data_5IOR # _model_server_result.job_id d4XhoVyYN_kvBwsFIdX-OQ _model_server_result.datetime_utc '2024-11-28 05:20:27' _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 5ior # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 5IOR # _exptl.entry_id 5IOR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 376.364 _entity.id 4 _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 5IOR _cell.length_a 109.679 _cell.length_b 109.679 _cell.length_c 119.864 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IOR _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 10_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 4 'crystal symmetry operation' 15_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _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 401 n n N1 C10 RBF doub 402 n n C2 O2 RBF doub 403 n n C2 N3 RBF sing 404 n n N3 C4 RBF sing 405 n n N3 HN3 RBF sing 406 n n C4 O4 RBF doub 407 n n C4 C4A RBF sing 408 n n C4A N5 RBF doub 409 n n C4A C10 RBF sing 410 n n N5 C5A RBF sing 411 n n C5A C6 RBF doub 412 n y C5A C9A RBF sing 413 n y C6 C7 RBF sing 414 n y C6 HC6 RBF sing 415 n n C7 C7M RBF sing 416 n n C7 C8 RBF doub 417 n y C7M HC71 RBF sing 418 n n C7M HC72 RBF sing 419 n n C7M HC73 RBF sing 420 n n C8 C8M RBF sing 421 n n C8 C9 RBF sing 422 n y C8M HC81 RBF sing 423 n n C8M HC82 RBF sing 424 n n C8M HC83 RBF sing 425 n n C9 C9A RBF doub 426 n y C9 HC9 RBF sing 427 n n C9A N10 RBF sing 428 n n N10 C10 RBF sing 429 n n N10 C1' RBF sing 430 n n C1' C2' RBF sing 431 n n C1' HC11 RBF sing 432 n n C1' HC12 RBF sing 433 n n C2' O2' RBF sing 434 n n C2' C3' RBF sing 435 n n C2' HC2' RBF sing 436 n n O2' HO2' RBF sing 437 n n C3' O3' RBF sing 438 n n C3' C4' RBF sing 439 n n C3' HC3' RBF sing 440 n n O3' HO3' RBF sing 441 n n C4' O4' RBF sing 442 n n C4' C5' RBF sing 443 n n C4' HC4' RBF sing 444 n n O4' HO4' RBF sing 445 n n C5' O5' RBF sing 446 n n C5' HC51 RBF sing 447 n n C5' HC52 RBF sing 448 n n O5' HO5' RBF sing 449 n n # _atom_sites.entry_id 5IOR _atom_sites.fract_transf_matrix[1][1] 0.009118 _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] 0.009118 _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] 0.008343 _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 FAD A 1 301 315 FAD FAD . C 3 DUS A 1 302 1 DUS DUS . D 4 RBF A 1 303 1 RBF RBF . E 5 HOH A 1 401 48 HOH HOH . E 5 HOH A 2 402 64 HOH HOH . E 5 HOH A 3 403 36 HOH HOH . E 5 HOH A 4 404 22 HOH HOH . E 5 HOH A 5 405 57 HOH HOH . E 5 HOH A 6 406 34 HOH HOH . E 5 HOH A 7 407 8 HOH HOH . E 5 HOH A 8 408 81 HOH HOH . E 5 HOH A 9 409 33 HOH HOH . E 5 HOH A 10 410 56 HOH HOH . E 5 HOH A 11 411 18 HOH HOH . E 5 HOH A 12 412 86 HOH HOH . E 5 HOH A 13 413 38 HOH HOH . E 5 HOH A 14 414 23 HOH HOH . E 5 HOH A 15 415 7 HOH HOH . E 5 HOH A 16 416 102 HOH HOH . E 5 HOH A 17 417 9 HOH HOH . E 5 HOH A 18 418 99 HOH HOH . E 5 HOH A 19 419 3 HOH HOH . E 5 HOH A 20 420 49 HOH HOH . E 5 HOH A 21 421 32 HOH HOH . E 5 HOH A 22 422 103 HOH HOH . E 5 HOH A 23 423 4 HOH HOH . E 5 HOH A 24 424 80 HOH HOH . E 5 HOH A 25 425 44 HOH HOH . E 5 HOH A 26 426 20 HOH HOH . E 5 HOH A 27 427 19 HOH HOH . E 5 HOH A 28 428 84 HOH HOH . E 5 HOH A 29 429 65 HOH HOH . E 5 HOH A 30 430 12 HOH HOH . E 5 HOH A 31 431 108 HOH HOH . E 5 HOH A 32 432 73 HOH HOH . E 5 HOH A 33 433 30 HOH HOH . E 5 HOH A 34 434 82 HOH HOH . E 5 HOH A 35 435 16 HOH HOH . E 5 HOH A 36 436 87 HOH HOH . E 5 HOH A 37 437 79 HOH HOH . E 5 HOH A 38 438 78 HOH HOH . E 5 HOH A 39 439 43 HOH HOH . E 5 HOH A 40 440 62 HOH HOH . E 5 HOH A 41 441 42 HOH HOH . E 5 HOH A 42 442 106 HOH HOH . E 5 HOH A 43 443 51 HOH HOH . E 5 HOH A 44 444 29 HOH HOH . E 5 HOH A 45 445 47 HOH HOH . E 5 HOH A 46 446 54 HOH HOH . E 5 HOH A 47 447 71 HOH HOH . E 5 HOH A 48 448 93 HOH HOH . E 5 HOH A 49 449 11 HOH HOH . E 5 HOH A 50 450 83 HOH HOH . E 5 HOH A 51 451 59 HOH HOH . E 5 HOH A 52 452 94 HOH HOH . E 5 HOH A 53 453 45 HOH HOH . E 5 HOH A 54 454 89 HOH HOH . E 5 HOH A 55 455 6 HOH HOH . E 5 HOH A 56 456 40 HOH HOH . E 5 HOH A 57 457 13 HOH HOH . E 5 HOH A 58 458 24 HOH HOH . E 5 HOH A 59 459 2 HOH HOH . E 5 HOH A 60 460 10 HOH HOH . E 5 HOH A 61 461 35 HOH HOH . E 5 HOH A 62 462 14 HOH HOH . E 5 HOH A 63 463 25 HOH HOH . E 5 HOH A 64 464 21 HOH HOH . E 5 HOH A 65 465 28 HOH HOH . E 5 HOH A 66 466 26 HOH HOH . E 5 HOH A 67 467 5 HOH HOH . E 5 HOH A 68 468 37 HOH HOH . E 5 HOH A 69 469 53 HOH HOH . E 5 HOH A 70 470 90 HOH HOH . E 5 HOH A 71 471 92 HOH HOH . E 5 HOH A 72 472 70 HOH HOH . E 5 HOH A 73 473 39 HOH HOH . E 5 HOH A 74 474 105 HOH HOH . E 5 HOH A 75 475 55 HOH HOH . E 5 HOH A 76 476 67 HOH HOH . E 5 HOH A 77 477 66 HOH HOH . E 5 HOH A 78 478 41 HOH HOH . E 5 HOH A 79 479 107 HOH HOH . E 5 HOH A 80 480 50 HOH HOH . E 5 HOH A 81 481 27 HOH HOH . E 5 HOH A 82 482 74 HOH HOH . E 5 HOH A 83 483 17 HOH HOH . E 5 HOH A 84 484 63 HOH HOH . E 5 HOH A 85 485 31 HOH HOH . E 5 HOH A 86 486 69 HOH HOH . E 5 HOH A 87 487 15 HOH HOH . E 5 HOH A 88 488 52 HOH HOH . E 5 HOH A 89 489 91 HOH HOH . E 5 HOH A 90 490 46 HOH HOH . E 5 HOH A 91 491 68 HOH HOH . E 5 HOH A 92 492 97 HOH HOH . E 5 HOH A 93 493 98 HOH HOH . E 5 HOH A 94 494 58 HOH HOH . E 5 HOH A 95 495 95 HOH HOH . E 5 HOH A 96 496 104 HOH HOH . E 5 HOH A 97 497 96 HOH HOH . E 5 HOH A 98 498 100 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 4 0.057 24.744 7.759 1 59.65 ? N1 RBF 303 A 1 HETATM 2 C C2 RBF . . . D 4 -0.436 25.64 6.859 1 56.99 ? C2 RBF 303 A 1 HETATM 3 O O2 RBF . . . D 4 -0.329 26.857 7.107 1 51.62 ? O2 RBF 303 A 1 HETATM 4 N N3 RBF . . . D 4 -1.022 25.254 5.703 1 60.84 ? N3 RBF 303 A 1 HETATM 5 C C4 RBF . . . D 4 -1.159 23.945 5.367 1 59.55 ? C4 RBF 303 A 1 HETATM 6 O O4 RBF . . . D 4 -1.708 23.62 4.283 1 55.94 ? O4 RBF 303 A 1 HETATM 7 C C4A RBF . . . D 4 -0.643 22.904 6.311 1 57.89 ? C4A RBF 303 A 1 HETATM 8 N N5 RBF . . . D 4 -0.735 21.573 6.049 1 55.93 ? N5 RBF 303 A 1 HETATM 9 C C5A RBF . . . D 4 -0.248 20.646 6.927 1 55.9 ? C5A RBF 303 A 1 HETATM 10 C C6 RBF . . . D 4 -0.368 19.291 6.603 1 54.98 ? C6 RBF 303 A 1 HETATM 11 C C7 RBF . . . D 4 0.107 18.296 7.449 1 52.22 ? C7 RBF 303 A 1 HETATM 12 C C7M RBF . . . D 4 -0.04 16.839 7.061 1 49.03 ? C7M RBF 303 A 1 HETATM 13 C C8 RBF . . . D 4 0.748 18.699 8.732 1 53.22 ? C8 RBF 303 A 1 HETATM 14 C C8M RBF . . . D 4 1.257 17.638 9.66 1 50.99 ? C8M RBF 303 A 1 HETATM 15 C C9 RBF . . . D 4 0.878 20.049 9.075 1 53.05 ? C9 RBF 303 A 1 HETATM 16 C C9A RBF . . . D 4 0.406 21.059 8.219 1 55.27 ? C9A RBF 303 A 1 HETATM 17 N N10 RBF . . . D 4 0.51 22.458 8.528 1 56.76 ? N10 RBF 303 A 1 HETATM 18 C C10 RBF . . . D 4 -0.003 23.393 7.572 1 57.81 ? C10 RBF 303 A 1 HETATM 19 C C1' RBF . . . D 4 1.168 22.946 9.77 1 56.18 ? C1' RBF 303 A 1 HETATM 20 C C2' RBF . . . D 4 0.281 23.137 11.015 1 57.99 ? C2' RBF 303 A 1 HETATM 21 O O2' RBF . . . D 4 -0.44 21.924 11.306 1 55.53 ? O2' RBF 303 A 1 HETATM 22 C C3' RBF . . . D 4 -0.673 24.346 10.933 1 60.29 ? C3' RBF 303 A 1 HETATM 23 O O3' RBF . . . D 4 -0.052 25.382 10.155 1 57.42 ? O3' RBF 303 A 1 HETATM 24 C C4' RBF . . . D 4 -1.038 24.947 12.306 1 66.3 ? C4' RBF 303 A 1 HETATM 25 O O4' RBF . . . D 4 -0.615 24.101 13.384 1 67.84 ? O4' RBF 303 A 1 HETATM 26 C C5' RBF . . . D 4 -2.53 25.211 12.508 1 70.17 ? C5' RBF 303 A 1 HETATM 27 O O5' RBF . . . D 4 -2.753 25.656 13.858 1 77.19 ? O5' RBF 303 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 27 #