data_8ACY # _model_server_result.job_id la8kyM7mu4uZBmQDg0_u3w _model_server_result.datetime_utc '2024-12-26 11:16:53' _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 8acy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":502}' # _entry.id 8ACY # _exptl.entry_id 8ACY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 376.364 _entity.id 8 _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 110.98 _cell.angle_gamma 90 _cell.entry_id 8ACY _cell.length_a 95.27 _cell.length_b 143.32 _cell.length_c 104.37 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8ACY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_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 _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 8 _struct_asym.id H _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 B OG1 THR 236 B THR 236 1_555 G P FMN . B FMN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.59 ? covale ? covale2 C OG1 THR 225 C THR 225 1_555 L P FMN . C FMN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.601 ? metalc ? metalc1 B O ILE 371 B ILE 371 1_555 K NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.73 ? metalc ? metalc2 B O ARG 372 B ARG 372 1_555 K NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc3 B O ASN 375 B ASN 375 1_555 K NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc4 B O TYR 378 B TYR 378 1_555 K NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc5 D SG CYS 29 D CYS 29 1_555 N FE2 FES . E FES 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc6 D SG CYS 112 D CYS 112 1_555 N FE1 FES . E FES 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc7 E SG CYS 26 E CYS 26 1_555 N FE1 FES . E FES 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc8 E SG CYS 120 E CYS 120 1_555 N FE2 FES . E FES 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc9 F SG CYS 70 F CYS 70 1_555 P FE1 FES . F FES 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc10 F SG CYS 76 F CYS 76 1_555 P FE1 FES . F FES 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc11 F SG CYS 79 F CYS 79 1_555 P FE2 FES . F FES 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc12 F SG CYS 111 F CYS 111 1_555 P FE2 FES . F FES 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? # _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 506 n n N1 C10 RBF doub 507 n n C2 O2 RBF doub 508 n n C2 N3 RBF sing 509 n n N3 C4 RBF sing 510 n n N3 HN3 RBF sing 511 n n C4 O4 RBF doub 512 n n C4 C4A RBF sing 513 n n C4A N5 RBF doub 514 n n C4A C10 RBF sing 515 n n N5 C5A RBF sing 516 n n C5A C6 RBF doub 517 n y C5A C9A RBF sing 518 n y C6 C7 RBF sing 519 n y C6 HC6 RBF sing 520 n n C7 C7M RBF sing 521 n n C7 C8 RBF doub 522 n y C7M HC71 RBF sing 523 n n C7M HC72 RBF sing 524 n n C7M HC73 RBF sing 525 n n C8 C8M RBF sing 526 n n C8 C9 RBF sing 527 n y C8M HC81 RBF sing 528 n n C8M HC82 RBF sing 529 n n C8M HC83 RBF sing 530 n n C9 C9A RBF doub 531 n y C9 HC9 RBF sing 532 n n C9A N10 RBF sing 533 n n N10 C10 RBF sing 534 n n N10 C1' RBF sing 535 n n C1' C2' RBF sing 536 n n C1' HC11 RBF sing 537 n n C1' HC12 RBF sing 538 n n C2' O2' RBF sing 539 n n C2' C3' RBF sing 540 n n C2' HC2' RBF sing 541 n n O2' HO2' RBF sing 542 n n C3' O3' RBF sing 543 n n C3' C4' RBF sing 544 n n C3' HC3' RBF sing 545 n n O3' HO3' RBF sing 546 n n C4' O4' RBF sing 547 n n C4' C5' RBF sing 548 n n C4' HC4' RBF sing 549 n n O4' HO4' RBF sing 550 n n C5' O5' RBF sing 551 n n C5' HC51 RBF sing 552 n n C5' HC52 RBF sing 553 n n O5' HO5' RBF sing 554 n n # _atom_sites.entry_id 8ACY _atom_sites.fract_transf_matrix[1][1] 0.010496 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004025 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006977 _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] 0.010262 _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 G 7 FMN B 1 501 600 FMN FMN . H 8 RBF B 1 502 601 RBF RBF . I 9 LMT B 1 503 603 LMT LMT . J 9 LMT B 1 504 605 LMT LMT . K 10 NA B 1 505 1 NA NA . L 7 FMN C 1 1000 1000 FMN FMN . M 9 LMT D 1 301 604 LMT LMT . N 11 FES E 1 1001 1001 FES FES . O 12 FAD F 1 1501 1501 FAD FAD . P 11 FES F 1 1502 1502 FES FES . # 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 . . . H 8 -14.944 11.262 -11.131 1 183.38 ? N1 RBF 502 B 1 HETATM 2 C C2 RBF . . . H 8 -13.897 12.063 -10.827 1 171.28 ? C2 RBF 502 B 1 HETATM 3 O O2 RBF . . . H 8 -13.736 13.148 -11.394 1 164.57 ? O2 RBF 502 B 1 HETATM 4 N N3 RBF . . . H 8 -12.983 11.714 -9.89 1 169.53 ? N3 RBF 502 B 1 HETATM 5 C C4 RBF . . . H 8 -13.066 10.531 -9.201 1 168.93 ? C4 RBF 502 B 1 HETATM 6 O O4 RBF . . . H 8 -12.22 10.262 -8.366 1 164.61 ? O4 RBF 502 B 1 HETATM 7 C C4A RBF . . . H 8 -14.136 9.67 -9.485 1 176.77 ? C4A RBF 502 B 1 HETATM 8 N N5 RBF . . . H 8 -14.227 8.539 -8.833 1 174.15 ? N5 RBF 502 B 1 HETATM 9 C C5A RBF . . . H 8 -15.28 7.717 -9.135 1 172.38 ? C5A RBF 502 B 1 HETATM 10 C C6 RBF . . . H 8 -15.389 6.496 -8.445 1 159.59 ? C6 RBF 502 B 1 HETATM 11 C C7 RBF . . . H 8 -16.414 5.616 -8.697 1 166.77 ? C7 RBF 502 B 1 HETATM 12 C C7M RBF . . . H 8 -16.487 4.319 -7.933 1 162.84 ? C7M RBF 502 B 1 HETATM 13 C C8 RBF . . . H 8 -17.392 5.95 -9.675 1 184.47 ? C8 RBF 502 B 1 HETATM 14 C C8M RBF . . . H 8 -18.536 5.017 -9.979 1 180.09 ? C8M RBF 502 B 1 HETATM 15 C C9 RBF . . . H 8 -17.296 7.147 -10.354 1 189.47 ? C9 RBF 502 B 1 HETATM 16 C C9A RBF . . . H 8 -16.246 8.048 -10.105 1 184.98 ? C9A RBF 502 B 1 HETATM 17 N N10 RBF . . . H 8 -16.112 9.264 -10.774 1 194.89 ? N10 RBF 502 B 1 HETATM 18 C C10 RBF . . . H 8 -15.063 10.118 -10.488 1 182.76 ? C10 RBF 502 B 1 HETATM 19 C C1' RBF . . . H 8 -17.092 9.657 -11.8 1 205.53 ? C1' RBF 502 B 1 HETATM 20 C C2' RBF . . . H 8 -16.706 9.14 -13.183 1 207.37 ? C2' RBF 502 B 1 HETATM 21 O O2' RBF . . . H 8 -16.72 7.716 -13.196 1 220.81 ? O2' RBF 502 B 1 HETATM 22 C C3' RBF . . . H 8 -15.292 9.61 -13.544 1 187.58 ? C3' RBF 502 B 1 HETATM 23 O O3' RBF . . . H 8 -15.32 11.037 -13.576 1 181.7 ? O3' RBF 502 B 1 HETATM 24 C C4' RBF . . . H 8 -14.718 9.088 -14.857 1 182.32 ? C4' RBF 502 B 1 HETATM 25 O O4' RBF . . . H 8 -13.307 9.354 -14.892 1 179.36 ? O4' RBF 502 B 1 HETATM 26 C C5' RBF . . . H 8 -15.343 9.693 -16.093 1 176.25 ? C5' RBF 502 B 1 HETATM 27 O O5' RBF . . . H 8 -16.67 10.145 -15.853 1 204.36 ? O5' RBF 502 B 1 HETATM 28 H HN3 RBF . . . H 8 -12.321 12.27 -9.726 1 203.44 ? HN3 RBF 502 B 1 HETATM 29 H HC6 RBF . . . H 8 -14.733 6.28 -7.787 1 191.5 ? HC6 RBF 502 B 1 HETATM 30 H HC71 RBF . . . H 8 -15.595 4.056 -7.653 1 195.41 ? HC71 RBF 502 B 1 HETATM 31 H HC72 RBF . . . H 8 -16.864 3.628 -8.501 1 195.41 ? HC72 RBF 502 B 1 HETATM 32 H HC73 RBF . . . H 8 -17.049 4.435 -7.15 1 195.41 ? HC73 RBF 502 B 1 HETATM 33 H HC81 RBF . . . H 8 -18.898 5.222 -10.856 1 216.11 ? HC81 RBF 502 B 1 HETATM 34 H HC82 RBF . . . H 8 -18.218 4.099 -9.968 1 216.11 ? HC82 RBF 502 B 1 HETATM 35 H HC83 RBF . . . H 8 -19.231 5.126 -9.309 1 216.11 ? HC83 RBF 502 B 1 HETATM 36 H HC9 RBF . . . H 8 -17.957 7.367 -11.008 1 227.36 ? HC9 RBF 502 B 1 HETATM 37 H HC11 RBF . . . H 8 -17.155 10.633 -11.824 1 246.63 ? HC11 RBF 502 B 1 HETATM 38 H HC12 RBF . . . H 8 -17.97 9.305 -11.554 1 246.63 ? HC12 RBF 502 B 1 HETATM 39 H HC2' RBF . . . H 8 -17.362 9.471 -13.849 1 248.84 ? HC2' RBF 502 B 1 HETATM 40 H HO2' RBF . . . H 8 -17.516 7.443 -13.085 1 264.97 ? HO2' RBF 502 B 1 HETATM 41 H HC3' RBF . . . H 8 -14.673 9.287 -12.839 1 225.09 ? HC3' RBF 502 B 1 HETATM 42 H HC4' RBF . . . H 8 -14.894 8.1 -14.886 1 218.79 ? HC4' RBF 502 B 1 HETATM 43 H HO4' RBF . . . H 8 -12.943 8.993 -15.567 1 215.24 ? HO4' RBF 502 B 1 HETATM 44 H HC51 RBF . . . H 8 -15.357 9.015 -16.812 1 211.5 ? HC51 RBF 502 B 1 HETATM 45 H HC52 RBF . . . H 8 -14.791 10.454 -16.395 1 211.5 ? HC52 RBF 502 B 1 HETATM 46 H HO5' RBF . . . H 8 -16.945 10.54 -16.549 1 245.23 ? HO5' RBF 502 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 50 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 46 #