW cW-W 7 B.DG7 C.5CM6 G-c WC 19-XIX cWW cW-W 8 B.DT8 C.DA5 T-A WC 20-XX cWW cW-W 9 B.DT9 C.DA4 T-A WC 20-XX cWW cW-W 10 B.DG10 C.DC3 G-C WC 19-XIX cWW cW-W 11 B.DG11 C.DC2 G-C WC 19-XIX cWW cW-W 12 B.DC12 C.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 17 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6d1t A-tyr B.DA5 A.TYR34 13.15 -160.47 -5.49 10.57 -5.56 48.46 56.49 -155.40 2 6d1t A-arg B.DA5 A.ARG44 11.24 -157.48 -2.38 10.95 0.92 10.37 63.55 -153.32 3 6d1t C-arg B.5CM6 A.ARG22 11.37 -121.90 -5.91 7.58 6.08 -15.29 -52.17 -113.84 4 6d1t C-asp B.5CM6 A.ASP32 10.32 -149.35 -3.31 9.77 -0.14 36.62 13.10 -147.44 5 6d1t C-tyr B.5CM6 A.TYR34 -12.76 178.43 1.50 -9.91 -7.90 -63.41 -37.32 178.04 6 6d1t C-arg B.5CM6 A.ARG44 10.48 178.76 -1.80 -10.21 -1.56 -28.52 -53.70 178.56 7 6d1t G-arg B.DG7 A.ARG22 -11.64 -159.48 -4.51 10.07 3.72 -28.53 -38.62 -157.52 8 6d1t G-arg B.DG7 A.ARG30 11.13 -169.31 -3.97 9.36 4.53 1.03 -0.86 -169.31 9 6d1t T-thr B.DT8 A.THR27 -10.66 -146.87 -3.32 9.84 -2.40 21.35 -15.26 -145.96 10 6d1t T-arg B.DT8 A.ARG30 -11.32 162.34 2.58 -11.02 0.36 8.06 3.72 162.29 11 6d1t C-arg C.DC3 A.ARG30 12.99 -89.41 -5.36 10.83 4.75 -2.09 -4.48 -89.30 12 6d1t A-arg C.DA4 A.ARG30 11.52 -128.33 -0.37 11.44 1.28 -4.91 -5.57 -128.21 13 6d1t A-arg C.DA5 A.ARG30 -11.36 -159.70 2.24 11.00 -1.75 -4.89 -8.60 -159.62 14 6d1t C-arg C.5CM6 A.ARG22 11.31 165.84 -4.65 -9.88 -2.96 -28.88 52.73 163.62 15 6d1t C-arg C.5CM6 A.ARG44 10.37 -147.61 -6.47 7.29 3.55 -56.15 33.76 -141.26 16 6d1t G-arg C.DG7 A.ARG44 -10.62 -177.38 -1.90 10.35 1.43 -32.02 60.81 -176.82 17 6d1t T-arg C.DT8 A.ARG44 -11.35 151.85 -2.48 -10.91 -1.88 18.10 -61.70 146.62 **************************************************************************** List of 13 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6d1t AT-arg B.DA5 C.DT8 A.ARG44 11.29 -154.65 -2.43 10.94 1.40 14.24 62.65 -149.97 2 6d1t AT-arg C.DA5 B.DT8 A.ARG30 -11.34 -160.98 2.40 11.03 -1.06 1.57 -6.11 -160.95 3 6d1t AT-arg C.DA4 B.DT9 A.ARG30 11.43 -126.92 -0.57 11.24 2.00 2.47 -7.27 -126.79 4 6d1t AT-thr C.DA5 B.DT8 A.THR27 10.62 148.02 -3.05 -9.97 2.03 26.02 20.50 146.60 5 6d1t AT-tyr B.DA5 C.DT8 A.TYR34 13.16 -158.02 -5.44 10.81 -5.18 52.41 56.11 -151.85 6 6d1t GC-arg C.DG7 B.5CM6 A.ARG22 -11.35 122.62 -5.64 -7.48 -6.40 -12.48 49.73 115.65 7 6d1t GC-arg C.DG7 B.5CM6 A.ARG44 -10.55 -178.06 -1.85 10.28 1.50 -30.25 57.26 -177.70 8 6d1t GC-arg B.DG7 C.5CM6 A.ARG22 -11.48 -162.65 -4.60 9.97 3.34 -28.70 -45.68 -160.51 9 6d1t GC-arg B.DG7 C.5CM6 A.ARG30 10.92 -170.12 -4.14 9.17 4.25 2.08 -8.24 -170.09 10 6d1t GC-arg B.DG7 C.5CM6 A.ARG44 -10.40 144.38 -6.16 -7.20 -4.28 -52.28 -39.72 137.31 11 6d1t GC-arg B.DG10 C.DC3 A.ARG30 -13.02 87.65 -5.41 -10.79 -4.89 -0.18 5.10 87.53 12 6d1t GC-asp C.DG7 B.5CM6 A.ASP32 -10.35 150.93 -3.17 -9.85 -0.16 39.16 -15.99 148.77 13 6d1t GC-tyr C.DG7 B.5CM6 A.TYR34 12.82 -176.51 1.63 10.06 7.77 -65.17 40.43 -175.56 **************************************************************************** List of 7 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 6d1t OP1@B.5CM6 N@A.LYS23 3.22 po4:backbone 2 6d1t OP1@B.5CM6 N@A.SER24 3.09 po4:backbone 3 6d1t OP1@B.DG7 N@A.ALA26 2.69 po4:backbone 4 6d1t OP2@B.DG7 N@A.THR27 2.97 po4:backbone 5 6d1t OP2@B.DG7 OG1@A.THR27 2.66 po4:sidechain 6 6d1t OP2@C.DA5 N@A.LYS46 2.95 po4:backbone 7 6d1t OP2@C.5CM6 OG@A.SER45 2.78 po4:sidechain **************************************************************************** List of 5 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 6d1t N7@B.DG7 NH1@A.ARG22 2.64 base:sidechain 2 6d1t O6@B.DG7 NH2@A.ARG22 2.79 base:sidechain 3 6d1t O4@B.DT8 NH1@A.ARG30 2.76 base:sidechain 4 6d1t N7@C.DG7 NH2@A.ARG44 2.85 base:sidechain 5 6d1t O6@C.DG7 NH1@A.ARG44 2.78 base:sidechain **************************************************************************** List of 3 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 6d1t G-arg B.DG7 A.ARG22 0.44 8 2 6d1t T-arg B.DT8 A.ARG30 0.58 58 3 6d1t G-arg C.DG7 A.ARG44 0.01 31 **************************************************************************** List of 2 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 6d1t C-arg B.5CM6 A.ARG22 3.55 4 2 6d1t C-arg C.5CM6 A.ARG44 3.34 19