data_3CVW # _model_server_result.job_id EHyTu4ekpo7wVbK3rfkVAQ _model_server_result.datetime_utc '2024-12-26 05:40:21' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3cvw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1422}' # _entry.id 3CVW # _exptl.entry_id 3CVW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 363.322 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 3CVW _cell.length_a 86.47 _cell.length_b 89.51 _cell.length_c 89.34 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CVW _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A O3' DG 7 C DG 7 1_555 A P 64T 8 C 64T 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.601 ? covale ? covale2 A O3' 64T 8 C 64T 8 1_555 A P 5PY 9 C 5PY 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? covale ? covale3 A C6 64T 8 C 64T 8 1_555 A C4 5PY 9 C 5PY 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.528 ? covale ? covale4 A O3' 5PY 9 C 5PY 9 1_555 A P DG 10 C DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.6 ? hydrog 'DC-DG PAIR' hydrog1 A N4 DC 2 C DC 2 1_555 B O6 DG 15 D DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N1 DA 3 C DA 3 1_555 B N3 DT 14 D DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N6 DA 3 C DA 3 1_555 B O4 DT 14 D DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog4 A N1 DG 4 C DG 4 1_555 B N3 DC 13 D DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N3 DC 5 C DC 5 1_555 B N1 DG 12 D DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N4 DC 5 C DC 5 1_555 B O6 DG 12 D DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A O2 DC 5 C DC 5 1_555 B N2 DG 12 D DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog8 A O6 DG 6 C DG 6 1_555 B N4 DC 10 D DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 DG 6 C DG 6 1_555 B N3 DC 11 D DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N2 DG 6 C DG 6 1_555 B O2 DC 11 D DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O6 DG 6 C DG 6 1_555 B N4 DC 11 D DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N1 DG 7 C DG 7 1_555 B N3 DC 10 D DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N2 DG 7 C DG 7 1_555 B O2 DC 10 D DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O6 DG 7 C DG 7 1_555 B N4 DC 10 D DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog15 A N1 DG 10 C DG 10 1_555 B O2 DC 7 D DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N3 DC 11 C DC 11 1_555 B N1 DG 6 D DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N4 DC 11 C DC 11 1_555 B O6 DG 6 D DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O2 DC 11 C DC 11 1_555 B N2 DG 6 D DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N1 DA 12 C DA 12 1_555 B N3 DT 5 D DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N6 DA 12 C DA 12 1_555 B O4 DT 5 D DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N1 DG 13 C DG 13 1_555 B N3 DC 4 D DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N2 DG 13 C DG 13 1_555 B O2 DC 4 D DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A O6 DG 13 C DG 13 1_555 B N4 DC 4 D DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N1 DG 14 C DG 14 1_555 B N3 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N2 DG 14 C DG 14 1_555 B O2 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A O6 DG 14 C DG 14 1_555 B N4 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog27 A N3 DT 15 C DT 15 1_555 B N1 DA 2 D DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C16 H17 N3 O7' _chem_comp.formula_weight 363.322 _chem_comp.id FO1 _chem_comp.mon_nstd_flag . _chem_comp.name 1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 7,8-didemethyl-8-hydroxy-5-deazariboflavin # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N1 C1 FO1 sing 399 n n N1 C13 FO1 doub 400 n n C1 O1 FO1 doub 401 n n C1 N2 FO1 sing 402 n n N2 C2 FO1 sing 403 n n N2 HN3 FO1 sing 404 n n C2 O2 FO1 doub 405 n n C2 C3 FO1 sing 406 n n C3 C4 FO1 doub 407 n n C3 C13 FO1 sing 408 n n C4 C5 FO1 sing 409 n n C4 H21 FO1 sing 410 n n C5 C6 FO1 doub 411 n y C5 C12 FO1 sing 412 n y C6 C7 FO1 sing 413 n y C6 HC6 FO1 sing 414 n n C7 C9 FO1 doub 415 n y C7 HC7 FO1 sing 416 n n C9 O10 FO1 sing 417 n n C9 C11 FO1 sing 418 n y O10 HC82 FO1 sing 419 n n C11 C12 FO1 doub 420 n y C11 HC9 FO1 sing 421 n n C12 N3 FO1 sing 422 n n N3 C13 FO1 sing 423 n n N3 C14 FO1 sing 424 n n C14 C15 FO1 sing 425 n n C14 HC11 FO1 sing 426 n n C14 HC12 FO1 sing 427 n n C15 O3 FO1 sing 428 n n C15 C16 FO1 sing 429 n n C15 HC2' FO1 sing 430 n n O3 HO2' FO1 sing 431 n n C16 O4 FO1 sing 432 n n C16 C17 FO1 sing 433 n n C16 HC3' FO1 sing 434 n n O4 HO3' FO1 sing 435 n n C17 O5 FO1 sing 436 n n C17 C18 FO1 sing 437 n n C17 HC4' FO1 sing 438 n n O5 HO4' FO1 sing 439 n n C18 O6 FO1 sing 440 n n C18 HC51 FO1 sing 441 n n C18 HC52 FO1 sing 442 n n O6 HO5' FO1 sing 443 n n # _atom_sites.entry_id 3CVW _atom_sites.fract_transf_matrix[1][1] 0.011565 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011172 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.011193 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code D 4 FAD A 1 521 1 FAD FAD . E 5 FO1 A 1 1422 1422 FO1 HDB . F 6 HOH C 1 16 16 HOH HOH . G 6 HOH A 1 1423 1 HOH HOH . G 6 HOH A 2 1424 2 HOH HOH . G 6 HOH A 3 1425 3 HOH HOH . G 6 HOH A 4 1426 4 HOH HOH . G 6 HOH A 5 1427 6 HOH HOH . G 6 HOH A 6 1428 7 HOH HOH . G 6 HOH A 7 1429 8 HOH HOH . G 6 HOH A 8 1430 9 HOH HOH . G 6 HOH A 9 1431 11 HOH HOH . G 6 HOH A 10 1432 12 HOH HOH . G 6 HOH A 11 1433 15 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N1 FO1 . . . E 5 3.191 12.94 -42.528 1 49.85 ? N1 FO1 1422 A 1 HETATM 2 C C1 FO1 . . . E 5 3.604 14.224 -42.684 1 49.85 ? C1 FO1 1422 A 1 HETATM 3 O O1 FO1 . . . E 5 4.438 14.5 -43.575 1 49.85 ? O1 FO1 1422 A 1 HETATM 4 N N2 FO1 . . . E 5 3.129 15.212 -41.891 1 49.85 ? N2 FO1 1422 A 1 HETATM 5 C C2 FO1 . . . E 5 2.229 14.947 -40.922 1 49.85 ? C2 FO1 1422 A 1 HETATM 6 O O2 FO1 . . . E 5 1.799 15.87 -40.197 1 49.85 ? O2 FO1 1422 A 1 HETATM 7 C C3 FO1 . . . E 5 1.766 13.544 -40.738 1 49.85 ? C3 FO1 1422 A 1 HETATM 8 C C4 FO1 . . . E 5 0.841 13.237 -39.748 1 49.85 ? C4 FO1 1422 A 1 HETATM 9 C C5 FO1 . . . E 5 0.429 11.924 -39.601 1 49.85 ? C5 FO1 1422 A 1 HETATM 10 C C6 FO1 . . . E 5 -0.493 11.56 -38.631 1 49.85 ? C6 FO1 1422 A 1 HETATM 11 C C7 FO1 . . . E 5 -0.847 10.217 -38.558 1 49.85 ? C7 FO1 1422 A 1 HETATM 12 C C9 FO1 . . . E 5 -0.28 9.294 -39.44 1 49.85 ? C9 FO1 1422 A 1 HETATM 13 O O10 FO1 . . . E 5 -0.641 7.983 -39.352 1 49.85 ? O10 FO1 1422 A 1 HETATM 14 C C11 FO1 . . . E 5 0.578 9.647 -40.342 1 49.85 ? C11 FO1 1422 A 1 HETATM 15 C C12 FO1 . . . E 5 0.98 10.869 -40.497 1 49.85 ? C12 FO1 1422 A 1 HETATM 16 N N3 FO1 . . . E 5 1.923 11.191 -41.509 1 49.85 ? N3 FO1 1422 A 1 HETATM 17 C C13 FO1 . . . E 5 2.291 12.563 -41.584 1 49.85 ? C13 FO1 1422 A 1 HETATM 18 C C14 FO1 . . . E 5 3.111 10.321 -41.453 1 49.85 ? C14 FO1 1422 A 1 HETATM 19 C C15 FO1 . . . E 5 3.027 9.394 -42.663 1 49.85 ? C15 FO1 1422 A 1 HETATM 20 O O3 FO1 . . . E 5 3.07 8.031 -42.219 1 49.85 ? O3 FO1 1422 A 1 HETATM 21 C C16 FO1 . . . E 5 4.134 9.658 -43.683 1 49.85 ? C16 FO1 1422 A 1 HETATM 22 O O4 FO1 . . . E 5 4.134 11.037 -44.076 1 49.85 ? O4 FO1 1422 A 1 HETATM 23 C C17 FO1 . . . E 5 3.992 8.779 -44.924 1 49.85 ? C17 FO1 1422 A 1 HETATM 24 O O5 FO1 . . . E 5 5.247 8.747 -45.612 1 49.85 ? O5 FO1 1422 A 1 HETATM 25 C C18 FO1 . . . E 5 2.905 9.263 -45.882 1 49.85 ? C18 FO1 1422 A 1 HETATM 26 O O6 FO1 . . . E 5 2.627 8.242 -46.847 1 49.85 ? O6 FO1 1422 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #