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{ "index": 79, "num_nts": 7, "nts_short": "CUCUCGG", "nts_long": "///d/81,///f/15,///f/14,///d/86,///f/13,///f/12,///f/11" } ], "nonStack": { "num_nts": 39, "nts_short": "CUACUCCACGGCCAUUUUUAUGAAUCACUCCCUUUCUUC", "nts_long": "///d/6,///d/21,///d/22,///d/25,///d/26,///d/61,///d/62,///d/73,///d/79,///d/80,///e/8,///e/23,///e/36,///e/88,///e/89,///e/91,///e/92,///e/93,///e/94,///e/96,///e/106,///f/19,///f/23,///f/64,///f/74,///f/78,///f/83,///f/84,c. g & i. \\-14,c. g & i. \\-13,///g/8,///g/22,///g/23,///g/136,///g/150,///g/151,///g/160,///g/161,///g/162" }, "num_atom2bases": 9, "atom2bases": [ { "index": 1, "type": "phosphate", "atom": "///d/67/OP2", "nt": "///d/65", "vert_dist": 3.284 }, { "index": 2, "type": "sugar", "atom": "///d/75/O4'", "nt": "///d/72", "vert_dist": 3.235 }, { "index": 3, "type": "sugar", "atom": "///e/19/O2'", "nt": "///e/20", "vert_dist": 2.866 }, { "index": 4, "type": "sugar", "atom": "///e/23/O2'", "nt": "///e/21", "vert_dist": 3.012 }, { "index": 5, "type": "sugar", "atom": "///e/45/O4'", "nt": "///e/44", "vert_dist": 3.357 }, { "index": 6, "type": "sugar", "atom": "///f/25/O4'", "nt": "///f/22", "vert_dist": 3.007 }, { "index": 7, "type": "sugar", "atom": "///f/47/O2'", "nt": "///f/48", "vert_dist": 3.087 }, { "index": 8, "type": "phosphate", "atom": "///f/57/OP2", "nt": "///f/55", "vert_dist": 3.076 }, { "index": 9, "type": "sugar", "atom": "///g/148/O2'", "nt": "///g/149", "vert_dist": 3.166 } ], "num_hairpins": 5, "hairpins": [ { "index": 1, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 2 ], "summary": "[1] 4 [d.8 d.13] 2", "num_nts": 6, "nts_short": "CUUCGG", "nts_long": "///d/8,///d/9,///d/10,///d/11,///d/12,///d/13", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUCG", "nts_long": "///d/9,///d/10,///d/11,///d/12" } ] }, { "index": 2, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 7 ], "summary": "[1] 5 [d.64 d.70] 3", "num_nts": 7, "nts_short": "UGCGCAA", "nts_long": "///d/64,///d/65,///d/66,///d/67,///d/68,///d/69,///d/70", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GCGCA", "nts_long": "///d/65,///d/66,///d/67,///d/68,///d/69" } ] }, { "index": 3, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ -4 ], "summary": "[1] 7 [e.37 e.45] 1", "num_nts": 9, "nts_short": "GCCUUUUAC", "nts_long": "///e/37,///e/38,///e/39,///e/40,///e/41,///e/42,///e/43,///e/44,///e/45", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "CCUUUUA", "nts_long": "///e/38,///e/39,///e/40,///e/41,///e/42,///e/43,///e/44" } ] }, { "index": 4, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 15 ], "summary": "[1] 4 [e.104 e.109] 4", "num_nts": 6, "nts_short": "CUUUGG", "nts_long": "///e/104,///e/105,///e/106,///e/107,///e/108,///e/109", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUUG", "nts_long": "///e/105,///e/106,///e/107,///e/108" } ] }, { "index": 5, "type": "hairpin loop", "bridging_nts": [ 10 ], "stem_indices": [ 18 ], "summary": "[1] 10 [f.51 f.62] 3", "num_nts": 12, "nts_short": "AGUUUAAUAUCU", "nts_long": "///f/51,///f/52,///f/53,///f/54,///f/55,///f/56,///f/57,///f/58,///f/59,///f/60,///f/61,///f/62", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 10, "nts_short": "GUUUAAUAUC", "nts_long": "///f/52,///f/53,///f/54,///f/55,///f/56,///f/57,///f/58,///f/59,///f/60,///f/61" } ] } ], "num_bulges": 5, "bulges": [ { "index": 1, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 1, 2 ], "summary": "[2] 1 0 [d.5 d.15 d.7 d.14] 5 2", "num_nts": 5, "nts_short": "UCGCA", "nts_long": "///d/5,///d/6,///d/7,///d/14,///d/15", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///d/6" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 2, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 14, -5 ], "summary": "[2] 1 0 [e.98 e.115 e.100 e.114] 2 1", "num_nts": 5, "nts_short": "GCCGC", "nts_long": "///e/98,///e/99,///e/100,///e/114,///e/115", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///e/99" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 3, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ -5, 15 ], "summary": "[2] 0 1 [e.100 e.114 e.101 e.112] 1 4", "num_nts": 5, "nts_short": "CUAGG", "nts_long": "///e/100,///e/101,///e/112,///e/113,///e/114", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///e/113" } ] }, { "index": 4, "type": "bulge", "bridging_nts": [ 0, 2 ], "stem_indices": [ 4, 5 ], "summary": "[2] 0 2 [d.52 f.25 d.53 f.22] 4 3", "num_nts": 6, "nts_short": "UAUAAG", "nts_long": "///d/52,///d/53,///f/22,///f/23,///f/24,///f/25", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 2, "nts_short": "AA", "nts_long": "///f/23,///f/24" } ] }, { "index": 5, "type": "bulge", "bridging_nts": [ 0, 2 ], "stem_indices": [ -2, 7 ], "summary": "[2] 0 2 [d.61 d.75 d.62 d.72] 1 3", "num_nts": 6, "nts_short": "CCGAUG", "nts_long": "///d/61,///d/62,///d/72,///d/73,///d/74,///d/75", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 2, "nts_short": "AU", "nts_long": "///d/73,///d/74" } ] } ], "num_iloops": 9, "iloops": [ { "index": 1, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 8, 9 ], "summary": "[2] 1 1 [d.88 f.10 d.90 f.8] 2 6", "num_nts": 6, "nts_short": "GUGCUC", "nts_long": "///d/88,///d/89,///d/90,///f/8,///f/9,///f/10", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///d/89" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///f/9" } ] }, { "index": 2, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 9, -3 ], "summary": "[2] 1 1 [d.95 f.3 d.97 f.1] 6 1", "num_nts": 6, "nts_short": "GUUAUC", "nts_long": "///d/95,///d/96,///d/97,///f/1,///f/2,///f/3", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///d/96" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///f/2" } ] }, { "index": 3, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 12, -4 ], "summary": "[2] 1 1 [e.35 e.47 e.37 e.45] 8 1", "num_nts": 6, "nts_short": "UCGCUA", "nts_long": "///e/35,///e/36,///e/37,///e/45,///e/46,///e/47", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///e/36" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///e/46" } ] }, { "index": 4, "type": "asymmetric internal loop", "bridging_nts": [ 2, 1 ], "stem_indices": [ 6, -2 ], "summary": "[2] 2 1 [d.58 d.77 d.61 d.75] 2 1", "num_nts": 7, "nts_short": "GGCCGAC", "nts_long": "///d/58,///d/59,///d/60,///d/61,///d/75,///d/76,///d/77", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GC", "nts_long": "///d/59,///d/60" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///d/76" } ] }, { "index": 5, "type": "asymmetric internal loop", "bridging_nts": [ 3, 1 ], "stem_indices": [ 11, 12 ], "summary": "[2] 3 1 [e.24 e.56 e.28 e.54] 2 8", "num_nts": 8, "nts_short": "GCAUAUCC", "nts_long": "///e/24,///e/25,///e/26,///e/27,///e/28,///e/54,///e/55,///e/56", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CAU", "nts_long": "///e/25,///e/26,///e/27" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///e/55" } ] }, { "index": 6, "type": "asymmetric internal loop", "bridging_nts": [ 4, 1 ], "stem_indices": [ 10, 11 ], "summary": "[2] 4 1 [e.18 e.59 e.23 e.57] 10 2", "num_nts": 9, "nts_short": "CAGAUCGUG", "nts_long": "///e/18,///e/19,///e/20,///e/21,///e/22,///e/23,///e/57,///e/58,///e/59", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AGAU", "nts_long": "///e/19,///e/20,///e/21,///e/22" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///e/58" } ] }, { "index": 7, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ 16, 17 ], "summary": "[2] 2 3 [f.39 g.138 f.42 g.134] 5 2", "num_nts": 9, "nts_short": "UCUGUGUCA", "nts_long": "///f/39,///f/40,///f/41,///f/42,///g/134,///g/135,///g/136,///g/137,///g/138", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CU", "nts_long": "///f/40,///f/41" }, { "index": 2, "num_nts": 3, "nts_short": "GUC", "nts_long": "///g/135,///g/136,///g/137" } ] }, { "index": 8, "type": "asymmetric internal loop", "bridging_nts": [ 3, 4 ], "stem_indices": [ -6, 16 ], "summary": "[2] 3 4 [f.31 g.147 f.35 g.142] 1 5", "num_nts": 11, "nts_short": "GUGUAUUAUCC", "nts_long": "///f/31,///f/32,///f/33,///f/34,///f/35,///g/142,///g/143,///g/144,///g/145,///g/146,///g/147", "num_stems": 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0.4000", " 2 N -2.2500 -5.0000 0.4000", " 3 N -2.2500 -5.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 2.2500 5.0000 0.4000", " 6 C 2.2500 -5.0000 0.4000", " 7 C 2.2500 -5.0000 -0.4000", " 8 C 2.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -5.0000 0.4000", " 11 C -2.2500 -5.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ] }, "metadata": { "license": "http://innovation.columbia.edu/technologies/CU20391", "url": "http://x3dna.org/", "url_alt": "http://home.x3dna.org/", "forum": "http://forum.x3dna.org/", "citation": "Lu et al. (2015). 'DSSR: an integrated software tool for dissecting the spatial structure of RNA.' Nucleic Acids Res., 43(21):e142 [doi:10.1093/nar/gkv716].", "str_id": "7qtt", "num_aaChains": 33, "aaChains": "A=1164,B=70,C=815,D=89,E=198,F=78,G=67,I=84,J=72,L=28,N=792,O=320,P=148,Q=100,T=142,U=295,V=285,W=459,X=241,Y=306,Z=95,a=1936,b=899,h=66,i=70,j=68,k=78,l=68,m=63,n=64,p=159,q=74,u=367", "num_naChains": 4, "naChains": "d=93,e=98,f=76,g=76", "num_atoms": 73537, "num_waters": 0, "num_metals": 19, "metals_desc": "Mg=7,Zn=12", "num_notes": 52, "notes": [ { "Aminors": "A-minor interactions (including types I and II)" }, { "Cstem_index": "stem index of the 'Canonical' helix in k-turn" }, { "Cstem_pair": "Cstem bp delineating the k-turn internal loop" }, { "Dp": "perpendicular distance of the 3' P atom to the glycosidic bond" }, { "GA_pair": "sheared G-A pair in k-turn" }, { "HtypePknot": "H-type pseudoknot" }, { "Kturn": "kink-turn (k-turn)" }, { "LW": "Leontis-Westhof" }, { "NCstem_index": "stem index of the 'Non-Canonical' helix in k-turn" }, { "NCstem_pair": "NCstem bp delineating the k-turn internal loop" }, { "Uturn": "U-turn of the UNR- or GNRA-type" }, { "aa": "amino acid" }, { "atom_pair": "symbols of the two atoms involved in an H-bond" }, { "auxfiles": "auxiliary files" }, { "glyco_bond": "conformation of base related to sugar (syn or anti)" }, { "bb_type": "backbone conformation, BI or BII" }, { "bending_angle": "angle between two helical axes" }, { "bp": "base pair" }, { "bseq": "base sequence in one-letter code" }, { "bulge": "bulge loop" }, { "coaxStacks": "coaxial stacking of stems within a helix" }, { "dbn": "dot bracket notation" }, { "desc": "description" }, { "donAcc_type": "donor/acceptor type of the atom pair in an H-bond" }, { "epsilon_zeta": "difference between epsilon and zeta torsion angles" }, { "hairpin": "hairpin loop" }, { "hbond": "hydrogen bond (H-bond)" }, { "helix": "defined by base-stacking interactions, regardless of bp type and backbone connectivity" }, { "id": "identifier" }, { "iloop": "internal loop" }, { "index": "serial number" }, { "isoCanonPairs": "isolated canonical pairs" }, { "junction": "(multi-branched) junction loop" }, { "kissingLoop": "kissing loop" }, { "multiplet": "3+ bases in a coplanar geometry" }, { "na": "nucleic acid" }, { "nonPair": "two nts not forming a pair, but with H-bonding/stacking interactions" }, { "nonStack": "nucleotide not involved in stacking interactions" }, { "nt": "nucleotide" }, { "num": "number" }, { "oArea": "overlap areas between two bases, including exocyclic atoms" }, { "oArea_ring": "overlap areas between two bases, including only ring atoms" }, { "phosContacts": "H-bonding and atom-capping interactions involving a phosphate" }, { "residue_pair": "types of the two residues involved in an H-bond" }, { "rmsd": "root-mean-squares deviation" }, { "serNum": "serial number" }, { "ssSegments": "single-stranded segments not involved in loops" }, { "ssZp": "Z-coordinate of the 3' phosphorus atom with reference to the 5' base plane" }, { "sstr": "secondary structure in dbn" }, { "stem": "helix consisting of only canonical pairs, with a continuous backbone" }, { "str_id": "structure identifier, derived from inpfile with extension removed" }, { "vert_dist": "vertical distance from an atom to a base plane" } ], "num_auxfiles": 19, "auxfiles": [ { "index": 1, "name": "dssr-pairs.pdb", "desc": "an ensemble of base pairs" }, { "index": 2, "name": "dssr-multiplets.pdb", "desc": "an ensemble of multiplets" }, { "index": 3, "name": "dssr-stems.pdb", "desc": "an ensemble of stems" }, { "index": 4, "name": "dssr-helices.pdb", "desc": "an ensemble of helices (coaxial stacking)" }, { "index": 5, "name": "dssr-hairpins.pdb", "desc": "an ensemble of hairpin loops" }, { "index": 6, "name": "dssr-bulges.pdb", "desc": "an ensemble of bulges" }, { "index": 7, "name": "dssr-iloops.pdb", "desc": "an ensemble of internal loops" }, { "index": 8, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 9, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 10, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 11, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 12, "name": "dssr-splays.pdb", "desc": "an ensemble of splayed-apart units" }, { "index": 13, "name": "dssr-Aminors.pdb", "desc": "an ensemble of A minor motifs (types I and II)" }, { "index": 14, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 15, "name": "dssr-atom2bases.pdb", "desc": "an ensemble of atom-base stacking interactions" }, { "index": 16, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 17, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 18, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 19, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }