**************************************************************************** Note: By default, each nucleotide is identified by chainId.name#. So a common case would be B.A1689, meaning adenosine #1689 on chain B. One-letter base names for modified nucleotides are put in lower case (e.g., 'c' for 5MC). For further information about the output notation, please refer to the DSSR User Manual. Questions and suggestions are *always* welcome on the 3DNA Forum. Command: x3dna-dssr -i=5e3h.pdb -o=5e3h.out File name: 5e3h.pdb no. of DNA/RNA chains: 2 [B=12,C=12] no. of nucleotides: 25 no. of atoms: 5517 no. of waters: 0 no. of metals: 5 [Be=1,Mg=3,Zn=1] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 ADP-a 1 A.ADP1006 **************************************************************************** List of 11 base pairs nt1 nt2 bp name Saenger LW DSSR 1 B.C1 C.G14 C-G WC 19-XIX cWW cW-W 2 B.G2 C.C13 G-C WC 19-XIX cWW cW-W 3 B.A3 C.U12 A-U WC 20-XX cWW cW-W 4 B.C4 C.G11 C-G WC 19-XIX cWW cW-W 5 B.G5 C.C10 G-C WC 19-XIX cWW cW-W 6 B.C6 C.G9 C-G WC 19-XIX cWW cW-W 7 B.U7 C.A8 U-A WC 20-XX cWW cW-W 8 B.A8 C.U7 A-U WC 20-XX cWW cW-W 9 B.G9 C.C6 G-C WC 19-XIX cWW cW-W 10 B.C10 C.G5 C-G WC 19-XIX cWW cW-W 11 B.G11 C.C4 G-C WC 19-XIX cWW cW-W **************************************************************************** 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[1] bps=11 strand-1 5'-CGACGCUAGCG-3' bp-type ||||||||||| strand-2 3'-GCUGCGAUCGC-5' helix-form AAAA.AAAAA 1 B.C1 C.G14 C-G WC 19-XIX cWW cW-W 2 B.G2 C.C13 G-C WC 19-XIX cWW cW-W 3 B.A3 C.U12 A-U WC 20-XX cWW cW-W 4 B.C4 C.G11 C-G WC 19-XIX cWW cW-W 5 B.G5 C.C10 G-C WC 19-XIX cWW cW-W 6 B.C6 C.G9 C-G WC 19-XIX cWW cW-W 7 B.U7 C.A8 U-A WC 20-XX cWW cW-W 8 B.A8 C.U7 A-U WC 20-XX cWW cW-W 9 B.G9 C.C6 G-C WC 19-XIX cWW cW-W 10 B.C10 C.G5 C-G WC 19-XIX cWW cW-W 11 B.G11 C.C4 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 stem Note: a stem is defined as a helix consisting of only canonical WC/wobble pairs, with a continuous backbone. stem#number[#helix-number containing this stem] Other terms are defined as in the above Helix section. -------------------------------------------------------------------- stem#1[#1] bps=11 strand-1 5'-CGACGCUAGCG-3' bp-type ||||||||||| strand-2 3'-GCUGCGAUCGC-5' helix-form AAAA.AAAAA 1 B.C1 C.G14 C-G WC 19-XIX cWW cW-W 2 B.G2 C.C13 G-C WC 19-XIX cWW cW-W 3 B.A3 C.U12 A-U WC 20-XX cWW cW-W 4 B.C4 C.G11 C-G WC 19-XIX cWW cW-W 5 B.G5 C.C10 G-C WC 19-XIX cWW cW-W 6 B.C6 C.G9 C-G WC 19-XIX cWW cW-W 7 B.U7 C.A8 U-A WC 20-XX cWW cW-W 8 B.A8 C.U7 A-U WC 20-XX cWW cW-W 9 B.G9 C.C6 G-C WC 19-XIX cWW cW-W 10 B.C10 C.G5 C-G WC 19-XIX cWW cW-W 11 B.G11 C.C4 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 3 base stacks Note: a stack is an ordered list of nucleotides assembled together via base-stacking interactions, regardless of backbone connectivity. Stacking interactions within a stem are *not* included. 1 nts=2 FC A.PHE853,B.C1 2 nts=2 GU B.G11,B.U12 3 nts=3 FaR A.PHE241,A.ADP1006,A.ARG244 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 A C.A3 **************************************************************************** List of 3 non-loop single-stranded segments 1 nts=1 U B.U12 2 nts=1 A C.A3 3 nts=1 a A.ADP1006 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5e3h nts=25 [whole] CGACGCUAGCGU&ACGCUAGCGUCG&a (((((((((((.&.)))))))))))&. >5e3h-B #1 nts=12 2.90(0.33) [chain] RNA CGACGCUAGCGU (((((((((((. >5e3h-C #2 nts=12 2.67(0.38) [chain] RNA ACGCUAGCGUCG .))))))))))) **************************************************************************** Summary of structural features of 25 nucleotides Note: the first five columns are: (1) serial number, (2) one-letter shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base ring atoms fitted against those in a standard base reference frame. The sixth (last) column contains a comma-separated list of features whose meanings are mostly self-explanatory, except for: turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees break: no backbone linkage between O3'(i-1) and P(i) 1 C ( B.C1 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 G ( B.G2 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 3 A ( B.A3 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 4 C ( B.C4 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 5 G ( B.G5 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 C ( B.C6 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 7 U ( B.U7 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 8 A ( B.A8 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 9 G ( B.G9 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 10 C ( B.C10 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 11 G ( B.G11 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 12 U . B.U12 0.003 anti,~C3'-endo,non-pair-contact,ss-non-loop 13 A . C.A3 0.002 anti,~C3'-endo,BI,non-stack,ss-non-loop 14 C ) C.C4 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 15 G ) C.G5 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 16 C ) C.C6 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 17 U ) C.U7 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 18 A ) C.A8 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 19 G ) C.G9 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 20 C ) C.C10 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 21 G ) C.G11 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 22 U ) C.U12 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 23 C ) C.C13 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 24 G ) C.G14 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 25 a . A.ADP1006 0.067 modified,anti,ss-non-loop **************************************************************************** List of 8 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-stems.pdb -- an ensemble of stems 3 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 4 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 5 dssr-2ndstrs.ct -- secondary structure in connectivity table format 6 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 7 dssr-torsions.txt -- backbone torsion angles and suite names 8 dssr-stacks.pdb -- an ensemble of base stacks