data_8A1Y
#
_model_server_result.job_id            vRloNB0TyNxTcK-tjUAK6Q 
_model_server_result.datetime_utc      '2024-11-23 04:37:51' 
_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          8a1y 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":601}' 
#
_entry.id    8A1Y 
#
_exptl.entry_id    8A1Y 
_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            8A1Y 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8A1Y 
_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 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.599 ? 
covale ? covale2 C OG1 THR 225 C THR 225 1_555 O P FMN . C FMN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? 
metalc ? metalc1 D SG CYS 29 D CYS 29 1_555 P FE2 FES . D FES 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? 
metalc ? metalc2 D SG CYS 112 D CYS 112 1_555 P FE1 FES . D FES 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc3 P FE1 FES . D FES 1001 1_555 E SG CYS 26 E CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? 
metalc ? metalc4 P FE2 FES . D FES 1001 1_555 E SG CYS 120 E CYS 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc5 F SG CYS 70 F CYS 70 1_555 T FE1 FES . F FES 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc6 F SG CYS 76 F CYS 76 1_555 T FE1 FES . F FES 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc7 F SG CYS 79 F CYS 79 1_555 T FE2 FES . F FES 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc8 F SG CYS 111 F CYS 111 1_555 T FE2 FES . F FES 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
#
_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 679 n n 
N1 C10 RBF doub 680 n n 
C2 O2 RBF doub 681 n n 
C2 N3 RBF sing 682 n n 
N3 C4 RBF sing 683 n n 
N3 HN3 RBF sing 684 n n 
C4 O4 RBF doub 685 n n 
C4 C4A RBF sing 686 n n 
C4A N5 RBF doub 687 n n 
C4A C10 RBF sing 688 n n 
N5 C5A RBF sing 689 n n 
C5A C6 RBF doub 690 n y 
C5A C9A RBF sing 691 n y 
C6 C7 RBF sing 692 n y 
C6 HC6 RBF sing 693 n n 
C7 C7M RBF sing 694 n n 
C7 C8 RBF doub 695 n y 
C7M HC71 RBF sing 696 n n 
C7M HC72 RBF sing 697 n n 
C7M HC73 RBF sing 698 n n 
C8 C8M RBF sing 699 n n 
C8 C9 RBF sing 700 n y 
C8M HC81 RBF sing 701 n n 
C8M HC82 RBF sing 702 n n 
C8M HC83 RBF sing 703 n n 
C9 C9A RBF doub 704 n y 
C9 HC9 RBF sing 705 n n 
C9A N10 RBF sing 706 n n 
N10 C10 RBF sing 707 n n 
N10 C1' RBF sing 708 n n 
C1' C2' RBF sing 709 n n 
C1' HC11 RBF sing 710 n n 
C1' HC12 RBF sing 711 n n 
C2' O2' RBF sing 712 n n 
C2' C3' RBF sing 713 n n 
C2' HC2' RBF sing 714 n n 
O2' HO2' RBF sing 715 n n 
C3' O3' RBF sing 716 n n 
C3' C4' RBF sing 717 n n 
C3' HC3' RBF sing 718 n n 
O3' HO3' RBF sing 719 n n 
C4' O4' RBF sing 720 n n 
C4' C5' RBF sing 721 n n 
C4' HC4' RBF sing 722 n n 
O4' HO4' RBF sing 723 n n 
C5' O5' RBF sing 724 n n 
C5' HC51 RBF sing 725 n n 
C5' HC52 RBF sing 726 n n 
O5' HO5' RBF sing 727 n n 
#
_atom_sites.entry_id                     8A1Y 
_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 1 600 600 FMN FMN . 
H 8 RBF B 1 601 601 RBF RBF . 
I 9 3PE B 1 602 602 3PE 3PE . 
J 10 LMT B 1 603 603 LMT LMT . 
K 9 3PE B 1 604 604 3PE 3PE . 
L 10 LMT B 1 605 605 LMT LMT . 
M 9 3PE B 1 606 606 3PE 3PE . 
N 11 HQO B 1 607 607 HQO HQO . 
O 7 FMN C 1 1000 1000 FMN FMN . 
P 12 FES D 1 1001 1001 FES FES . 
Q 10 LMT D 1 1002 1002 LMT LMT . 
R 10 LMT E 1 201 201 LMT LMT . 
S 13 FAD F 1 1501 1501 FAD FAD . 
T 12 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 8 114.708 125.139 141.08 1 103.95 ? N1 RBF 601 B 1 
HETATM 2 C C2 RBF . . . H 8 115.535 126.201 141.181 1 103.96 ? C2 RBF 601 B 1 
HETATM 3 O O2 RBF . . . H 8 115.315 127.237 140.55 1 105.05 ? O2 RBF 601 B 1 
HETATM 4 N N3 RBF . . . H 8 116.634 126.184 141.975 1 106.31 ? N3 RBF 601 B 1 
HETATM 5 C C4 RBF . . . H 8 116.972 125.083 142.72 1 106.97 ? C4 RBF 601 B 1 
HETATM 6 O O4 RBF . . . H 8 117.972 125.11 143.423 1 101.95 ? O4 RBF 601 B 1 
HETATM 7 C C4A RBF . . . H 8 116.138 123.953 142.641 1 104.08 ? C4A RBF 601 B 1 
HETATM 8 N N5 RBF . . . H 8 116.447 122.898 143.346 1 96.78 ? N5 RBF 601 B 1 
HETATM 9 C C5A RBF . . . H 8 115.619 121.812 143.253 1 98.04 ? C5A RBF 601 B 1 
HETATM 10 C C6 RBF . . . H 8 115.942 120.672 144.009 1 98.54 ? C6 RBF 601 B 1 
HETATM 11 C C7 RBF . . . H 8 115.164 119.54 143.974 1 102.71 ? C7 RBF 601 B 1 
HETATM 12 C C7M RBF . . . H 8 115.547 118.34 144.803 1 92.55 ? C7M RBF 601 B 1 
HETATM 13 C C8 RBF . . . H 8 114.009 119.521 143.153 1 103.84 ? C8 RBF 601 B 1 
HETATM 14 C C8M RBF . . . H 8 113.129 118.3 143.087 1 96.35 ? C8M RBF 601 B 1 
HETATM 15 C C9 RBF . . . H 8 113.681 120.634 142.407 1 105.23 ? C9 RBF 601 B 1 
HETATM 16 C C9A RBF . . . H 8 114.469 121.798 142.436 1 105.67 ? C9A RBF 601 B 1 
HETATM 17 N N10 RBF . . . H 8 114.174 122.946 141.696 1 107.07 ? N10 RBF 601 B 1 
HETATM 18 C C10 RBF . . . H 8 114.993 124.059 141.776 1 104.37 ? C10 RBF 601 B 1 
HETATM 19 C C1' RBF . . . H 8 112.981 122.994 140.828 1 104.23 ? C1' RBF 601 B 1 
HETATM 20 C C2' RBF . . . H 8 113.277 122.563 139.4 1 103.15 ? C2' RBF 601 B 1 
HETATM 21 O O2' RBF . . . H 8 114.036 121.358 139.386 1 97.97 ? O2' RBF 601 B 1 
HETATM 22 C C3' RBF . . . H 8 114.022 123.654 138.627 1 103.34 ? C3' RBF 601 B 1 
HETATM 23 O O3' RBF . . . H 8 113.318 124.885 138.762 1 103.15 ? O3' RBF 601 B 1 
HETATM 24 C C4' RBF . . . H 8 114.201 123.337 137.142 1 101.39 ? C4' RBF 601 B 1 
HETATM 25 O O4' RBF . . . H 8 115.439 122.652 136.942 1 101.16 ? O4' RBF 601 B 1 
HETATM 26 C C5' RBF . . . H 8 114.155 124.582 136.283 1 100.5 ? C5' RBF 601 B 1 
HETATM 27 O O5' RBF . . . H 8 114.311 124.268 134.903 1 100.94 ? O5' RBF 601 B 1 
HETATM 28 H HN3 RBF . . . H 8 117.136 126.904 142.007 1 96.35 ? HN3 RBF 601 B 1 
HETATM 29 H HC6 RBF . . . H 8 116.721 120.691 144.559 1 95.91 ? HC6 RBF 601 B 1 
HETATM 30 H HC71 RBF . . . H 8 115.311 117.526 144.329 1 95.71 ? HC71 RBF 601 B 1 
HETATM 31 H HC72 RBF . . . H 8 115.074 118.366 145.65 1 95.04 ? HC72 RBF 601 B 1 
HETATM 32 H HC73 RBF . . . H 8 116.504 118.35 144.968 1 95.37 ? HC73 RBF 601 B 1 
HETATM 33 H HC81 RBF . . . H 8 113.106 117.867 143.954 1 96.33 ? HC81 RBF 601 B 1 
HETATM 34 H HC82 RBF . . . H 8 113.482 117.681 142.427 1 96.74 ? HC82 RBF 601 B 1 
HETATM 35 H HC83 RBF . . . H 8 112.229 118.562 142.833 1 96.44 ? HC83 RBF 601 B 1 
HETATM 36 H HC9 RBF . . . H 8 112.9 120.606 141.858 1 97.46 ? HC9 RBF 601 B 1 
HETATM 37 H HC11 RBF . . . H 8 112.635 123.908 140.819 1 97.2 ? HC11 RBF 601 B 1 
HETATM 38 H HC12 RBF . . . H 8 112.284 122.423 141.201 1 97.55 ? HC12 RBF 601 B 1 
HETATM 39 H HC2' RBF . . . H 8 112.417 122.388 138.938 1 97.35 ? HC2' RBF 601 B 1 
HETATM 40 H HO2' RBF . . . H 8 113.569 120.73 139.711 1 97 ? HO2' RBF 601 B 1 
HETATM 41 H HC3' RBF . . . H 8 114.921 123.764 139.03 1 97.55 ? HC3' RBF 601 B 1 
HETATM 42 H HO3' RBF . . . H 8 112.526 124.777 138.479 1 97.58 ? HO3' RBF 601 B 1 
HETATM 43 H HC4' RBF . . . H 8 113.455 122.734 136.85 1 97.37 ? HC4' RBF 601 B 1 
HETATM 44 H HO4' RBF . . . H 8 116.097 123.129 137.184 1 96.82 ? HO4' RBF 601 B 1 
HETATM 45 H HC51 RBF . . . H 8 114.875 125.197 136.561 1 96.09 ? HC51 RBF 601 B 1 
HETATM 46 H HC52 RBF . . . H 8 113.289 125.037 136.414 1 97.38 ? HC52 RBF 601 B 1 
HETATM 47 H HO5' RBF . . . H 8 114.183 124.981 134.47 1 96.62 ? HO5' RBF 601 B 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    39 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           47 
#