data_8RBQ # _model_server_result.job_id BopGqLQWkq1PWGv2hDOx2A _model_server_result.datetime_utc '2024-10-19 01:42:01' _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 8rbq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":404}' # _entry.id 8RBQ # _exptl.entry_id 8RBQ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 376.364 _entity.id 13 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RIBOFLAVIN _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 8RBQ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RBQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details heptameric _pdbx_struct_assembly.oligomeric_count 7 _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,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X _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 13 _struct_asym.id T _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 D OG1 THR 202 G THR 202 1_555 N P FMN . G FMN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.628 ? metalc ? metalc1 A SG CYS 25 A CYS 25 1_555 H FE1 FES . A FES 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc2 A SG CYS 113 A CYS 113 1_555 H FE2 FES . A FES 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc3 H FE2 FES . A FES 200 1_555 C SG CYS 39 E CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc4 H FE1 FES . A FES 200 1_555 C SG CYS 122 E CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc5 B SG CYS 370 C CYS 370 1_555 K FE3 SF4 . C SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc6 B SG CYS 373 C CYS 373 1_555 K FE4 SF4 . C SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc7 B SG CYS 376 C CYS 376 1_555 K FE1 SF4 . C SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc8 B SG CYS 380 C CYS 380 1_555 L FE4 SF4 . C SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc9 B SG CYS 409 C CYS 409 1_555 L FE1 SF4 . C SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc10 B SG CYS 412 C CYS 412 1_555 L FE2 SF4 . C SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc11 B SG CYS 415 C CYS 415 1_555 L FE3 SF4 . C SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc12 B SG CYS 419 C CYS 419 1_555 K FE2 SF4 . C SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc13 F SG CYS 109 B CYS 109 1_555 P FE1 SF4 . B SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc14 F SG CYS 112 B CYS 112 1_555 P FE2 SF4 . B SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc15 F SG CYS 115 B CYS 115 1_555 P FE3 SF4 . B SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc16 F SG CYS 119 B CYS 119 1_555 O FE1 SF4 . B SF4 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc17 F SG CYS 139 B CYS 139 1_555 O FE4 SF4 . B SF4 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc18 F SG CYS 142 B CYS 142 1_555 O FE3 SF4 . B SF4 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc19 F SG CYS 145 B CYS 145 1_555 O FE2 SF4 . B SF4 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc20 F SG CYS 149 B CYS 149 1_555 P FE4 SF4 . B SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? # _chem_comp.formula 'C17 H20 N4 O6' _chem_comp.formula_weight 376.364 _chem_comp.id RBF _chem_comp.mon_nstd_flag . _chem_comp.name RIBOFLAVIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'RIBOFLAVINE;VITAMIN B2' # 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 C2 RBF sing 544 n n N1 C10 RBF doub 545 n n C2 O2 RBF doub 546 n n C2 N3 RBF sing 547 n n N3 C4 RBF sing 548 n n N3 HN3 RBF sing 549 n n C4 O4 RBF doub 550 n n C4 C4A RBF sing 551 n n C4A N5 RBF doub 552 n n C4A C10 RBF sing 553 n n N5 C5A RBF sing 554 n n C5A C6 RBF doub 555 n y C5A C9A RBF sing 556 n y C6 C7 RBF sing 557 n y C6 HC6 RBF sing 558 n n C7 C7M RBF sing 559 n n C7 C8 RBF doub 560 n y C7M HC71 RBF sing 561 n n C7M HC72 RBF sing 562 n n C7M HC73 RBF sing 563 n n C8 C8M RBF sing 564 n n C8 C9 RBF sing 565 n y C8M HC81 RBF sing 566 n n C8M HC82 RBF sing 567 n n C8M HC83 RBF sing 568 n n C9 C9A RBF doub 569 n y C9 HC9 RBF sing 570 n n C9A N10 RBF sing 571 n n N10 C10 RBF sing 572 n n N10 C1' RBF sing 573 n n C1' C2' RBF sing 574 n n C1' HC11 RBF sing 575 n n C1' HC12 RBF sing 576 n n C2' O2' RBF sing 577 n n C2' C3' RBF sing 578 n n C2' HC2' RBF sing 579 n n O2' HO2' RBF sing 580 n n C3' O3' RBF sing 581 n n C3' C4' RBF sing 582 n n C3' HC3' RBF sing 583 n n O3' HO3' RBF sing 584 n n C4' O4' RBF sing 585 n n C4' C5' RBF sing 586 n n C4' HC4' RBF sing 587 n n O4' HO4' RBF sing 588 n n C5' O5' RBF sing 589 n n C5' HC51 RBF sing 590 n n C5' HC52 RBF sing 591 n n O5' HO5' RBF sing 592 n n # _atom_sites.entry_id 8RBQ _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 H 8 FES A 1 200 200 FES FES . I 9 LMT A 1 201 201 LMT LMT . J 10 FMN C 1 500 500 FMN FMN . K 11 SF4 C 1 501 501 SF4 SF4 . L 11 SF4 C 1 502 502 SF4 SF4 . M 9 LMT E 1 301 409 LMT LMT . N 10 FMN G 1 301 202 FMN T1F . O 11 SF4 B 1 201 201 SF4 SF4 . P 11 SF4 B 1 202 202 SF4 SF4 . Q 9 LMT D 1 401 202 LMT LMT . R 9 LMT D 1 402 204 LMT LMT . S 12 PTY D 1 403 301 PTY PTY . T 13 RBF D 1 404 402 RBF RBF . U 9 LMT D 1 405 406 LMT LMT . V 9 LMT D 1 406 407 LMT LMT . W 9 LMT D 1 407 412 LMT LMT . X 12 PTY D 1 408 413 PTY PTY . # 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 RBF . . . T 13 110.418 132.665 119.126 1 47.48 ? N1 RBF 404 D 1 HETATM 2 C C2 RBF . . . T 13 110.563 132.754 117.721 1 46.45 ? C2 RBF 404 D 1 HETATM 3 O O2 RBF . . . T 13 109.662 132.431 116.973 1 55.59 ? O2 RBF 404 D 1 HETATM 4 N N3 RBF . . . T 13 111.784 133.243 117.187 1 41.75 ? N3 RBF 404 D 1 HETATM 5 C C4 RBF . . . T 13 112.891 133.646 117.946 1 47.23 ? C4 RBF 404 D 1 HETATM 6 O O4 RBF . . . T 13 113.901 134.054 117.409 1 55.65 ? O4 RBF 404 D 1 HETATM 7 C C4A RBF . . . T 13 112.735 133.543 119.419 1 51.53 ? C4A RBF 404 D 1 HETATM 8 N N5 RBF . . . T 13 113.724 133.901 120.187 1 55.71 ? N5 RBF 404 D 1 HETATM 9 C C5A RBF . . . T 13 113.528 133.784 121.563 1 48.41 ? C5A RBF 404 D 1 HETATM 10 C C6 RBF . . . T 13 114.589 134.169 122.404 1 48.5 ? C6 RBF 404 D 1 HETATM 11 C C7 RBF . . . T 13 114.447 134.072 123.766 1 46.76 ? C7 RBF 404 D 1 HETATM 12 C C7M RBF . . . T 13 115.549 134.471 124.672 1 44.1 ? C7M RBF 404 D 1 HETATM 13 C C8 RBF . . . T 13 113.245 133.59 124.332 1 52.24 ? C8 RBF 404 D 1 HETATM 14 C C8M RBF . . . T 13 113.103 133.489 125.807 1 52.74 ? C8M RBF 404 D 1 HETATM 15 C C9 RBF . . . T 13 112.196 133.215 123.529 1 50.64 ? C9 RBF 404 D 1 HETATM 16 C C9A RBF . . . T 13 112.319 133.312 122.13 1 47.49 ? C9A RBF 404 D 1 HETATM 17 N N10 RBF . . . T 13 111.303 132.9 121.262 1 51.77 ? N10 RBF 404 D 1 HETATM 18 C C10 RBF . . . T 13 111.445 133.029 119.879 1 51.57 ? C10 RBF 404 D 1 HETATM 19 C C1' RBF . . . T 13 110 132.419 121.75 1 51.4 ? C1' RBF 404 D 1 HETATM 20 C C2' RBF . . . T 13 110.053 130.906 122.064 1 56.41 ? C2' RBF 404 D 1 HETATM 21 O O2' RBF . . . T 13 111.38 130.472 122.033 1 63.35 ? O2' RBF 404 D 1 HETATM 22 C C3' RBF . . . T 13 109.256 130.203 120.959 1 51.06 ? C3' RBF 404 D 1 HETATM 23 O O3' RBF . . . T 13 107.934 130.275 121.407 1 59.43 ? O3' RBF 404 D 1 HETATM 24 C C4' RBF . . . T 13 109.68 128.73 120.687 1 49.41 ? C4' RBF 404 D 1 HETATM 25 O O4' RBF . . . T 13 109.667 128.425 119.329 1 50.55 ? O4' RBF 404 D 1 HETATM 26 C C5' RBF . . . T 13 108.58 127.906 121.403 1 51.89 ? C5' RBF 404 D 1 HETATM 27 O O5' RBF . . . T 13 108.072 127.114 120.376 1 55.86 ? O5' RBF 404 D 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 76 _model_server_stats.query_time_ms 381 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #