data_8RB8 # _model_server_result.job_id Lg3FTzfpGfFAYq43FduEPA _model_server_result.datetime_utc '2024-11-22 20:47:02' _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 8rb8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":403}' # _entry.id 8RB8 # _exptl.entry_id 8RB8 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 376.364 _entity.id 12 _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 8RB8 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RB8 _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,Y,Z,AA,BA,CA _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 12 _struct_asym.id O _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 C OG1 THR 177 D THR 177 1_555 V P FMN . D FMN 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.624 ? covale ? covale2 E OG1 THR 202 G THR 202 1_555 AA P FMN . G FMN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.631 ? metalc ? metalc1 A SG CYS 25 A CYS 25 1_555 H FE1 FES . A FES 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc2 A SG CYS 113 A CYS 113 1_555 H FE2 FES . A FES 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc3 H FE2 FES . A FES 200 1_555 D SG CYS 39 E CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc4 H FE1 FES . A FES 200 1_555 D SG CYS 122 E CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc5 B SG CYS 370 C CYS 370 1_555 K FE3 SF4 . C SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc6 B SG CYS 373 C CYS 373 1_555 K FE4 SF4 . C SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc7 B SG CYS 376 C CYS 376 1_555 K FE1 SF4 . C SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc8 B SG CYS 380 C CYS 380 1_555 L FE4 SF4 . C SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc11 B SG CYS 415 C CYS 415 1_555 L FE3 SF4 . C SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc12 B SG CYS 419 C CYS 419 1_555 K FE2 SF4 . C SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc13 G SG CYS 109 B CYS 109 1_555 CA FE1 SF4 . B SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc14 G SG CYS 112 B CYS 112 1_555 CA FE2 SF4 . B SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc15 G SG CYS 115 B CYS 115 1_555 CA FE3 SF4 . B SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc16 G SG CYS 119 B CYS 119 1_555 BA FE1 SF4 . B SF4 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc17 G SG CYS 139 B CYS 139 1_555 BA FE4 SF4 . B SF4 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc18 G SG CYS 142 B CYS 142 1_555 BA FE3 SF4 . B SF4 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc19 G SG CYS 145 B CYS 145 1_555 BA FE2 SF4 . B SF4 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc20 G SG CYS 149 B CYS 149 1_555 CA FE4 SF4 . B SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? # _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 415 n n N1 C10 RBF doub 416 n n C2 O2 RBF doub 417 n n C2 N3 RBF sing 418 n n N3 C4 RBF sing 419 n n N3 HN3 RBF sing 420 n n C4 O4 RBF doub 421 n n C4 C4A RBF sing 422 n n C4A N5 RBF doub 423 n n C4A C10 RBF sing 424 n n N5 C5A RBF sing 425 n n C5A C6 RBF doub 426 n y C5A C9A RBF sing 427 n y C6 C7 RBF sing 428 n y C6 HC6 RBF sing 429 n n C7 C7M RBF sing 430 n n C7 C8 RBF doub 431 n y C7M HC71 RBF sing 432 n n C7M HC72 RBF sing 433 n n C7M HC73 RBF sing 434 n n C8 C8M RBF sing 435 n n C8 C9 RBF sing 436 n y C8M HC81 RBF sing 437 n n C8M HC82 RBF sing 438 n n C8M HC83 RBF sing 439 n n C9 C9A RBF doub 440 n y C9 HC9 RBF sing 441 n n C9A N10 RBF sing 442 n n N10 C10 RBF sing 443 n n N10 C1' RBF sing 444 n n C1' C2' RBF sing 445 n n C1' HC11 RBF sing 446 n n C1' HC12 RBF sing 447 n n C2' O2' RBF sing 448 n n C2' C3' RBF sing 449 n n C2' HC2' RBF sing 450 n n O2' HO2' RBF sing 451 n n C3' O3' RBF sing 452 n n C3' C4' RBF sing 453 n n C3' HC3' RBF sing 454 n n O3' HO3' RBF sing 455 n n C4' O4' RBF sing 456 n n C4' C5' RBF sing 457 n n C4' HC4' RBF sing 458 n n O4' HO4' RBF sing 459 n n C5' O5' RBF sing 460 n n C5' HC51 RBF sing 461 n n C5' HC52 RBF sing 462 n n O5' HO5' RBF sing 463 n n # _atom_sites.entry_id 8RB8 _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 D 1 401 202 LMT LMT . N 9 LMT D 1 402 204 LMT LMT . O 12 RBF D 1 403 402 RBF RBF . P 9 LMT D 1 404 404 LMT LMT . Q 9 LMT D 1 405 405 LMT LMT . R 9 LMT D 1 406 406 LMT LMT . S 9 LMT D 1 407 407 LMT LMT . T 9 LMT D 1 408 409 LMT LMT . U 9 LMT D 1 409 411 LMT LMT . V 10 FMN D 1 410 177 FMN T1F . W 9 LMT E 1 301 408 LMT LMT . X 9 LMT E 1 302 301 LMT LMT . Y 9 LMT E 1 303 302 LMT LMT . Z 9 LMT E 1 304 303 LMT LMT . AA 10 FMN G 1 301 202 FMN T1F . BA 11 SF4 B 1 201 201 SF4 SF4 . CA 11 SF4 B 1 202 202 SF4 SF4 . # 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 . . . O 12 117.829 98.917 120.748 1 19.27 ? N1 RBF 403 D 1 HETATM 2 C C2 RBF . . . O 12 117.675 98.732 119.353 1 24.2 ? C2 RBF 403 D 1 HETATM 3 O O2 RBF . . . O 12 118.6 98.91 118.587 1 30.77 ? O2 RBF 403 D 1 HETATM 4 N N3 RBF . . . O 12 116.411 98.327 118.85 1 10.86 ? N3 RBF 403 D 1 HETATM 5 C C4 RBF . . . O 12 115.269 98.091 119.63 1 10.98 ? C4 RBF 403 D 1 HETATM 6 O O4 RBF . . . O 12 114.232 97.747 119.124 1 19.86 ? O4 RBF 403 D 1 HETATM 7 C C4A RBF . . . O 12 115.436 98.289 121.092 1 14.07 ? C4A RBF 403 D 1 HETATM 8 N N5 RBF . . . O 12 114.421 98.088 121.882 1 21.63 ? N5 RBF 403 D 1 HETATM 9 C C5A RBF . . . O 12 114.634 98.291 123.247 1 17.28 ? C5A RBF 403 D 1 HETATM 10 C C6 RBF . . . O 12 113.546 98.078 124.116 1 16.26 ? C6 RBF 403 D 1 HETATM 11 C C7 RBF . . . O 12 113.709 98.265 125.467 1 20.06 ? C7 RBF 403 D 1 HETATM 12 C C7M RBF . . . O 12 112.584 98.049 126.406 1 17.12 ? C7M RBF 403 D 1 HETATM 13 C C8 RBF . . . O 12 114.955 98.669 125.991 1 23.65 ? C8 RBF 403 D 1 HETATM 14 C C8M RBF . . . O 12 115.114 98.867 127.453 1 21.07 ? C8M RBF 403 D 1 HETATM 15 C C9 RBF . . . O 12 116.029 98.877 125.159 1 21.84 ? C9 RBF 403 D 1 HETATM 16 C C9A RBF . . . O 12 115.88 98.69 123.773 1 21.79 ? C9A RBF 403 D 1 HETATM 17 N N10 RBF . . . O 12 116.928 98.911 122.882 1 21.51 ? N10 RBF 403 D 1 HETATM 18 C C10 RBF . . . O 12 116.771 98.705 121.518 1 17.04 ? C10 RBF 403 D 1 HETATM 19 C C1' RBF . . . O 12 118.262 99.313 123.341 1 18.21 ? C1' RBF 403 D 1 HETATM 20 C C2' RBF . . . O 12 118.302 100.838 123.565 1 19.35 ? C2' RBF 403 D 1 HETATM 21 O O2' RBF . . . O 12 117.014 101.291 123.866 1 25.76 ? O2' RBF 403 D 1 HETATM 22 C C3' RBF . . . O 12 118.768 101.45 122.239 1 18.86 ? C3' RBF 403 D 1 HETATM 23 O O3' RBF . . . O 12 120.144 101.213 122.237 1 27.85 ? O3' RBF 403 D 1 HETATM 24 C C4' RBF . . . O 12 118.487 102.97 122.091 1 17.32 ? C4' RBF 403 D 1 HETATM 25 O O4' RBF . . . O 12 118.227 103.325 120.77 1 11.54 ? O4' RBF 403 D 1 HETATM 26 C C5' RBF . . . O 12 119.838 103.59 122.522 1 21.17 ? C5' RBF 403 D 1 HETATM 27 O O5' RBF . . . O 12 119.993 104.642 121.62 1 20.3 ? O5' RBF 403 D 1 # _model_server_stats.io_time_ms 75 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 102 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #