data_8EW3
#
_model_server_result.job_id            RK1Mtfv4P2_fCFgEr5Yt_Q 
_model_server_result.datetime_utc      '2025-06-22 18:09:25' 
_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          8ew3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":601}' 
#
_entry.id    8EW3 
#
_exptl.entry_id    8EW3 
_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            8EW3 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8EW3 
_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 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
covale ? covale2 C OG1 THR 225 C THR 225 1_555 J P FMN . C FMN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
metalc ? metalc1 D SG CYS 29 D CYS 29 1_555 K FE2 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc2 D SG CYS 112 D CYS 112 1_555 K FE1 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc3 E SG CYS 26 E CYS 26 1_555 K FE1 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc4 E SG CYS 120 E CYS 120 1_555 K FE2 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
#
_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 333 n n 
N1 C10 RBF doub 334 n n 
C2 O2 RBF doub 335 n n 
C2 N3 RBF sing 336 n n 
N3 C4 RBF sing 337 n n 
N3 HN3 RBF sing 338 n n 
C4 O4 RBF doub 339 n n 
C4 C4A RBF sing 340 n n 
C4A N5 RBF doub 341 n n 
C4A C10 RBF sing 342 n n 
N5 C5A RBF sing 343 n n 
C5A C6 RBF doub 344 n y 
C5A C9A RBF sing 345 n y 
C6 C7 RBF sing 346 n y 
C6 HC6 RBF sing 347 n n 
C7 C7M RBF sing 348 n n 
C7 C8 RBF doub 349 n y 
C7M HC71 RBF sing 350 n n 
C7M HC72 RBF sing 351 n n 
C7M HC73 RBF sing 352 n n 
C8 C8M RBF sing 353 n n 
C8 C9 RBF sing 354 n y 
C8M HC81 RBF sing 355 n n 
C8M HC82 RBF sing 356 n n 
C8M HC83 RBF sing 357 n n 
C9 C9A RBF doub 358 n y 
C9 HC9 RBF sing 359 n n 
C9A N10 RBF sing 360 n n 
N10 C10 RBF sing 361 n n 
N10 C1' RBF sing 362 n n 
C1' C2' RBF sing 363 n n 
C1' HC11 RBF sing 364 n n 
C1' HC12 RBF sing 365 n n 
C2' O2' RBF sing 366 n n 
C2' C3' RBF sing 367 n n 
C2' HC2' RBF sing 368 n n 
O2' HO2' RBF sing 369 n n 
C3' O3' RBF sing 370 n n 
C3' C4' RBF sing 371 n n 
C3' HC3' RBF sing 372 n n 
O3' HO3' RBF sing 373 n n 
C4' O4' RBF sing 374 n n 
C4' C5' RBF sing 375 n n 
C4' HC4' RBF sing 376 n n 
O4' HO4' RBF sing 377 n n 
C5' O5' RBF sing 378 n n 
C5' HC51 RBF sing 379 n n 
C5' HC52 RBF sing 380 n n 
O5' HO5' RBF sing 381 n n 
#
_atom_sites.entry_id                     8EW3 
_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 UQ1 B 1 602 602 UQ1 UQ1 . 
J 7 FMN C 1 301 301 FMN FMN . 
K 10 FES E 1 301 301 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 8 177.997 206.907 203.051 1 41.43 ? N1 RBF 601 B 1 
HETATM 2 C C2 RBF . . . H 8 178.495 206.055 203.972 1 41.9 ? C2 RBF 601 B 1 
HETATM 3 O O2 RBF . . . H 8 179.668 206.134 204.337 1 53.39 ? O2 RBF 601 B 1 
HETATM 4 N N3 RBF . . . H 8 177.738 205.082 204.534 1 37.06 ? N3 RBF 601 B 1 
HETATM 5 C C4 RBF . . . H 8 176.42 204.903 204.199 1 40.86 ? C4 RBF 601 B 1 
HETATM 6 O O4 RBF . . . H 8 175.774 204.014 204.733 1 43.75 ? O4 RBF 601 B 1 
HETATM 7 C C4A RBF . . . H 8 175.862 205.772 203.246 1 40.88 ? C4A RBF 601 B 1 
HETATM 8 N N5 RBF . . . H 8 174.606 205.616 202.92 1 39.45 ? N5 RBF 601 B 1 
HETATM 9 C C5A RBF . . . H 8 174.085 206.477 201.992 1 37.99 ? C5A RBF 601 B 1 
HETATM 10 C C6 RBF . . . H 8 172.734 206.326 201.635 1 40.14 ? C6 RBF 601 B 1 
HETATM 11 C C7 RBF . . . H 8 172.14 207.154 200.714 1 44.43 ? C7 RBF 601 B 1 
HETATM 12 C C7M RBF . . . H 8 170.688 206.964 200.356 1 35.95 ? C7M RBF 601 B 1 
HETATM 13 C C8 RBF . . . H 8 172.904 208.178 200.106 1 45.94 ? C8 RBF 601 B 1 
HETATM 14 C C8M RBF . . . H 8 172.277 209.097 199.089 1 45.1 ? C8M RBF 601 B 1 
HETATM 15 C C9 RBF . . . H 8 174.231 208.335 200.447 1 39.53 ? C9 RBF 601 B 1 
HETATM 16 C C9A RBF . . . H 8 174.848 207.497 201.39 1 42.62 ? C9A RBF 601 B 1 
HETATM 17 N N10 RBF . . . H 8 176.188 207.626 201.756 1 44.47 ? N10 RBF 601 B 1 
HETATM 18 C C10 RBF . . . H 8 176.737 206.777 202.7 1 42.06 ? C10 RBF 601 B 1 
HETATM 19 C C1' RBF . . . H 8 177.018 208.687 201.153 1 38.56 ? C1' RBF 601 B 1 
HETATM 20 C C2' RBF . . . H 8 177.697 208.263 199.848 1 43.95 ? C2' RBF 601 B 1 
HETATM 21 O O2' RBF . . . H 8 176.729 207.913 198.865 1 50.41 ? O2' RBF 601 B 1 
HETATM 22 C C3' RBF . . . H 8 178.683 207.104 200.022 1 41.01 ? C3' RBF 601 B 1 
HETATM 23 O O3' RBF . . . H 8 179.649 207.451 201.007 1 51.62 ? O3' RBF 601 B 1 
HETATM 24 C C4' RBF . . . H 8 179.398 206.679 198.738 1 44.89 ? C4' RBF 601 B 1 
HETATM 25 O O4' RBF . . . H 8 180.086 205.446 198.961 1 48.01 ? O4' RBF 601 B 1 
HETATM 26 C C5' RBF . . . H 8 180.383 207.721 198.255 1 46.72 ? C5' RBF 601 B 1 
HETATM 27 O O5' RBF . . . H 8 181.086 207.269 197.102 1 47.33 ? O5' RBF 601 B 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#