data_8AD0 # _model_server_result.job_id nElz5kFfrNHjF-BiDm5gSA _model_server_result.datetime_utc '2024-10-19 13:19:53' _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 8ad0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":502}' # _entry.id 8AD0 # _exptl.entry_id 8AD0 _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 109.83 _cell.angle_gamma 90 _cell.entry_id 8AD0 _cell.length_a 89.31 _cell.length_b 142.15 _cell.length_c 105.93 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8AD0 _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,Q,R,S,T,U,V _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.587 ? covale ? covale2 C OG1 THR 225 C THR 225 1_555 M P FMN . C FMN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.598 ? metalc ? metalc1 B O VAL 275 B VAL 275 1_555 K NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc2 B O VAL 332 B VAL 332 1_555 K NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? metalc ? metalc3 D SG CYS 29 D CYS 29 1_555 P FE2 FES . D FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc4 D SG CYS 112 D CYS 112 1_555 P FE1 FES . D FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc5 P FE1 FES . D FES 302 1_555 E SG CYS 26 E CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc6 P FE2 FES . D FES 302 1_555 E SG CYS 120 E CYS 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc7 F SG CYS 70 F CYS 70 1_555 S FE1 FES . F FES 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc8 F SG CYS 76 F CYS 76 1_555 S FE1 FES . F FES 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc9 F SG CYS 79 F CYS 79 1_555 S FE2 FES . F FES 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc10 F SG CYS 111 F CYS 111 1_555 S FE2 FES . F FES 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? # _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 640 n n N1 C10 RBF doub 641 n n C2 O2 RBF doub 642 n n C2 N3 RBF sing 643 n n N3 C4 RBF sing 644 n n N3 HN3 RBF sing 645 n n C4 O4 RBF doub 646 n n C4 C4A RBF sing 647 n n C4A N5 RBF doub 648 n n C4A C10 RBF sing 649 n n N5 C5A RBF sing 650 n n C5A C6 RBF doub 651 n y C5A C9A RBF sing 652 n y C6 C7 RBF sing 653 n y C6 HC6 RBF sing 654 n n C7 C7M RBF sing 655 n n C7 C8 RBF doub 656 n y C7M HC71 RBF sing 657 n n C7M HC72 RBF sing 658 n n C7M HC73 RBF sing 659 n n C8 C8M RBF sing 660 n n C8 C9 RBF sing 661 n y C8M HC81 RBF sing 662 n n C8M HC82 RBF sing 663 n n C8M HC83 RBF sing 664 n n C9 C9A RBF doub 665 n y C9 HC9 RBF sing 666 n n C9A N10 RBF sing 667 n n N10 C10 RBF sing 668 n n N10 C1' RBF sing 669 n n C1' C2' RBF sing 670 n n C1' HC11 RBF sing 671 n n C1' HC12 RBF sing 672 n n C2' O2' RBF sing 673 n n C2' C3' RBF sing 674 n n C2' HC2' RBF sing 675 n n O2' HO2' RBF sing 676 n n C3' O3' RBF sing 677 n n C3' C4' RBF sing 678 n n C3' HC3' RBF sing 679 n n O3' HO3' RBF sing 680 n n C4' O4' RBF sing 681 n n C4' C5' RBF sing 682 n n C4' HC4' RBF sing 683 n n O4' HO4' RBF sing 684 n n C5' O5' RBF sing 685 n n C5' HC51 RBF sing 686 n n C5' HC52 RBF sing 687 n n O5' HO5' RBF sing 688 n n # _atom_sites.entry_id 8AD0 _atom_sites.fract_transf_matrix[1][1] 0.011197 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004038 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007035 _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] 0.010035 _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 1 504 608 3PE 3PE . K 11 NA B 1 505 1 NA NA . L 12 K B 1 506 2 K K . M 7 FMN C 1 301 1000 FMN FMN . N 13 BR C 1 302 3 BR BR . O 9 LMT D 1 301 604 LMT LMT . P 14 FES D 1 302 1001 FES FES . Q 9 LMT E 1 201 603 LMT LMT . R 15 FAD F 1 1501 1501 FAD FAD . S 14 FES F 1 1502 1502 FES FES . T 16 HOH A 1 501 5 HOH HOH . U 16 HOH B 1 601 3 HOH HOH . U 16 HOH B 2 602 2 HOH HOH . U 16 HOH B 3 603 4 HOH HOH . V 16 HOH E 1 301 1 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 RBF . . . H 8 16.364 9.929 34.607 1 125.65 ? N1 RBF 502 B 1 HETATM 2 C C2 RBF . . . H 8 17.448 10.71 34.853 1 123.22 ? C2 RBF 502 B 1 HETATM 3 O O2 RBF . . . H 8 17.656 11.739 34.198 1 122.76 ? O2 RBF 502 B 1 HETATM 4 N N3 RBF . . . H 8 18.346 10.4 35.823 1 121.97 ? N3 RBF 502 B 1 HETATM 5 C C4 RBF . . . H 8 18.208 9.28 36.604 1 120.74 ? C4 RBF 502 B 1 HETATM 6 O O4 RBF . . . H 8 19.045 9.055 37.461 1 118.28 ? O4 RBF 502 B 1 HETATM 7 C C4A RBF . . . H 8 17.087 8.434 36.381 1 124 ? C4A RBF 502 B 1 HETATM 8 N N5 RBF . . . H 8 16.934 7.36 37.12 1 122.47 ? N5 RBF 502 B 1 HETATM 9 C C5A RBF . . . H 8 15.843 6.566 36.873 1 125.37 ? C5A RBF 502 B 1 HETATM 10 C C6 RBF . . . H 8 15.666 5.409 37.657 1 124.79 ? C6 RBF 502 B 1 HETATM 11 C C7 RBF . . . H 8 14.599 4.562 37.466 1 128.67 ? C7 RBF 502 B 1 HETATM 12 C C7M RBF . . . H 8 14.45 3.334 38.328 1 128.41 ? C7M RBF 502 B 1 HETATM 13 C C8 RBF . . . H 8 13.645 4.866 36.446 1 144.14 ? C8 RBF 502 B 1 HETATM 14 C C8M RBF . . . H 8 12.459 3.967 36.204 1 142.82 ? C8M RBF 502 B 1 HETATM 15 C C9 RBF . . . H 8 13.81 6.004 35.675 1 135.35 ? C9 RBF 502 B 1 HETATM 16 C C9A RBF . . . H 8 14.902 6.869 35.866 1 127.73 ? C9A RBF 502 B 1 HETATM 17 N N10 RBF . . . H 8 15.098 8.024 35.108 1 127.63 ? N10 RBF 502 B 1 HETATM 18 C C10 RBF . . . H 8 16.188 8.844 35.336 1 126.27 ? C10 RBF 502 B 1 HETATM 19 C C1' RBF . . . H 8 14.138 8.383 34.048 1 138.41 ? C1' RBF 502 B 1 HETATM 20 C C2' RBF . . . H 8 14.473 7.777 32.695 1 130.6 ? C2' RBF 502 B 1 HETATM 21 O O2' RBF . . . H 8 14.407 6.365 32.78 1 129.57 ? O2' RBF 502 B 1 HETATM 22 C C3' RBF . . . H 8 15.897 8.177 32.31 1 126.08 ? C3' RBF 502 B 1 HETATM 23 O O3' RBF . . . H 8 15.966 9.607 32.202 1 125.95 ? O3' RBF 502 B 1 HETATM 24 C C4' RBF . . . H 8 16.396 7.605 30.982 1 123.63 ? C4' RBF 502 B 1 HETATM 25 O O4' RBF . . . H 8 17.812 7.783 30.882 1 122.63 ? O4' RBF 502 B 1 HETATM 26 C C5' RBF . . . H 8 15.722 8.273 29.799 1 126.43 ? C5' RBF 502 B 1 HETATM 27 O O5' RBF . . . H 8 15.999 7.594 28.577 1 137.62 ? O5' RBF 502 B 1 HETATM 28 H HN3 RBF . . . H 8 19.032 10.938 35.946 1 147.15 ? HN3 RBF 502 B 1 HETATM 29 H HC6 RBF . . . H 8 16.306 5.213 38.337 1 150.54 ? HC6 RBF 502 B 1 HETATM 30 H HC71 RBF . . . H 8 13.866 3.534 39.078 1 154.88 ? HC71 RBF 502 B 1 HETATM 31 H HC72 RBF . . . H 8 14.066 2.614 37.802 1 154.88 ? HC72 RBF 502 B 1 HETATM 32 H HC73 RBF . . . H 8 15.321 3.063 38.66 1 154.88 ? HC73 RBF 502 B 1 HETATM 33 H HC81 RBF . . . H 8 12.71 3.256 35.592 1 172.18 ? HC81 RBF 502 B 1 HETATM 34 H HC82 RBF . . . H 8 11.733 4.483 35.818 1 172.18 ? HC82 RBF 502 B 1 HETATM 35 H HC83 RBF . . . H 8 12.167 3.58 37.045 1 172.18 ? HC83 RBF 502 B 1 HETATM 36 H HC9 RBF . . . H 8 13.166 6.205 34.997 1 163.21 ? HC9 RBF 502 B 1 HETATM 37 H HC11 RBF . . . H 8 14.117 9.357 33.964 1 166.88 ? HC11 RBF 502 B 1 HETATM 38 H HC12 RBF . . . H 8 13.247 8.085 34.319 1 166.88 ? HC12 RBF 502 B 1 HETATM 39 H HC2' RBF . . . H 8 13.826 8.082 32.009 1 157.51 ? HC2' RBF 502 B 1 HETATM 40 H HO2' RBF . . . H 8 15.036 6.085 33.276 1 156.28 ? HO2' RBF 502 B 1 HETATM 41 H HC3' RBF . . . H 8 16.491 7.855 33.036 1 152.09 ? HC3' RBF 502 B 1 HETATM 42 H HC4' RBF . . . H 8 16.196 6.621 30.954 1 149.15 ? HC4' RBF 502 B 1 HETATM 43 H HO4' RBF . . . H 8 18.016 8.606 30.86 1 147.95 ? HO4' RBF 502 B 1 HETATM 44 H HC51 RBF . . . H 8 14.745 8.286 29.949 1 152.51 ? HC51 RBF 502 B 1 HETATM 45 H HC52 RBF . . . H 8 16.038 9.206 29.731 1 152.51 ? HC52 RBF 502 B 1 HETATM 46 H HO5' RBF . . . H 8 15.695 8.06 27.94 1 165.93 ? HO5' RBF 502 B 1 # _model_server_stats.io_time_ms 34 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 46 #