**************************************************************************** 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=7mlb.pdb -o=7mlb.out File name: 7mlb.pdb no. of DNA/RNA chains: 3 [G=15,H=18,I=5] no. of nucleotides: 38 no. of atoms: 28400 no. of waters: 0 no. of metals: 7 [Mg=5,Zn=2] **************************************************************************** List of 13 base pairs nt1 nt2 bp name Saenger LW DSSR 1 G.DC6 H.DG22 C-G WC 19-XIX cWW cW-W 2 G.DT7 H.DA21 T-A WC 20-XX cWW cW-W 3 G.DG8 H.DC20 G-C WC 19-XIX cWW cW-W 4 G.DC9 H.DG19 C-G WC 19-XIX cWW cW-W 5 G.DA10 H.DT18 A-T WC 20-XX cWW cW-W 6 G.DT11 H.DA17 T-A WC 20-XX cWW cW-W 7 G.DC12 H.DG16 C-G WC 19-XIX cWW cW-W 8 G.DC13 H.DG15 C-G WC 19-XIX cWW cW-W 9 G.DT15 I.A5 T-A WC 20-XX cWW cW-W 10 G.DG16 I.C4 G-C WC 19-XIX cWW cW-W 11 G.DA17 I.U3 A-U WC 20-XX cWW cW-W 12 G.DG18 I.C2 G-C WC 19-XIX cWW cW-W 13 G.DT19 I.A1 T-A WC 20-XX cWW cW-W **************************************************************************** List of 2 helices 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=8 strand-1 5'-CTGCATCC-3' bp-type |||||||| strand-2 3'-GACGTAGG-5' helix-form ..BBBB. 1 G.DC6 H.DG22 C-G WC 19-XIX cWW cW-W 2 G.DT7 H.DA21 T-A WC 20-XX cWW cW-W 3 G.DG8 H.DC20 G-C WC 19-XIX cWW cW-W 4 G.DC9 H.DG19 C-G WC 19-XIX cWW cW-W 5 G.DA10 H.DT18 A-T WC 20-XX cWW cW-W 6 G.DT11 H.DA17 T-A WC 20-XX cWW cW-W 7 G.DC12 H.DG16 C-G WC 19-XIX cWW cW-W 8 G.DC13 H.DG15 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=5 strand-1 5'-TGAGT-3' bp-type ||||| strand-2 3'-ACUCA-5' helix-form .A.. 1 G.DT15 I.A5 T-A WC 20-XX cWW cW-W 2 G.DG16 I.C4 G-C WC 19-XIX cWW cW-W 3 G.DA17 I.U3 A-U WC 20-XX cWW cW-W 4 G.DG18 I.C2 G-C WC 19-XIX cWW cW-W 5 G.DT19 I.A1 T-A WC 20-XX cWW cW-W **************************************************************************** List of 2 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=8 strand-1 5'-CTGCATCC-3' bp-type |||||||| strand-2 3'-GACGTAGG-5' helix-form ..BBBB. 1 G.DC6 H.DG22 C-G WC 19-XIX cWW cW-W 2 G.DT7 H.DA21 T-A WC 20-XX cWW cW-W 3 G.DG8 H.DC20 G-C WC 19-XIX cWW cW-W 4 G.DC9 H.DG19 C-G WC 19-XIX cWW cW-W 5 G.DA10 H.DT18 A-T WC 20-XX cWW cW-W 6 G.DT11 H.DA17 T-A WC 20-XX cWW cW-W 7 G.DC12 H.DG16 C-G WC 19-XIX cWW cW-W 8 G.DC13 H.DG15 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=5 strand-1 5'-TGAGT-3' bp-type ||||| strand-2 3'-ACUCA-5' helix-form .A.. 1 G.DT15 I.A5 T-A WC 20-XX cWW cW-W 2 G.DG16 I.C4 G-C WC 19-XIX cWW cW-W 3 G.DA17 I.U3 A-U WC 20-XX cWW cW-W 4 G.DG18 I.C2 G-C WC 19-XIX cWW cW-W 5 G.DT19 I.A1 T-A WC 20-XX cWW cW-W **************************************************************************** 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 WA C.TRP171,H.DA13 2 nts=2 CT G.DC14,G.DT15 3 nts=2 TG G.DT19,G.DG20 4 nts=3 RAY F.ARG231,H.DA2,F.TYR238 5 nts=3 TAA H.DT3,H.DA4,H.DA5 **************************************************************************** Nucleotides not involved in stacking interactions nts=3 TTG H.DT1,H.DT6,H.DG14 **************************************************************************** List of 3 non-loop single-stranded segments 1 nts=1 C G.DC14 2 nts=1 G G.DG20 3 nts=10* TATAATGGAG H.DT1,H.DA2,H.DT3,H.DA4,H.DA5,H.DT6,H.DG7,H.DG8,H.DA13,H.DG14 **************************************************************************** List of 6 splayed-apart dinucleotides 1 G.DC13 G.DC14 angle=124 distance=16.6 ratio=0.88 2 H.DA2 H.DT3 angle=147 distance=19.2 ratio=0.96 3 H.DA5 H.DT6 angle=90 distance=14.3 ratio=0.71 4 H.DT6 H.DG7 angle=101 distance=15.3 ratio=0.77 5 H.DA13 H.DG14 angle=116 distance=18.1 ratio=0.85 6 H.DG14 H.DG15 angle=121 distance=17.3 ratio=0.87 ---------------------------------------------------------------- Summary of 4 splayed-apart units 1 nts=2 CC G.DC13,G.DC14 2 nts=2 AT H.DA2,H.DT3 3 nts=3 ATG H.DA5,H.DT6,H.DG7 4 nts=3 AGG H.DA13,H.DG14,H.DG15 **************************************************************************** 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 >7mlb nts=38 [whole] CTGCATCCCTGAGTG&TATAATGG&AGGGATGCAG&ACUCA ((((((((.