data_8XSM # _model_server_result.job_id IrmO3Pbvyx8zSFWGuFW-hQ _model_server_result.datetime_utc '2025-01-18 05:00:43' _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 8xsm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8XSM # _exptl.entry_id 8XSM _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 376.364 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RIBOFLAVIN _entity.pdbx_number_of_molecules 2 _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 8XSM _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XSM _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N # _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 275 n n N1 C10 RBF doub 276 n n C2 O2 RBF doub 277 n n C2 N3 RBF sing 278 n n N3 C4 RBF sing 279 n n N3 HN3 RBF sing 280 n n C4 O4 RBF doub 281 n n C4 C4A RBF sing 282 n n C4A N5 RBF doub 283 n n C4A C10 RBF sing 284 n n N5 C5A RBF sing 285 n n C5A C6 RBF doub 286 n y C5A C9A RBF sing 287 n y C6 C7 RBF sing 288 n y C6 HC6 RBF sing 289 n n C7 C7M RBF sing 290 n n C7 C8 RBF doub 291 n y C7M HC71 RBF sing 292 n n C7M HC72 RBF sing 293 n n C7M HC73 RBF sing 294 n n C8 C8M RBF sing 295 n n C8 C9 RBF sing 296 n y C8M HC81 RBF sing 297 n n C8M HC82 RBF sing 298 n n C8M HC83 RBF sing 299 n n C9 C9A RBF doub 300 n y C9 HC9 RBF sing 301 n n C9A N10 RBF sing 302 n n N10 C10 RBF sing 303 n n N10 C1' RBF sing 304 n n C1' C2' RBF sing 305 n n C1' HC11 RBF sing 306 n n C1' HC12 RBF sing 307 n n C2' O2' RBF sing 308 n n C2' C3' RBF sing 309 n n C2' HC2' RBF sing 310 n n O2' HO2' RBF sing 311 n n C3' O3' RBF sing 312 n n C3' C4' RBF sing 313 n n C3' HC3' RBF sing 314 n n O3' HO3' RBF sing 315 n n C4' O4' RBF sing 316 n n C4' C5' RBF sing 317 n n C4' HC4' RBF sing 318 n n O4' HO4' RBF sing 319 n n C5' O5' RBF sing 320 n n C5' HC51 RBF sing 321 n n C5' HC52 RBF sing 322 n n O5' HO5' RBF sing 323 n n # _atom_sites.entry_id 8XSM _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 B 2 RBF A 1 501 501 RBF RIB . C 2 RBF A 1 502 601 RBF RIB . # 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 . . . B 2 141.267 134.277 131.116 1 45.3 ? N1 RBF 501 A 1 HETATM 2 C C2 RBF . . . B 2 140.684 133.264 131.761 1 45.3 ? C2 RBF 501 A 1 HETATM 3 O O2 RBF . . . B 2 139.704 133.414 132.386 1 45.3 ? O2 RBF 501 A 1 HETATM 4 N N3 RBF . . . B 2 141.243 132.062 131.688 1 45.3 ? N3 RBF 501 A 1 HETATM 5 C C4 RBF . . . B 2 142.341 131.867 130.999 1 45.3 ? C4 RBF 501 A 1 HETATM 6 O O4 RBF . . . B 2 142.8 130.787 130.956 1 45.3 ? O4 RBF 501 A 1 HETATM 7 C C4A RBF . . . B 2 142.935 132.884 130.354 1 45.3 ? C4A RBF 501 A 1 HETATM 8 N N5 RBF . . . B 2 144.035 132.721 129.656 1 45.3 ? N5 RBF 501 A 1 HETATM 9 C C5A RBF . . . B 2 144.587 133.732 129.05 1 45.3 ? C5A RBF 501 A 1 HETATM 10 C C6 RBF . . . B 2 145.739 133.59 128.312 1 45.3 ? C6 RBF 501 A 1 HETATM 11 C C7 RBF . . . B 2 146.312 134.676 127.669 1 45.3 ? C7 RBF 501 A 1 HETATM 12 C C7M RBF . . . B 2 147.583 134.512 126.855 1 45.3 ? C7M RBF 501 A 1 HETATM 13 C C8 RBF . . . B 2 145.727 135.907 127.775 1 45.3 ? C8 RBF 501 A 1 HETATM 14 C C8M RBF . . . B 2 146.307 137.128 127.092 1 45.3 ? C8M RBF 501 A 1 HETATM 15 C C9 RBF . . . B 2 144.581 136.035 128.512 1 45.3 ? C9 RBF 501 A 1 HETATM 16 C C9A RBF . . . B 2 144.017 134.956 129.137 1 45.3 ? C9A RBF 501 A 1 HETATM 17 N N10 RBF . . . B 2 142.923 135.123 129.821 1 45.3 ? N10 RBF 501 A 1 HETATM 18 C C10 RBF . . . B 2 142.372 134.094 130.431 1 45.3 ? C10 RBF 501 A 1 HETATM 19 C C1' RBF . . . B 2 142.371 136.432 129.891 1 45.3 ? C1' RBF 501 A 1 HETATM 20 C C2' RBF . . . B 2 140.935 136.425 129.475 1 45.3 ? C2' RBF 501 A 1 HETATM 21 O O2' RBF . . . B 2 140.885 137.021 128.213 1 45.3 ? O2' RBF 501 A 1 HETATM 22 C C3' RBF . . . B 2 140.259 137.254 130.555 1 45.3 ? C3' RBF 501 A 1 HETATM 23 O O3' RBF . . . B 2 139.091 136.701 131.061 1 45.3 ? O3' RBF 501 A 1 HETATM 24 C C4' RBF . . . B 2 139.828 138.583 130.034 1 45.3 ? C4' RBF 501 A 1 HETATM 25 O O4' RBF . . . B 2 140.986 139.052 129.452 1 45.3 ? O4' RBF 501 A 1 HETATM 26 C C5' RBF . . . B 2 139.423 139.378 131.249 1 45.3 ? C5' RBF 501 A 1 HETATM 27 O O5' RBF . . . B 2 138.458 138.619 131.897 1 45.3 ? O5' RBF 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #