data_4E0F # _model_server_result.job_id gywjhaZOoDxdFrWNLkYXKg _model_server_result.datetime_utc '2025-07-19 03:30:46' _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 4e0f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 4E0F # _exptl.entry_id 4E0F _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 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 4E0F _cell.length_a 69.98 _cell.length_b 91.82 _cell.length_c 98.77 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4E0F _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 2 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 277 n n N1 C10 RBF doub 278 n n C2 O2 RBF doub 279 n n C2 N3 RBF sing 280 n n N3 C4 RBF sing 281 n n N3 HN3 RBF sing 282 n n C4 O4 RBF doub 283 n n C4 C4A RBF sing 284 n n C4A N5 RBF doub 285 n n C4A C10 RBF sing 286 n n N5 C5A RBF sing 287 n n C5A C6 RBF doub 288 n y C5A C9A RBF sing 289 n y C6 C7 RBF sing 290 n y C6 HC6 RBF sing 291 n n C7 C7M RBF sing 292 n n C7 C8 RBF doub 293 n y C7M HC71 RBF sing 294 n n C7M HC72 RBF sing 295 n n C7M HC73 RBF sing 296 n n C8 C8M RBF sing 297 n n C8 C9 RBF sing 298 n y C8M HC81 RBF sing 299 n n C8M HC82 RBF sing 300 n n C8M HC83 RBF sing 301 n n C9 C9A RBF doub 302 n y C9 HC9 RBF sing 303 n n C9A N10 RBF sing 304 n n N10 C10 RBF sing 305 n n N10 C1' RBF sing 306 n n C1' C2' RBF sing 307 n n C1' HC11 RBF sing 308 n n C1' HC12 RBF sing 309 n n C2' O2' RBF sing 310 n n C2' C3' RBF sing 311 n n C2' HC2' RBF sing 312 n n O2' HO2' RBF sing 313 n n C3' O3' RBF sing 314 n n C3' C4' RBF sing 315 n n C3' HC3' RBF sing 316 n n O3' HO3' RBF sing 317 n n C4' O4' RBF sing 318 n n C4' C5' RBF sing 319 n n C4' HC4' RBF sing 320 n n O4' HO4' RBF sing 321 n n C5' O5' RBF sing 322 n n C5' HC51 RBF sing 323 n n C5' HC52 RBF sing 324 n n O5' HO5' RBF sing 325 n n # _atom_sites.entry_id 4E0F _atom_sites.fract_transf_matrix[1][1] 0.01429 _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] 0.010891 _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] 0.010125 _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 D 2 RBF A 1 301 1 RBF RBF . E 3 HOH A 1 401 1 HOH HOH . E 3 HOH A 2 402 2 HOH HOH . E 3 HOH A 3 403 3 HOH HOH . E 3 HOH A 4 404 4 HOH HOH . E 3 HOH A 5 405 5 HOH HOH . E 3 HOH A 6 406 6 HOH HOH . E 3 HOH A 7 407 7 HOH HOH . E 3 HOH A 8 408 8 HOH HOH . E 3 HOH A 9 409 9 HOH HOH . E 3 HOH A 10 410 11 HOH HOH . E 3 HOH A 11 411 12 HOH HOH . E 3 HOH A 12 412 13 HOH HOH . E 3 HOH A 13 413 14 HOH HOH . E 3 HOH A 14 414 15 HOH HOH . E 3 HOH A 15 415 29 HOH HOH . E 3 HOH A 16 416 30 HOH HOH . E 3 HOH A 17 417 31 HOH HOH . E 3 HOH A 18 418 32 HOH HOH . E 3 HOH A 19 419 33 HOH HOH . E 3 HOH A 20 420 34 HOH HOH . E 3 HOH A 21 421 35 HOH HOH . E 3 HOH A 22 422 36 HOH HOH . E 3 HOH A 23 423 39 HOH HOH . E 3 HOH A 24 424 40 HOH HOH . E 3 HOH A 25 425 42 HOH HOH . E 3 HOH A 26 426 43 HOH HOH . E 3 HOH A 27 427 66 HOH HOH . F 3 HOH B 1 301 10 HOH HOH . F 3 HOH B 2 302 16 HOH HOH . F 3 HOH B 3 303 17 HOH HOH . F 3 HOH B 4 304 27 HOH HOH . F 3 HOH B 5 305 28 HOH HOH . F 3 HOH B 6 306 37 HOH HOH . F 3 HOH B 7 307 38 HOH HOH . F 3 HOH B 8 308 45 HOH HOH . F 3 HOH B 9 309 46 HOH HOH . F 3 HOH B 10 310 47 HOH HOH . F 3 HOH B 11 311 48 HOH HOH . F 3 HOH B 12 312 49 HOH HOH . F 3 HOH B 13 313 50 HOH HOH . F 3 HOH B 14 314 51 HOH HOH . F 3 HOH B 15 315 52 HOH HOH . F 3 HOH B 16 316 53 HOH HOH . F 3 HOH B 17 317 54 HOH HOH . F 3 HOH B 18 318 63 HOH HOH . F 3 HOH B 19 319 64 HOH HOH . G 3 HOH C 1 301 18 HOH HOH . G 3 HOH C 2 302 19 HOH HOH . G 3 HOH C 3 303 20 HOH HOH . G 3 HOH C 4 304 21 HOH HOH . G 3 HOH C 5 305 22 HOH HOH . G 3 HOH C 6 306 23 HOH HOH . G 3 HOH C 7 307 24 HOH HOH . G 3 HOH C 8 308 25 HOH HOH . G 3 HOH C 9 309 26 HOH HOH . G 3 HOH C 10 310 41 HOH HOH . G 3 HOH C 11 311 44 HOH HOH . G 3 HOH C 12 312 55 HOH HOH . G 3 HOH C 13 313 56 HOH HOH . G 3 HOH C 14 314 57 HOH HOH . G 3 HOH C 15 315 58 HOH HOH . G 3 HOH C 16 316 59 HOH HOH . G 3 HOH C 17 317 60 HOH HOH . G 3 HOH C 18 318 61 HOH HOH . G 3 HOH C 19 319 62 HOH HOH . G 3 HOH C 20 320 65 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 -12.707 8.103 31.175 1 30.17 ? N1 RBF 301 A 1 HETATM 2 C C2 RBF . . . D 2 -13.992 8.089 31.607 1 30.27 ? C2 RBF 301 A 1 HETATM 3 O O2 RBF . . . D 2 -14.812 8.844 31.047 1 30.26 ? O2 RBF 301 A 1 HETATM 4 N N3 RBF . . . D 2 -14.408 7.298 32.616 1 30.51 ? N3 RBF 301 A 1 HETATM 5 C C4 RBF . . . D 2 -13.585 6.46 33.268 1 30.31 ? C4 RBF 301 A 1 HETATM 6 O O4 RBF . . . D 2 -14.005 5.737 34.197 1 29.89 ? O4 RBF 301 A 1 HETATM 7 C C4A RBF . . . D 2 -12.161 6.416 32.852 1 30.37 ? C4A RBF 301 A 1 HETATM 8 N N5 RBF . . . D 2 -11.263 5.603 33.452 1 30.69 ? N5 RBF 301 A 1 HETATM 9 C C5A RBF . . . D 2 -9.968 5.581 33.054 1 30.8 ? C5A RBF 301 A 1 HETATM 10 C C6 RBF . . . D 2 -9.073 4.731 33.701 1 31.06 ? C6 RBF 301 A 1 HETATM 11 C C7 RBF . . . D 2 -7.735 4.686 33.316 1 31.05 ? C7 RBF 301 A 1 HETATM 12 C C7M RBF . . . D 2 -6.794 3.751 34.038 1 30.94 ? C7M RBF 301 A 1 HETATM 13 C C8 RBF . . . D 2 -7.262 5.556 32.197 1 31 ? C8 RBF 301 A 1 HETATM 14 C C8M RBF . . . D 2 -5.823 5.532 31.758 1 31.13 ? C8M RBF 301 A 1 HETATM 15 C C9 RBF . . . D 2 -8.154 6.41 31.548 1 30.83 ? C9 RBF 301 A 1 HETATM 16 C C9A RBF . . . D 2 -9.496 6.458 31.934 1 30.63 ? C9A RBF 301 A 1 HETATM 17 N N10 RBF . . . D 2 -10.425 7.317 31.29 1 30.21 ? N10 RBF 301 A 1 HETATM 18 C C10 RBF . . . D 2 -11.763 7.312 31.736 1 30.23 ? C10 RBF 301 A 1 HETATM 19 C C1' RBF . . . D 2 -10.023 8.197 30.185 1 29.99 ? C1' RBF 301 A 1 HETATM 20 C C2' RBF . . . D 2 -10.573 7.663 28.861 1 29.61 ? C2' RBF 301 A 1 HETATM 21 O O2' RBF . . . D 2 -10.025 6.363 28.598 1 29.6 ? O2' RBF 301 A 1 HETATM 22 C C3' RBF . . . D 2 -10.262 8.621 27.712 1 29.34 ? C3' RBF 301 A 1 HETATM 23 O O3' RBF . . . D 2 -10.808 9.912 28.016 1 29.26 ? O3' RBF 301 A 1 HETATM 24 C C4' RBF . . . D 2 -10.817 8.143 26.368 1 28.99 ? C4' RBF 301 A 1 HETATM 25 O O4' RBF . . . D 2 -10.212 6.898 25.988 1 28.09 ? O4' RBF 301 A 1 HETATM 26 C C5' RBF . . . D 2 -10.566 9.173 25.271 1 28.86 ? C5' RBF 301 A 1 HETATM 27 O O5' RBF . . . D 2 -9.169 9.205 24.954 1 28.69 ? O5' RBF 301 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #