data_8A1T # _model_server_result.job_id DU6uBz5Yc5Zn6KNIQIG0Aw _model_server_result.datetime_utc '2024-10-19 15:42:51' _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 8a1t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":502}' # _entry.id 8A1T # _exptl.entry_id 8A1T _exptl.method 'ELECTRON MICROSCOPY' # _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 90 _cell.angle_gamma 90 _cell.entry_id 8A1T _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8A1T _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 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,Q,R,S,T _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 ? _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? covale ? covale2 C OG1 THR 225 C THR 225 1_555 O P FMN . C FMN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? metalc ? metalc1 B O ALA 263 B ALA 263 1_555 M NA NA . B NA 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc2 B O VAL 275 B VAL 275 1_555 M NA NA . B NA 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc3 B O VAL 332 B VAL 332 1_555 M NA NA . B NA 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc4 B O ILE 371 B ILE 371 1_555 N K K . B K 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc5 B O ARG 372 B ARG 372 1_555 N K K . B K 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc6 B O ASN 375 B ASN 375 1_555 N K K . B K 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc7 B O TYR 378 B TYR 378 1_555 N K K . B K 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc8 D SG CYS 29 D CYS 29 1_555 Q FE2 FES . D FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc9 D SG CYS 112 D CYS 112 1_555 Q FE1 FES . D FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc10 Q FE1 FES . D FES 302 1_555 E SG CYS 26 E CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc11 Q FE2 FES . D FES 302 1_555 E SG CYS 120 E CYS 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc12 F SG CYS 70 F CYS 70 1_555 T FE1 FES . F FES 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc13 F SG CYS 76 F CYS 76 1_555 T FE1 FES . F FES 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc14 F SG CYS 79 F CYS 79 1_555 T FE2 FES . F FES 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc15 F SG CYS 111 F CYS 111 1_555 T FE2 FES . F FES 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? # _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 638 n n N1 C10 RBF doub 639 n n C2 O2 RBF doub 640 n n C2 N3 RBF sing 641 n n N3 C4 RBF sing 642 n n N3 HN3 RBF sing 643 n n C4 O4 RBF doub 644 n n C4 C4A RBF sing 645 n n C4A N5 RBF doub 646 n n C4A C10 RBF sing 647 n n N5 C5A RBF sing 648 n n C5A C6 RBF doub 649 n y C5A C9A RBF sing 650 n y C6 C7 RBF sing 651 n y C6 HC6 RBF sing 652 n n C7 C7M RBF sing 653 n n C7 C8 RBF doub 654 n y C7M HC71 RBF sing 655 n n C7M HC72 RBF sing 656 n n C7M HC73 RBF sing 657 n n C8 C8M RBF sing 658 n n C8 C9 RBF sing 659 n y C8M HC81 RBF sing 660 n n C8M HC82 RBF sing 661 n n C8M HC83 RBF sing 662 n n C9 C9A RBF doub 663 n y C9 HC9 RBF sing 664 n n C9A N10 RBF sing 665 n n N10 C10 RBF sing 666 n n N10 C1' RBF sing 667 n n C1' C2' RBF sing 668 n n C1' HC11 RBF sing 669 n n C1' HC12 RBF sing 670 n n C2' O2' RBF sing 671 n n C2' C3' RBF sing 672 n n C2' HC2' RBF sing 673 n n O2' HO2' RBF sing 674 n n C3' O3' RBF sing 675 n n C3' C4' RBF sing 676 n n C3' HC3' RBF sing 677 n n O3' HO3' RBF sing 678 n n C4' O4' RBF sing 679 n n C4' C5' RBF sing 680 n n C4' HC4' RBF sing 681 n n O4' HO4' RBF sing 682 n n C5' O5' RBF sing 683 n n C5' HC51 RBF sing 684 n n C5' HC52 RBF sing 685 n n O5' HO5' RBF sing 686 n n # _atom_sites.entry_id 8A1T _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 G 7 FMN B 1 501 600 FMN FMN . H 8 RBF B 1 502 601 RBF RBF . I 9 LMT B 1 503 605 LMT LMT . J 10 3PE B 1 504 606 3PE 3PE . K 10 3PE B 1 505 608 3PE 3PE . L 9 LMT B 1 506 1002 LMT LMT . M 11 NA B 1 507 1 NA NA . N 12 K B 1 508 2 K K . O 7 FMN C 1 1000 1000 FMN FMN . P 10 3PE D 1 301 602 3PE 3PE . Q 13 FES D 1 302 1001 FES FES . R 9 LMT E 1 201 603 LMT LMT . S 14 FAD F 1 1501 1501 FAD FAD . T 13 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 8 113.634 124.164 138.677 1 39.59 ? N1 RBF 502 B 1 HETATM 2 C C2 RBF . . . H 8 114.456 125.221 138.845 1 48.09 ? C2 RBF 502 B 1 HETATM 3 O O2 RBF . . . H 8 114.261 126.275 138.239 1 51.04 ? O2 RBF 502 B 1 HETATM 4 N N3 RBF . . . H 8 115.523 125.176 139.68 1 53.21 ? N3 RBF 502 B 1 HETATM 5 C C4 RBF . . . H 8 115.831 124.051 140.404 1 53.16 ? C4 RBF 502 B 1 HETATM 6 O O4 RBF . . . H 8 116.802 124.054 141.146 1 50.01 ? O4 RBF 502 B 1 HETATM 7 C C4A RBF . . . H 8 114.998 122.927 140.257 1 44.98 ? C4A RBF 502 B 1 HETATM 8 N N5 RBF . . . H 8 115.277 121.849 140.94 1 36.29 ? N5 RBF 502 B 1 HETATM 9 C C5A RBF . . . H 8 114.452 120.77 140.778 1 37.88 ? C5A RBF 502 B 1 HETATM 10 C C6 RBF . . . H 8 114.744 119.606 141.509 1 35.06 ? C6 RBF 502 B 1 HETATM 11 C C7 RBF . . . H 8 113.967 118.478 141.411 1 42.24 ? C7 RBF 502 B 1 HETATM 12 C C7M RBF . . . H 8 114.32 117.251 142.212 1 35.36 ? C7M RBF 502 B 1 HETATM 13 C C8 RBF . . . H 8 112.844 118.486 140.546 1 45.21 ? C8 RBF 502 B 1 HETATM 14 C C8M RBF . . . H 8 111.971 117.266 140.406 1 35.85 ? C8M RBF 502 B 1 HETATM 15 C C9 RBF . . . H 8 112.547 119.623 139.82 1 44.63 ? C9 RBF 502 B 1 HETATM 16 C C9A RBF . . . H 8 113.335 120.784 139.917 1 46.32 ? C9A RBF 502 B 1 HETATM 17 N N10 RBF . . . H 8 113.07 121.957 139.203 1 44.25 ? N10 RBF 502 B 1 HETATM 18 C C10 RBF . . . H 8 113.887 123.064 139.353 1 42.42 ? C10 RBF 502 B 1 HETATM 19 C C1' RBF . . . H 8 111.917 122.039 138.284 1 38.3 ? C1' RBF 502 B 1 HETATM 20 C C2' RBF . . . H 8 112.261 121.588 136.87 1 40.92 ? C2' RBF 502 B 1 HETATM 21 O O2' RBF . . . H 8 112.644 120.216 136.867 1 37.81 ? O2' RBF 502 B 1 HETATM 22 C C3' RBF . . . H 8 113.389 122.422 136.256 1 47.13 ? C3' RBF 502 B 1 HETATM 23 O O3' RBF . . . H 8 112.967 123.778 136.155 1 36.41 ? O3' RBF 502 B 1 HETATM 24 C C4' RBF . . . H 8 113.841 121.935 134.878 1 42.9 ? C4' RBF 502 B 1 HETATM 25 O O4' RBF . . . H 8 115.068 122.576 134.524 1 37.69 ? O4' RBF 502 B 1 HETATM 26 C C5' RBF . . . H 8 112.808 122.205 133.806 1 38.14 ? C5' RBF 502 B 1 HETATM 27 O O5' RBF . . . H 8 113.231 121.695 132.545 1 40.84 ? O5' RBF 502 B 1 HETATM 28 H HN3 RBF . . . H 8 116.024 125.894 139.754 1 37.53 ? HN3 RBF 502 B 1 HETATM 29 H HC6 RBF . . . H 8 115.501 119.606 142.09 1 35.91 ? HC6 RBF 502 B 1 HETATM 30 H HC71 RBF . . . H 8 114.864 116.655 141.672 1 36.06 ? HC71 RBF 502 B 1 HETATM 31 H HC72 RBF . . . H 8 113.509 116.792 142.483 1 35.9 ? HC72 RBF 502 B 1 HETATM 32 H HC73 RBF . . . H 8 114.819 117.513 143.003 1 35.51 ? HC73 RBF 502 B 1 HETATM 33 H HC81 RBF . . . H 8 111.294 117.268 141.102 1 36.67 ? HC81 RBF 502 B 1 HETATM 34 H HC82 RBF . . . H 8 112.512 116.464 140.483 1 36.1 ? HC82 RBF 502 B 1 HETATM 35 H HC83 RBF . . . H 8 111.536 117.277 139.537 1 36.29 ? HC83 RBF 502 B 1 HETATM 36 H HC9 RBF . . . H 8 111.787 119.614 139.243 1 37.59 ? HC9 RBF 502 B 1 HETATM 37 H HC11 RBF . . . H 8 111.6 122.964 138.255 1 37.42 ? HC11 RBF 502 B 1 HETATM 38 H HC12 RBF . . . H 8 111.188 121.491 138.63 1 37.1 ? HC12 RBF 502 B 1 HETATM 39 H HC2' RBF . . . H 8 111.454 121.684 136.3 1 37.16 ? HC2' RBF 502 B 1 HETATM 40 H HO2' RBF . . . H 8 111.982 119.739 137.093 1 37.68 ? HO2' RBF 502 B 1 HETATM 41 H HC3' RBF . . . H 8 114.171 122.386 136.863 1 39 ? HC3' RBF 502 B 1 HETATM 42 H HC4' RBF . . . H 8 113.995 120.944 134.92 1 37.4 ? HC4' RBF 502 B 1 HETATM 43 H HO4' RBF . . . H 8 114.976 123.418 134.495 1 36.45 ? HO4' RBF 502 B 1 HETATM 44 H HC51 RBF . . . H 8 112.66 123.179 133.733 1 36.18 ? HC51 RBF 502 B 1 HETATM 45 H HC52 RBF . . . H 8 111.955 121.779 134.061 1 36.5 ? HC52 RBF 502 B 1 HETATM 46 H HO5' RBF . . . H 8 113.984 122.033 132.366 1 35.94 ? HO5' RBF 502 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 46 #