data_5KBW # _model_server_result.job_id F534r72FqQu50i4GqgQzig _model_server_result.datetime_utc '2025-02-18 07:10:10' _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 5kbw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 5KBW # _exptl.entry_id 5KBW _exptl.method 'X-RAY DIFFRACTION' # _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 95.81 _cell.angle_gamma 90 _cell.entry_id 5KBW _cell.length_a 40.142 _cell.length_b 94.365 _cell.length_c 50.986 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KBW _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 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 C N N ? 2 D 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 264 n n N1 C10 RBF doub 265 n n C2 O2 RBF doub 266 n n C2 N3 RBF sing 267 n n N3 C4 RBF sing 268 n n N3 HN3 RBF sing 269 n n C4 O4 RBF doub 270 n n C4 C4A RBF sing 271 n n C4A N5 RBF doub 272 n n C4A C10 RBF sing 273 n n N5 C5A RBF sing 274 n n C5A C6 RBF doub 275 n y C5A C9A RBF sing 276 n y C6 C7 RBF sing 277 n y C6 HC6 RBF sing 278 n n C7 C7M RBF sing 279 n n C7 C8 RBF doub 280 n y C7M HC71 RBF sing 281 n n C7M HC72 RBF sing 282 n n C7M HC73 RBF sing 283 n n C8 C8M RBF sing 284 n n C8 C9 RBF sing 285 n y C8M HC81 RBF sing 286 n n C8M HC82 RBF sing 287 n n C8M HC83 RBF sing 288 n n C9 C9A RBF doub 289 n y C9 HC9 RBF sing 290 n n C9A N10 RBF sing 291 n n N10 C10 RBF sing 292 n n N10 C1' RBF sing 293 n n C1' C2' RBF sing 294 n n C1' HC11 RBF sing 295 n n C1' HC12 RBF sing 296 n n C2' O2' RBF sing 297 n n C2' C3' RBF sing 298 n n C2' HC2' RBF sing 299 n n O2' HO2' RBF sing 300 n n C3' O3' RBF sing 301 n n C3' C4' RBF sing 302 n n C3' HC3' RBF sing 303 n n O3' HO3' RBF sing 304 n n C4' O4' RBF sing 305 n n C4' C5' RBF sing 306 n n C4' HC4' RBF sing 307 n n O4' HO4' RBF sing 308 n n C5' O5' RBF sing 309 n n C5' HC51 RBF sing 310 n n C5' HC52 RBF sing 311 n n O5' HO5' RBF sing 312 n n # _atom_sites.entry_id 5KBW _atom_sites.fract_transf_matrix[1][1] 0.024912 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002534 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010597 _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] 0.019714 _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 C 2 RBF A 1 201 192 RBF RBF . D 2 RBF B 1 201 193 RBF RBF . E 3 HOH A 1 301 2 HOH HOH . F 3 HOH B 1 301 1 HOH HOH . F 3 HOH B 2 302 4 HOH HOH . F 3 HOH B 3 303 5 HOH HOH . F 3 HOH B 4 304 3 HOH HOH . F 3 HOH B 5 305 6 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 . . . D 2 -24.315 -2.522 83.373 1 52.64 ? N1 RBF 201 B 1 HETATM 2 C C2 RBF . . . D 2 -23.534 -3.521 82.897 1 41.05 ? C2 RBF 201 B 1 HETATM 3 O O2 RBF . . . D 2 -23.077 -4.317 83.636 1 58.65 ? O2 RBF 201 B 1 HETATM 4 N N3 RBF . . . D 2 -23.272 -3.607 81.563 1 54.53 ? N3 RBF 201 B 1 HETATM 5 C C4 RBF . . . D 2 -23.782 -2.722 80.732 1 51.72 ? C4 RBF 201 B 1 HETATM 6 O O4 RBF . . . D 2 -23.559 -2.801 79.594 1 52.62 ? O4 RBF 201 B 1 HETATM 7 C C4A RBF . . . D 2 -24.591 -1.696 81.217 1 60.92 ? C4A RBF 201 B 1 HETATM 8 N N5 RBF . . . D 2 -25.118 -0.773 80.343 1 47.46 ? N5 RBF 201 B 1 HETATM 9 C C5A RBF . . . D 2 -25.892 0.225 80.803 1 44.93 ? C5A RBF 201 B 1 HETATM 10 C C6 RBF . . . D 2 -26.427 1.167 79.88 1 51.32 ? C6 RBF 201 B 1 HETATM 11 C C7 RBF . . . D 2 -27.237 2.212 80.332 1 68.03 ? C7 RBF 201 B 1 HETATM 12 C C7M RBF . . . D 2 -27.718 3.111 79.253 1 52.38 ? C7M RBF 201 B 1 HETATM 13 C C8 RBF . . . D 2 -27.522 2.333 81.688 1 62.24 ? C8 RBF 201 B 1 HETATM 14 C C8M RBF . . . D 2 -28.403 3.46 82.26 1 53.33 ? C8M RBF 201 B 1 HETATM 15 C C9 RBF . . . D 2 -26.997 1.404 82.598 1 46.11 ? C9 RBF 201 B 1 HETATM 16 C C9A RBF . . . D 2 -26.167 0.331 82.146 1 53.2 ? C9A RBF 201 B 1 HETATM 17 N N10 RBF . . . D 2 -25.641 -0.567 83.006 1 48.45 ? N10 RBF 201 B 1 HETATM 18 C C10 RBF . . . D 2 -24.846 -1.6 82.521 1 63.13 ? C10 RBF 201 B 1 HETATM 19 C C1' RBF . . . D 2 -25.749 -0.751 84.477 1 59.63 ? C1' RBF 201 B 1 HETATM 20 C C2' RBF . . . D 2 -25.351 0.484 85.345 1 67.21 ? C2' RBF 201 B 1 HETATM 21 O O2' RBF . . . D 2 -24.061 0.344 85.809 1 68.65 ? O2' RBF 201 B 1 HETATM 22 C C3' RBF . . . D 2 -26.325 0.525 86.532 1 73.49 ? C3' RBF 201 B 1 HETATM 23 O O3' RBF . . . D 2 -27.609 0.158 86.085 1 95.55 ? O3' RBF 201 B 1 HETATM 24 C C4' RBF . . . D 2 -26.403 1.899 87.153 1 82.64 ? C4' RBF 201 B 1 HETATM 25 O O4' RBF . . . D 2 -27.436 1.901 88.139 1 78.33 ? O4' RBF 201 B 1 HETATM 26 C C5' RBF . . . D 2 -26.738 2.961 86.072 1 86.91 ? C5' RBF 201 B 1 HETATM 27 O O5' RBF . . . D 2 -26.873 4.257 86.702 1 112.35 ? O5' RBF 201 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #