**************************************************************************** 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=6wr9.pdb -o=6wr9.out File name: 6wr9.pdb no. of DNA/RNA chains: 4 [A=21,B=5,C=9,D=7] no. of nucleotides: 42 no. of atoms: 858 no. of waters: 0 no. of metals: 1 [Mg=1] **************************************************************************** List of 19 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DG3 D.DC16 G-C WC 19-XIX cWW cW-W 2 A.DC4 D.DG15 C-G WC 19-XIX cWW cW-W 3 A.DA5 D.DT14 A-T WC 20-XX cWW cW-W 4 A.DG6 D.DC13 G-C WC 19-XIX cWW cW-W 5 A.DA7 D.DT12 A-T WC 20-XX cWW cW-W 6 A.DC8 D.DG11 C-G WC 19-XIX cWW cW-W 7 A.DT9 D.DA10 T-A WC 20-XX cWW cW-W 8 A.DA10 B.DT5 A-T WC 20-XX cWW cW-W 9 A.DG11 B.DC4 G-C WC 19-XIX cWW cW-W 10 A.DA12 B.DT3 A-T WC 20-XX cWW cW-W 11 A.DC13 B.DG2 C-G WC 19-XIX cWW cW-W 12 A.DA14 B.DT1 A-T WC 20-XX cWW cW-W 13 A.DC15 C.DG9 C-G WC 19-XIX cWW cW-W 14 A.DC16 C.DG8 C-G WC 19-XIX cWW cW-W 15 A.DA17 C.DT7 A-T WC 20-XX cWW cW-W 16 A.DC18 C.DG6 C-G WC 19-XIX cWW cW-W 17 A.DT19 C.DA5 T-A WC 20-XX cWW cW-W 18 A.DC20 C.DG4 C-G WC 19-XIX cWW cW-W 19 A.DA21 C.DT3 A-T WC 20-XX 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[3] bps=19 strand-1 5'-GCAGACTAGACACCACTCA-3' bp-type ||||||||||||||||||| strand-2 3'-CGTCTGATCTGTGGTGAGT-5' helix-form BBBB..xBBBBxB.BBB. 1 A.DG3 D.DC16 G-C WC 19-XIX cWW cW-W 2 A.DC4 D.DG15 C-G WC 19-XIX cWW cW-W 3 A.DA5 D.DT14 A-T WC 20-XX cWW cW-W 4 A.DG6 D.DC13 G-C WC 19-XIX cWW cW-W 5 A.DA7 D.DT12 A-T WC 20-XX cWW cW-W 6 A.DC8 D.DG11 C-G WC 19-XIX cWW cW-W 7 A.DT9 D.DA10 T-A WC 20-XX cWW cW-W 8 A.DA10 B.DT5 A-T WC 20-XX cWW cW-W 9 A.DG11 B.DC4 G-C WC 19-XIX cWW cW-W 10 A.DA12 B.DT3 A-T WC 20-XX cWW cW-W 11 A.DC13 B.DG2 C-G WC 19-XIX cWW cW-W 12 A.DA14 B.DT1 A-T WC 20-XX cWW cW-W 13 A.DC15 C.DG9 C-G WC 19-XIX cWW cW-W 14 A.DC16 C.DG8 C-G WC 19-XIX cWW cW-W 15 A.DA17 C.DT7 A-T WC 20-XX cWW cW-W 16 A.DC18 C.DG6 C-G WC 19-XIX cWW cW-W 17 A.DT19 C.DA5 T-A WC 20-XX cWW cW-W 18 A.DC20 C.DG4 C-G WC 19-XIX cWW cW-W 19 A.DA21 C.DT3 A-T WC 20-XX cWW cW-W **************************************************************************** List of 3 stems 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=7 strand-1 5'-GCAGACT-3' bp-type ||||||| strand-2 3'-CGTCTGA-5' helix-form BBBB.. 1 A.DG3 D.DC16 G-C WC 19-XIX cWW cW-W 2 A.DC4 D.DG15 C-G WC 19-XIX cWW cW-W 3 A.DA5 D.DT14 A-T WC 20-XX cWW cW-W 4 A.DG6 D.DC13 G-C WC 19-XIX cWW cW-W 5 A.DA7 D.DT12 A-T WC 20-XX cWW cW-W 6 A.DC8 D.DG11 C-G WC 19-XIX cWW cW-W 7 A.DT9 D.DA10 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=5 strand-1 5'-AGACA-3' bp-type ||||| strand-2 3'-TCTGT-5' helix-form BBBB 1 A.DA10 B.DT5 A-T WC 20-XX cWW cW-W 2 A.DG11 B.DC4 G-C WC 19-XIX cWW cW-W 3 A.DA12 B.DT3 A-T WC 20-XX cWW cW-W 4 A.DC13 B.DG2 C-G WC 19-XIX cWW cW-W 5 A.DA14 B.DT1 A-T WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#3[#1] bps=7 strand-1 5'-CCACTCA-3' bp-type ||||||| strand-2 3'-GGTGAGT-5' helix-form B.BBB. 1 A.DC15 C.DG9 C-G WC 19-XIX cWW cW-W 2 A.DC16 C.DG8 C-G WC 19-XIX cWW cW-W 3 A.DA17 C.DT7 A-T WC 20-XX cWW cW-W 4 A.DC18 C.DG6 C-G WC 19-XIX cWW cW-W 5 A.DT19 C.DA5 T-A WC 20-XX cWW cW-W 6 A.DC20 C.DG4 C-G WC 19-XIX cWW cW-W 7 A.DA21 C.DT3 A-T WC 20-XX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 3 stems: [#1,#2,#3] **************************************************************************** List of 5 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 AC A.DA14,A.DC15 2 nts=2 TG B.DT1,C.DG9 3 nts=2 TA B.DT5,D.DA10 4 nts=3 GAG A.DG1,A.DA2,A.DG3 5 nts=3 TCT C.DT1,C.DC2,C.DT3 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=2 GA A.DG1,A.DA2 2 nts=2 TC C.DT1,C.DC2 **************************************************************************** Special notes: o cross-paired segments in separate chains, be *careful* with .dbn **************************************************************************** This structure contains *1-order pseudoknot o You may want to run DSSR again with the '--nested' option which removes pseudoknots to get a fully nested secondary structure representation. o The DSSR-derived dbn may be problematic (see notes above). **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6wr9 nts=42 [whole] GAGCAGACTAGACACCACTCA&TGTCT&TCTGAGTGG&AGTCTGC ..((((((([[[[[(((((((&]]]]]&..)))))))&))))))) >6wr9-A #1 nts=21 3.33(0.40) [chain] DNA GAGCAGACTAGACACCACTCA ..((((((([[[[[((((((( >6wr9-B #2 nts=5 4.00(0.25) [chain] DNA TGTCT ]]]]] >6wr9-C #3 nts=9 3.42(0.17) [chain] DNA TCTGAGTGG ..))))))) >6wr9-D #4 nts=7 3.13(0.20) [chain] DNA AGTCTGC ))))))) **************************************************************************** Summary of structural features of 42 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 G . A.DG1 0.012 syn,~C3'-endo,BI,non-pair-contact,ss-non-loop 2 A . A.DA2 0.008 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 3 G ( A.DG3 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 4 C ( A.DC4 0.007 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 5 A ( A.DA5 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 6 G ( A.DG6 0.006 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 7 A ( A.DA7 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 8 C ( A.DC8 0.004 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 9 T ( A.DT9 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 10 A [ A.DA10 0.004 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 11 G [ A.DG11 0.008 pseudoknotted,anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 12 A [ A.DA12 0.005 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 13 C [ A.DC13 0.007 pseudoknotted,anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 14 A [ A.DA14 0.005 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 15 C ( A.DC15 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 16 C ( A.DC16 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 17 A ( A.DA17 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 18 C ( A.DC18 0.006 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 19 T ( A.DT19 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 20 C ( A.DC20 0.009 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 21 A ( A.DA21 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 22 T ] B.DT1 0.007 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 23 G ] B.DG2 0.015 pseudoknotted,anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 24 T ] B.DT3 0.007 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 25 C ] B.DC4 0.012 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 26 T ] B.DT5 0.009 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 27 T . C.DT1 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop 28 C . C.DC2 0.005 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 29 T ) C.DT3 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 30 G ) C.DG4 0.007 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 31 A ) C.DA5 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 32 G ) C.DG6 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 33 T ) C.DT7 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 34 G ) C.DG8 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 35 G ) C.DG9 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 36 A ) D.DA10 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 37 G ) D.DG11 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 38 T ) D.DT12 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 39 C ) D.DC13 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 40 T ) D.DT14 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 41 G ) D.DG15 0.014 anti,canonical,non-pair-contact,helix,stem,coaxial-stack 42 C ) D.DC16 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** 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