[[[[[.&........&..))))))))&]]]]] >7mlb-G #1 nts=15 3.21(1.28) [chain] DNA CTGCATCCCTGAGTG ((((((((.[[[[[. >7mlb-H #2 nts=18 2.39(2.41) [chain] DNA* TATAATGG&AGGGATGCAG ........&..)))))))) >7mlb-I #3 nts=5 3.22(0.05) [chain] RNA ACUCA ]]]]] **************************************************************************** Summary of structural features of 38 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 ( G.DC6 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 T ( G.DT7 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 G ( G.DG8 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 C ( G.DC9 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 A ( G.DA10 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 T ( G.DT11 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 7 C ( G.DC12 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 8 C ( G.DC13 0.004 anti,~C3'-endo,BII,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart 9 C . G.DC14 0.003 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 10 T [ G.DT15 0.004 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 11 G [ G.DG16 0.006 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 A [ G.DA17 0.004 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 13 G [ G.DG18 0.002 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 14 T [ G.DT19 0.002 pseudoknotted,anti,BI,canonical,non-pair-contact,helix-end,stem-end 15 G . G.DG20 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop 16 T . H.DT1 0.002 syn,~C3'-endo,BI,non-stack,ss-non-loop 17 A . H.DA2 0.003 anti,BII,ss-non-loop,splayed-apart 18 T . H.DT3 0.002 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 19 A . H.DA4 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 20 A . H.DA5 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 21 T . H.DT6 0.002 anti,~C2'-endo,BII,non-stack,ss-non-loop,splayed-apart 22 G . H.DG7 0.004 anti,~C2'-endo,ss-non-loop,splayed-apart 23 G . H.DG8 0.004 break,anti,~C2'-endo,ss-non-loop,phosphate 24 A . H.DA13 0.003 anti,~C2'-endo,ss-non-loop,splayed-apart 25 G . H.DG14 0.003 anti,~C2'-endo,BII,non-stack,ss-non-loop,splayed-apart 26 G ) H.DG15 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 27 G ) H.DG16 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 28 A ) H.DA17 0.006 anti,BI,canonical,non-pair-contact,helix,stem 29 T ) H.DT18 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 30 G ) H.DG19 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 31 C ) H.DC20 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 32 A ) H.DA21 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 33 G ) H.DG22 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 34 A ] I.A1 0.012 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 35 C ] I.C2 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 36 U ] I.U3 0.002 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 37 C ] I.C4 0.008 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 38 A ] I.A5 0.014 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate **************************************************************************** List of 9 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-splays.pdb -- an ensemble of splayed-apart units 9 dssr-stacks.pdb -- an ensemble of base stacks