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"G", "nt_code": "G", "nt_id": "///B/9", "linked_nts": [ "///B/8", "///B/10" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack", "alpha": -76.217, "beta": 177.614, "gamma": 63.402, "delta": 79.733, "epsilon": -157.049, "zeta": -60.117, "epsilon_zeta": -96.932, "bb_type": "BI", "chi": -159.218, "glyco_bond": "anti", "C5prime_xyz": [ -1.314, 8.773, 0.531 ], "P_xyz": [ 1.269, 9.202, 0.899 ], "form": "A", "ssZp": 4.223, "Dp": 4.650, "splay_angle": 23.004, "splay_distance": 3.738, "splay_ratio": 0.202, "d22": null, "d64": null, "eta": 170.359, "theta": -138.005, "eta_prime": -178.642, "theta_prime": -138.237, "eta_base": -137.046, "theta_base": -107.437, "v0": 9.603, "v1": -31.448, "v2": 38.887, "v3": -34.996, "v4": 16.465, "amplitude": 39.034, "phase_angle": 4.971, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.700, "filter_rmsd": 0.027, "frame": { "rmsd": 0.027, "origin": [ 4.634, 10.602, 0.606 ], "x_axis": [ -0.922, 0.045, -0.385 ], "y_axis": [ -0.385, 0.028, 0.923 ], "z_axis": [ 0.052, 0.999, -0.008 ], "quaternion": [ 0.156, -0.121, 0.700, 0.687 ] } }, { "index": 20, "index_chain": 10, "chain_name": "B", "nt_resnum": 10, "nt_name": "C", "nt_code": "C", "nt_id": "///B/10", "linked_nts": [ "///B/9", null ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack", "alpha": -78.261, "beta": 179.776, "gamma": 54.110, "delta": 78.043, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -161.432, "glyco_bond": "anti", "C5prime_xyz": [ -1.511, 8.838, 0.747 ], "P_xyz": [ 1.060, 9.448, 0.959 ], "form": "-", "ssZp": null, "Dp": null, "splay_angle": null, "splay_distance": null, "splay_ratio": null, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": 2.404, "v1": -25.808, "v2": 37.098, "v3": -37.447, "v4": 22.307, "amplitude": 38.488, "phase_angle": 15.444, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.770, "filter_rmsd": 0.065, "frame": { "rmsd": 0.010, "origin": [ 3.935, 13.919, -0.967 ], "x_axis": [ -0.971, -0.019, 0.240 ], "y_axis": [ 0.240, 0.001, 0.971 ], "z_axis": [ -0.019, 1.000, 0.004 ], "quaternion": [ -0.092, 0.079, 0.701, 0.702 ] } } ], "num_hbonds": 32, "hbonds": [ { "index": 1, "atom1_serNum": 15, "atom2_serNum": 637, "donAcc_type": "standard", "distance": 2.956, "atom1_id": "///A/1/O6", "atom2_id": "///B/10/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 2, "atom1_serNum": 16, "atom2_serNum": 635, "donAcc_type": "standard", "distance": 2.966, "atom1_id": "///A/1/N1", "atom2_id": "///B/10/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 3, "atom1_serNum": 18, "atom2_serNum": 634, "donAcc_type": "standard", "distance": 2.859, "atom1_id": "///A/1/N2", "atom2_id": "///B/10/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 4, "atom1_serNum": 47, "atom2_serNum": 606, "donAcc_type": "standard", "distance": 2.874, "atom1_id": "///A/2/O2", "atom2_id": "///B/9/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 5, "atom1_serNum": 48, "atom2_serNum": 604, "donAcc_type": "standard", "distance": 2.952, "atom1_id": "///A/2/N3", "atom2_id": "///B/9/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 6, "atom1_serNum": 50, "atom2_serNum": 603, "donAcc_type": "standard", "distance": 2.923, "atom1_id": "///A/2/N4", "atom2_id": "///B/9/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 7, "atom1_serNum": 74, "atom2_serNum": 103, "donAcc_type": "acceptable", "distance": 2.979, "atom1_id": "///A/3/O2'", "atom2_id": "///A/4/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 8, "atom1_serNum": 81, "atom2_serNum": 573, "donAcc_type": "standard", "distance": 2.965, "atom1_id": "///A/3/N6", "atom2_id": "///B/8/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 9, "atom1_serNum": 82, "atom2_serNum": 571, "donAcc_type": "standard", "distance": 2.974, "atom1_id": "///A/3/N1", "atom2_id": "///B/8/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 10, "atom1_serNum": 99, "atom2_serNum": 117, "donAcc_type": "standard", "distance": 2.820, "atom1_id": "///A/4/OP2", "atom2_id": "///A/4/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 11, "atom1_serNum": 111, "atom2_serNum": 542, "donAcc_type": "standard", "distance": 2.921, "atom1_id": "///A/4/N7", "atom2_id": "///B/7/N2", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 12, "atom1_serNum": 114, "atom2_serNum": 540, "donAcc_type": "standard", "distance": 2.846, "atom1_id": "///A/4/O6", "atom2_id": "///B/7/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 13, "atom1_serNum": 148, "atom2_serNum": 508, "donAcc_type": "standard", "distance": 2.954, "atom1_id": "///A/5/O6", "atom2_id": "///B/6/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 14, "atom1_serNum": 149, "atom2_serNum": 506, "donAcc_type": "standard", "distance": 2.981, "atom1_id": "///A/5/N1", "atom2_id": "///B/6/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 15, "atom1_serNum": 151, "atom2_serNum": 505, "donAcc_type": "standard", "distance": 2.904, "atom1_id": "///A/5/N2", "atom2_id": "///B/6/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 16, "atom1_serNum": 179, "atom2_serNum": 477, "donAcc_type": "standard", "distance": 2.894, "atom1_id": "///A/6/O2", "atom2_id": "///B/5/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 17, "atom1_serNum": 180, "atom2_serNum": 475, "donAcc_type": "standard", "distance": 2.969, "atom1_id": "///A/6/N3", "atom2_id": "///B/5/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 18, "atom1_serNum": 182, "atom2_serNum": 474, "donAcc_type": "standard", "distance": 2.952, "atom1_id": "///A/6/N4", "atom2_id": "///B/5/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 19, "atom1_serNum": 206, "atom2_serNum": 236, "donAcc_type": "acceptable", "distance": 2.813, "atom1_id": "///A/7/O2'", "atom2_id": "///A/8/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 20, "atom1_serNum": 214, "atom2_serNum": 440, "donAcc_type": "standard", "distance": 2.855, "atom1_id": "///A/7/N1", "atom2_id": "///B/4/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 21, "atom1_serNum": 216, "atom2_serNum": 437, "donAcc_type": "standard", "distance": 2.933, "atom1_id": "///A/7/N2", "atom2_id": "///B/4/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 22, "atom1_serNum": 216, "atom2_serNum": 440, "donAcc_type": "standard", "distance": 3.125, "atom1_id": "///A/7/N2", "atom2_id": "///B/4/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 23, "atom1_serNum": 245, "atom2_serNum": 408, "donAcc_type": "standard", "distance": 3.006, "atom1_id": "///A/8/N3", "atom2_id": "///B/3/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 24, "atom1_serNum": 247, "atom2_serNum": 407, "donAcc_type": "standard", "distance": 2.937, "atom1_id": "///A/8/O4", "atom2_id": "///B/3/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 25, "atom1_serNum": 277, "atom2_serNum": 376, "donAcc_type": "standard", "distance": 2.925, "atom1_id": "///A/9/O6", "atom2_id": "///B/2/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 26, "atom1_serNum": 278, "atom2_serNum": 374, "donAcc_type": "standard", "distance": 2.946, "atom1_id": "///A/9/N1", "atom2_id": "///B/2/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 27, "atom1_serNum": 280, "atom2_serNum": 373, "donAcc_type": "standard", "distance": 2.873, "atom1_id": "///A/9/N2", "atom2_id": "///B/2/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 28, "atom1_serNum": 308, "atom2_serNum": 344, "donAcc_type": "standard", "distance": 2.856, "atom1_id": "///A/10/O2", "atom2_id": "///B/1/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 29, "atom1_serNum": 309, "atom2_serNum": 342, "donAcc_type": "standard", "distance": 2.964, "atom1_id": "///A/10/N3", "atom2_id": "///B/1/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 30, "atom1_serNum": 311, "atom2_serNum": 341, "donAcc_type": "standard", "distance": 2.963, "atom1_id": "///A/10/N4", "atom2_id": "///B/1/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 31, "atom1_serNum": 425, "atom2_serNum": 443, "donAcc_type": "standard", "distance": 2.821, "atom1_id": "///B/4/OP2", "atom2_id": "///B/4/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 32, "atom1_serNum": 532, "atom2_serNum": 562, "donAcc_type": "acceptable", "distance": 2.910, "atom1_id": "///B/7/O2'", "atom2_id": "///B/8/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" } ], "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": "1f5h", "num_naChains": 2, "naChains": "A=10,B=10", "num_atoms": 650, "num_waters": 0, "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": 13, "auxfiles": [ { "index": 1, "name": "dssr-pairs.pdb", "desc": "an ensemble of base pairs" }, { "index": 2, "name": "dssr-stems.pdb", "desc": "an ensemble of stems" }, { "index": 3, "name": "dssr-helices.pdb", "desc": "an ensemble of helices (coaxial stacking)" }, { "index": 4, "name": "dssr-iloops.pdb", "desc": "an ensemble of internal loops" }, { "index": 5, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 6, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 7, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 8, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 9, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 10, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 11, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 12, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 13, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }