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"///A/44,///A/45,///A/46,///A/47,///A/56,///A/57,///A/58", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/45,///A/46" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/57" } ] }, { "index": 3, "type": "asymmetric internal loop", "bridging_nts": [ 3, 6 ], "stem_indices": [ 2, 3 ], "summary": "[2] 3 6 [A.17 A.38 A.21 A.31] 3 3 k-turn:normal", "num_nts": 13, "nts_short": "UGGAGCGACGAAA", "nts_long": "///A/17,///A/18,///A/19,///A/20,///A/21,///A/31,///A/32,///A/33,///A/34,///A/35,///A/36,///A/37,///A/38", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GGA", "nts_long": "///A/18,///A/19,///A/20" }, { "index": 2, "num_nts": 6, "nts_short": "GACGAA", "nts_long": "///A/32,///A/33,///A/34,///A/35,///A/36,///A/37" } ] } ], "num_junctions": 2, "junctions": [ { "index": 1, "type": "4-way junction", "bridging_nts": [ 4, 0, 3, 0 ], "stem_indices": [ 1, -1, 5, -3 ], "summary": "[4] 4 0 3 0 [A.8 A.86 A.13 A.41 A.42 A.60 A.64 A.85] 8 1 3 1", "num_nts": 15, "nts_short": "CAAGAGCGCAAUUAG", "nts_long": "///A/8,///A/9,///A/10,///A/11,///A/12,///A/13,///A/41,///A/42,///A/60,///A/61,///A/62,///A/63,///A/64,///A/85,///A/86", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AAGA", "nts_long": "///A/9,///A/10,///A/11,///A/12" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 3, "nts_short": "AAU", "nts_long": "///A/61,///A/62,///A/63" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 2, "type": "5-way junction", "bridging_nts": [ 1, 0, 2, 0, 0 ], "stem_indices": [ 3, -2, 7, -3, 4 ], "summary": "[5] 1 0 2 0 0 [A.23 A.29 A.25 A.68 A.69 A.82 A.85 A.64 A.65 A.28] 3 1 5 1 2", "num_nts": 13, "nts_short": "GACGCGAAAUCGC", "nts_long": "///A/23,///A/24,///A/25,///A/68,///A/69,///A/82,///A/83,///A/84,///A/85,///A/64,///A/65,///A/28,///A/29", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/24" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/83,///A/84" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 5, "num_nts": 0, "nts_short": "", "nts_long": "" } ] } ], "num_ssSegments": 1, "ssSegments": [ { "index": 1, "is_broken": true, "num_nts": 2, "nts_short": "Ga", "nts_long": "///A/94,///A/301" } ], "num_Aminors": 4, "Aminors": [ { "index": 1, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/12 vs ///A/43,///A/59", "A_nt1": { "desc": "///A/12 vs ///A/43", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.97],N3-N2(amino)[2.99]" }, "A_nt2": { "desc": "///A/12 vs ///A/59", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.69]" } }, { "index": 2, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/24 vs ///A/64,///A/85", "A_nt1": { "desc": "///A/24 vs ///A/64", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/24 vs ///A/85", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.26]" } }, { "index": 3, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/61 vs ///A/22,///A/30", "A_nt1": { "desc": "///A/61 vs ///A/22", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)*N2(amino)[3.43]" }, "A_nt2": { "desc": "///A/61 vs ///A/30", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.89],N1-O2'(hydroxyl)[2.61]" } }, { "index": 4, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/62 vs ///A/23,///A/29", "A_nt1": { "desc": "///A/62 vs ///A/23", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.00],N6(amino)-N3[3.37],N1-N2(amino)[3.06]" }, "A_nt2": { "desc": "///A/62 vs ///A/29", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } } ], "num_riboseZippers": 1, "riboseZippers": [ { "index": 1, "num_nts": 4, "nts_short": "GAGC", "nts_long": "///A/11,///A/12,///A/43,///A/44" } ], "num_Kturns": 1, "Kturns": [ { "index": 1, "type": "Normal k-turn", "iloop_index": 3, "bounding_stems": [ 3, 2 ], "Cstem_index": 3, "NCstem_index": 2, "Cstem_pair": "C-G (///A/31,///A/21) WC", "NCstem_pair": "A-U (///A/38,///A/17) WC", "GA_pair": "G-A (///A/35,///A/20) Sheared", "bending_angle": 60.491, "strand1": { "num_nts": 12, "nts_short": "CCCGACGAAACC", "nts_long": "///A/29,///A/30,///A/31,///A/32,///A/33,///A/34,///A/35,///A/36,///A/37,///A/38,///A/39,///A/40" }, "strand2": { "num_nts": 9, "nts_short": "GGUGGAGGG", "nts_long": "///A/15,///A/16,///A/17,///A/18,///A/19,///A/20,///A/21,///A/22,///A/23" } } ], "num_splayUnits": 8, "splayUnits": [ { "index": 1, "num_nts": 3, "nts_short": "CAA", "nts_long": "///A/8,///A/9,///A/10" }, { "index": 2, "num_nts": 4, "nts_short": "AGAG", "nts_long": "///A/12,///A/13,///A/14,///A/15" }, { "index": 3, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/23,///A/24" }, { "index": 4, "num_nts": 3, "nts_short": "ACG", "nts_long": "///A/33,///A/34,///A/35" }, { "index": 5, "num_nts": 2, "nts_short": "CA", "nts_long": "///A/60,///A/61" }, { "index": 6, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/62,///A/63" }, { "index": 7, "num_nts": 2, "nts_short": "UC", "nts_long": "///A/64,///A/65" }, { "index": 8, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/74,///A/75" } ], "pseudoknot_order": 1, "pseudoknot_nts": [ { "index": 1, "symbols": "[]", "num_nts": 6, "nts_short": "CGGCCG", "nts_long": "///A/25,///A/27,///A/28,///A/65,///A/66,///A/68" } ], "dbn": { "all_chains": { "num_nts": 95, "num_chars": 96, "bseq": "GGCUUAUCAAGAGAGGUGGAGGGACUGGCCCGACGAAACCCGGCAACCAGAAAUGGUGCCAAUUCCUGCAGCGGAAACGUUGAAAGAUGAGCCG&a", "bseqUP": "GGCUUAUCAAGAGAGGUGGAGGGACUGGCCCGACGAAACCCGGCAACCAGAAAUGGUGCCAAUUCCUGCAGCGGAAACGUUGAAAGAUGAGCCG&A", "sstr": "((((((((....(.(((...(((.[.[[)))......))))(((..(((....))).)))...(]].](((((....)))))..))))))))).&.", "form": 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65.519, "delta": 83.762, "epsilon": -152.886, "zeta": -74.448, "epsilon_zeta": -78.437, "bb_type": "BI", "chi": -173.024, "glyco_bond": "anti", "C5prime_xyz": [ -1.249, 8.497, 1.264 ], "P_xyz": [ 1.355, 8.800, 1.457 ], "form": "A", "ssZp": 4.635, "Dp": 4.650, "splay_angle": 22.095, "splay_distance": 3.455, "splay_ratio": 0.197, "d22": null, "d64": null, "eta": 160.673, "theta": -147.131, "eta_prime": 178.495, "theta_prime": -144.775, "eta_base": -133.148, "theta_base": -124.915, "v0": 9.915, "v1": -33.960, "v2": 43.463, "v3": -38.650, "v4": 18.465, "amplitude": 43.676, "phase_angle": 5.652, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.480, "filter_rmsd": 0.007, "frame": { "rmsd": 0.007, "origin": [ -0.443, -10.418, -2.250 ], "x_axis": [ 0.304, 0.697, 0.649 ], "y_axis": [ -0.558, -0.422, 0.715 ], "z_axis": [ 0.772, -0.579, 0.261 ], "quaternion": [ 0.534, 0.605, 0.058, 0.587 ] } }, { "index": 3, "index_chain": 3, "chain_name": "A", 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"residue_pair": "nt:nt" }, { "index": 166, "atom1_serNum": 1569, "atom2_serNum": 1678, "donAcc_type": "standard", "distance": 3.014, "atom1_id": "///A/73/N1", "atom2_id": "///A/78/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 167, "atom1_serNum": 1571, "atom2_serNum": 1677, "donAcc_type": "standard", "distance": 2.658, "atom1_id": "///A/73/N2", "atom2_id": "///A/78/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 168, "atom1_serNum": 1584, "atom2_serNum": 1633, "donAcc_type": "acceptable", "distance": 2.922, "atom1_id": "///A/74/O2'", "atom2_id": "///A/76/N7", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 169, "atom1_serNum": 1594, "atom2_serNum": 1643, "donAcc_type": "standard", "distance": 2.823, "atom1_id": "///A/74/N2", "atom2_id": "///A/77/OP2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 170, "atom1_serNum": 1594, "atom2_serNum": 1655, "donAcc_type": "standard", "distance": 2.981, "atom1_id": "///A/74/N2", "atom2_id": "///A/77/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 171, "atom1_serNum": 1716, "atom2_serNum": 1732, "donAcc_type": "acceptable", "distance": 3.283, "atom1_id": "///A/80/O2'", "atom2_id": "///A/81/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 172, "atom1_serNum": 1736, "atom2_serNum": 1752, "donAcc_type": "acceptable", "distance": 3.072, "atom1_id": "///A/81/O2'", "atom2_id": "///A/82/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 173, "atom1_serNum": 1894, "atom2_serNum": 2043, "donAcc_type": "questionable", "distance": 3.130, "atom1_id": "///A/88/O2", "atom2_id": "///A/301/O4'", "atom_pair": "O:O", "residue_pair": "nt:ligand" } ], "refCoords": { "purine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -0.5000 0.4000", " 3 N -2.2500 -0.5000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 -0.5000 0.4000", " 7 C 1.2500 -0.5000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -0.5000 0.4000", " 11 C -2.2500 -0.5000 -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" ], "pyrimidine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 1.0000 0.4000", " 3 N -2.2500 1.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 1.0000 0.4000", " 7 C 1.2500 1.0000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 1.0000 0.4000", " 11 C -2.2500 1.0000 -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" ], "wc_pair": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 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": "3gx5", "num_naChains": 1, "naChains": "A=95", "num_atoms": 2193, "num_waters": 103, "num_metals": 9, "metals_desc": "Mg=8,K=1", "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": 21, "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-junctions.pdb", "desc": "an ensemble of junctions (multi-branch)" }, { "index": 9, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 10, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 11, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 12, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 13, "name": "dssr-splays.pdb", "desc": "an ensemble of splayed-apart units" }, { "index": 14, "name": "dssr-Aminors.pdb", "desc": "an ensemble of A minor motifs (types I and II)" }, { "index": 15, "name": "dssr-Kturns.pdb", "desc": "an ensemble of kink-turn motifs" }, { "index": 16, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 17, "name": "dssr-atom2bases.pdb", "desc": "an ensemble of atom-base stacking interactions" }, { "index": 18, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 19, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 20, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 21, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }