data_8RAF # _model_server_result.job_id T85VPg8TgThks_c6qRPuaA _model_server_result.datetime_utc '2024-11-14 05:07:12' _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 8raf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 8RAF # _exptl.entry_id 8RAF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _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 100.8 _cell.angle_gamma 90 _cell.entry_id 8RAF _cell.length_a 85.392 _cell.length_b 72.627 _cell.length_c 52.244 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RAF _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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 1,2 # 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' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 75.602451 0 51.318615 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 145 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 143 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C4A _struct_conn.ptnr2_label_comp_id PLP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id PLP _struct_conn.ptnr2_auth_seq_id 301 _struct_conn.ptnr2_symmetry 1_555 _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 1.318 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C8 H10 N O6 P' _chem_comp.formula_weight 247.142 _chem_comp.id PLP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN B6 Phosphate' # 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 PLP doub 260 n y N1 C6 PLP sing 261 n y C2 C2A PLP sing 262 n n C2 C3 PLP sing 263 n y C2A H2A1 PLP sing 264 n n C2A H2A2 PLP sing 265 n n C2A H2A3 PLP sing 266 n n C3 O3 PLP sing 267 n n C3 C4 PLP doub 268 n y O3 HO3 PLP sing 269 n n C4 C4A PLP sing 270 n n C4 C5 PLP sing 271 n y C4A O4A PLP doub 272 n n C4A H4A PLP sing 273 n n C5 C6 PLP doub 274 n y C5 C5A PLP sing 275 n n C6 H6 PLP sing 276 n n C5A O4P PLP sing 277 n n C5A H5A1 PLP sing 278 n n C5A H5A2 PLP sing 279 n n O4P P PLP sing 280 n n P O1P PLP doub 281 n n P O2P PLP sing 282 n n P O3P PLP sing 283 n n O2P HOP2 PLP sing 284 n n O3P HOP3 PLP sing 285 n n # _atom_sites.entry_id 8RAF _atom_sites.fract_transf_matrix[1][1] 0.011711 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002233 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013769 _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] 0.019486 _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 PLP A 1 301 301 PLP PLP . C 3 HOH A 1 401 153 HOH HOH . C 3 HOH A 2 402 120 HOH HOH . C 3 HOH A 3 403 91 HOH HOH . C 3 HOH A 4 404 116 HOH HOH . C 3 HOH A 5 405 118 HOH HOH . C 3 HOH A 6 406 92 HOH HOH . C 3 HOH A 7 407 95 HOH HOH . C 3 HOH A 8 408 186 HOH HOH . C 3 HOH A 9 409 131 HOH HOH . C 3 HOH A 10 410 105 HOH HOH . C 3 HOH A 11 411 22 HOH HOH . C 3 HOH A 12 412 45 HOH HOH . C 3 HOH A 13 413 17 HOH HOH . C 3 HOH A 14 414 179 HOH HOH . C 3 HOH A 15 415 117 HOH HOH . C 3 HOH A 16 416 80 HOH HOH . C 3 HOH A 17 417 44 HOH HOH . C 3 HOH A 18 418 71 HOH HOH . C 3 HOH A 19 419 112 HOH HOH . C 3 HOH A 20 420 65 HOH HOH . C 3 HOH A 21 421 34 HOH HOH . C 3 HOH A 22 422 19 HOH HOH . C 3 HOH A 23 423 30 HOH HOH . C 3 HOH A 24 424 134 HOH HOH . C 3 HOH A 25 425 170 HOH HOH . C 3 HOH A 26 426 130 HOH HOH . C 3 HOH A 27 427 162 HOH HOH . C 3 HOH A 28 428 78 HOH HOH . C 3 HOH A 29 429 108 HOH HOH . C 3 HOH A 30 430 175 HOH HOH . C 3 HOH A 31 431 190 HOH HOH . C 3 HOH A 32 432 82 HOH HOH . C 3 HOH A 33 433 40 HOH HOH . C 3 HOH A 34 434 2 HOH HOH . C 3 HOH A 35 435 79 HOH HOH . C 3 HOH A 36 436 169 HOH HOH . C 3 HOH A 37 437 89 HOH HOH . C 3 HOH A 38 438 27 HOH HOH . C 3 HOH A 39 439 145 HOH HOH . C 3 HOH A 40 440 47 HOH HOH . C 3 HOH A 41 441 3 HOH HOH . C 3 HOH A 42 442 52 HOH HOH . C 3 HOH A 43 443 33 HOH HOH . C 3 HOH A 44 444 191 HOH HOH . C 3 HOH A 45 445 63 HOH HOH . C 3 HOH A 46 446 150 HOH HOH . C 3 HOH A 47 447 64 HOH HOH . C 3 HOH A 48 448 123 HOH HOH . C 3 HOH A 49 449 125 HOH HOH . C 3 HOH A 50 450 15 HOH HOH . C 3 HOH A 51 451 146 HOH HOH . C 3 HOH A 52 452 121 HOH HOH . C 3 HOH A 53 453 51 HOH HOH . C 3 HOH A 54 454 18 HOH HOH . C 3 HOH A 55 455 159 HOH HOH . C 3 HOH A 56 456 5 HOH HOH . C 3 HOH A 57 457 1 HOH HOH . C 3 HOH A 58 458 9 HOH HOH . C 3 HOH A 59 459 60 HOH HOH . C 3 HOH A 60 460 53 HOH HOH . C 3 HOH A 61 461 119 HOH HOH . C 3 HOH A 62 462 35 HOH HOH . C 3 HOH A 63 463 11 HOH HOH . C 3 HOH A 64 464 61 HOH HOH . C 3 HOH A 65 465 70 HOH HOH . C 3 HOH A 66 466 96 HOH HOH . C 3 HOH A 67 467 180 HOH HOH . C 3 HOH A 68 468 100 HOH HOH . C 3 HOH A 69 469 56 HOH HOH . C 3 HOH A 70 470 85 HOH HOH . C 3 HOH A 71 471 21 HOH HOH . C 3 HOH A 72 472 43 HOH HOH . C 3 HOH A 73 473 42 HOH HOH . C 3 HOH A 74 474 83 HOH HOH . C 3 HOH A 75 475 67 HOH HOH . C 3 HOH A 76 476 62 HOH HOH . C 3 HOH A 77 477 86 HOH HOH . C 3 HOH A 78 478 93 HOH HOH . C 3 HOH A 79 479 172 HOH HOH . C 3 HOH A 80 480 84 HOH HOH . C 3 HOH A 81 481 38 HOH HOH . C 3 HOH A 82 482 8 HOH HOH . C 3 HOH A 83 483 148 HOH HOH . C 3 HOH A 84 484 20 HOH HOH . C 3 HOH A 85 485 66 HOH HOH . C 3 HOH A 86 486 25 HOH HOH . C 3 HOH A 87 487 32 HOH HOH . C 3 HOH A 88 488 74 HOH HOH . C 3 HOH A 89 489 132 HOH HOH . C 3 HOH A 90 490 14 HOH HOH . C 3 HOH A 91 491 49 HOH HOH . C 3 HOH A 92 492 111 HOH HOH . C 3 HOH A 93 493 16 HOH HOH . C 3 HOH A 94 494 68 HOH HOH . C 3 HOH A 95 495 7 HOH HOH . C 3 HOH A 96 496 98 HOH HOH . C 3 HOH A 97 497 13 HOH HOH . C 3 HOH A 98 498 4 HOH HOH . C 3 HOH A 99 499 94 HOH HOH . C 3 HOH A 100 500 142 HOH HOH . C 3 HOH A 101 501 50 HOH HOH . C 3 HOH A 102 502 133 HOH HOH . C 3 HOH A 103 503 183 HOH HOH . C 3 HOH A 104 504 151 HOH HOH . C 3 HOH A 105 505 182 HOH HOH . C 3 HOH A 106 506 156 HOH HOH . C 3 HOH A 107 507 36 HOH HOH . C 3 HOH A 108 508 37 HOH HOH . C 3 HOH A 109 509 10 HOH HOH . C 3 HOH A 110 510 6 HOH HOH . C 3 HOH A 111 511 26 HOH HOH . C 3 HOH A 112 512 28 HOH HOH . C 3 HOH A 113 513 124 HOH HOH . C 3 HOH A 114 514 185 HOH HOH . C 3 HOH A 115 515 54 HOH HOH . C 3 HOH A 116 516 101 HOH HOH . C 3 HOH A 117 517 160 HOH HOH . C 3 HOH A 118 518 161 HOH HOH . C 3 HOH A 119 519 171 HOH HOH . C 3 HOH A 120 520 73 HOH HOH . C 3 HOH A 121 521 168 HOH HOH . C 3 HOH A 122 522 77 HOH HOH . C 3 HOH A 123 523 23 HOH HOH . C 3 HOH A 124 524 48 HOH HOH . C 3 HOH A 125 525 69 HOH HOH . C 3 HOH A 126 526 29 HOH HOH . C 3 HOH A 127 527 76 HOH HOH . C 3 HOH A 128 528 122 HOH HOH . C 3 HOH A 129 529 39 HOH HOH . C 3 HOH A 130 530 174 HOH HOH . C 3 HOH A 131 531 157 HOH HOH . C 3 HOH A 132 532 106 HOH HOH . C 3 HOH A 133 533 166 HOH HOH . C 3 HOH A 134 534 176 HOH HOH . C 3 HOH A 135 535 184 HOH HOH . C 3 HOH A 136 536 55 HOH HOH . C 3 HOH A 137 537 141 HOH HOH . C 3 HOH A 138 538 178 HOH HOH . C 3 HOH A 139 539 41 HOH HOH . C 3 HOH A 140 540 143 HOH HOH . C 3 HOH A 141 541 155 HOH HOH . C 3 HOH A 142 542 138 HOH HOH . C 3 HOH A 143 543 109 HOH HOH . C 3 HOH A 144 544 31 HOH HOH . C 3 HOH A 145 545 113 HOH HOH . C 3 HOH A 146 546 177 HOH HOH . C 3 HOH A 147 547 107 HOH HOH . C 3 HOH A 148 548 129 HOH HOH . C 3 HOH A 149 549 24 HOH HOH . C 3 HOH A 150 550 104 HOH HOH . C 3 HOH A 151 551 12 HOH HOH . C 3 HOH A 152 552 75 HOH HOH . C 3 HOH A 153 553 72 HOH HOH . C 3 HOH A 154 554 81 HOH HOH . C 3 HOH A 155 555 128 HOH HOH . C 3 HOH A 156 556 58 HOH HOH . C 3 HOH A 157 557 102 HOH HOH . C 3 HOH A 158 558 147 HOH HOH . C 3 HOH A 159 559 165 HOH HOH . C 3 HOH A 160 560 87 HOH HOH . C 3 HOH A 161 561 136 HOH HOH . C 3 HOH A 162 562 181 HOH HOH . C 3 HOH A 163 563 149 HOH HOH . C 3 HOH A 164 564 127 HOH HOH . C 3 HOH A 165 565 103 HOH HOH . C 3 HOH A 166 566 115 HOH HOH . C 3 HOH A 167 567 114 HOH HOH . C 3 HOH A 168 568 126 HOH HOH . C 3 HOH A 169 569 57 HOH HOH . C 3 HOH A 170 570 163 HOH HOH . C 3 HOH A 171 571 97 HOH HOH . C 3 HOH A 172 572 187 HOH HOH . C 3 HOH A 173 573 137 HOH HOH . C 3 HOH A 174 574 139 HOH HOH . C 3 HOH A 175 575 152 HOH HOH . C 3 HOH A 176 576 59 HOH HOH . C 3 HOH A 177 577 164 HOH HOH . C 3 HOH A 178 578 88 HOH HOH . C 3 HOH A 179 579 144 HOH HOH . C 3 HOH A 180 580 189 HOH HOH . C 3 HOH A 181 581 135 HOH HOH . C 3 HOH A 182 582 173 HOH HOH . C 3 HOH A 183 583 110 HOH HOH . C 3 HOH A 184 584 90 HOH HOH . C 3 HOH A 185 585 158 HOH HOH . C 3 HOH A 186 586 46 HOH HOH . C 3 HOH A 187 587 188 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 PLP . . . B 2 27.146 4.212 16.952 1 14.44 ? N1 PLP 301 A 1 HETATM 2 C C2 PLP . . . B 2 28.02 3.353 17.46 1 14.96 ? C2 PLP 301 A 1 HETATM 3 C C2A PLP . . . B 2 29.008 3.824 18.481 1 14.46 ? C2A PLP 301 A 1 HETATM 4 C C3 PLP . . . B 2 28.03 2.035 17.037 1 15.75 ? C3 PLP 301 A 1 HETATM 5 O O3 PLP . . . B 2 28.942 1.186 17.568 1 17.96 ? O3 PLP 301 A 1 HETATM 6 C C4 PLP . . . B 2 27.16 1.609 16.022 1 15.07 ? C4 PLP 301 A 1 HETATM 7 C C4A PLP . . . B 2 27.322 0.217 15.59 1 16.21 ? C4A PLP 301 A 1 HETATM 8 C C5 PLP . . . B 2 26.237 2.538 15.512 1 14.65 ? C5 PLP 301 A 1 HETATM 9 C C6 PLP . . . B 2 26.266 3.814 16.012 1 14.77 ? C6 PLP 301 A 1 HETATM 10 C C5A PLP . . . B 2 25.189 2.167 14.505 1 13.48 ? C5A PLP 301 A 1 HETATM 11 O O4P PLP . . . B 2 25.726 1.606 13.28 1 11.25 ? O4P PLP 301 A 1 HETATM 12 P P PLP . . . B 2 24.745 0.727 12.323 1 11.22 ? P PLP 301 A 1 HETATM 13 O O1P PLP . . . B 2 25.738 0.311 11.243 1 9.77 ? O1P PLP 301 A 1 HETATM 14 O O2P PLP . . . B 2 24.268 -0.41 13.233 1 10.45 ? O2P PLP 301 A 1 HETATM 15 O O3P PLP . . . B 2 23.508 1.54 11.859 1 10.33 ? O3P PLP 301 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 15 #