data_2D63 # _model_server_result.job_id jGSsR5ZpXksE23WY5Og2-A _model_server_result.datetime_utc '2025-03-06 09:53:22' _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 2d63 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":413}' # _entry.id 2D63 # _exptl.entry_id 2D63 _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 90 _cell.angle_gamma 90 _cell.entry_id 2D63 _cell.length_a 157.658 _cell.length_b 85.481 _cell.length_c 78.295 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2D63 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _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 246 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 258 _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 413 _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 1.366 _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' # _atom_sites.entry_id 2D63 _atom_sites.fract_transf_matrix[1][1] 0.006343 _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] 0.011699 _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] 0.012772 _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 1 413 413 PLP PLP . C 3 IVA A 1 414 414 IVA IVA . D 4 HOH A 1 415 1 HOH HOH . D 4 HOH A 2 416 2 HOH HOH . D 4 HOH A 3 417 3 HOH HOH . D 4 HOH A 4 418 4 HOH HOH . D 4 HOH A 5 419 5 HOH HOH . D 4 HOH A 6 420 6 HOH HOH . D 4 HOH A 7 421 7 HOH HOH . D 4 HOH A 8 422 8 HOH HOH . D 4 HOH A 9 423 9 HOH HOH . D 4 HOH A 10 424 10 HOH HOH . D 4 HOH A 11 425 11 HOH HOH . D 4 HOH A 12 426 12 HOH HOH . D 4 HOH A 13 427 13 HOH HOH . D 4 HOH A 14 428 14 HOH HOH . D 4 HOH A 15 429 15 HOH HOH . D 4 HOH A 16 430 16 HOH HOH . D 4 HOH A 17 431 17 HOH HOH . D 4 HOH A 18 432 18 HOH HOH . D 4 HOH A 19 433 19 HOH HOH . D 4 HOH A 20 434 20 HOH HOH . D 4 HOH A 21 435 21 HOH HOH . D 4 HOH A 22 436 22 HOH HOH . D 4 HOH A 23 437 23 HOH HOH . D 4 HOH A 24 438 24 HOH HOH . D 4 HOH A 25 439 25 HOH HOH . D 4 HOH A 26 440 26 HOH HOH . D 4 HOH A 27 441 27 HOH HOH . D 4 HOH A 28 442 28 HOH HOH . D 4 HOH A 29 443 29 HOH HOH . D 4 HOH A 30 444 30 HOH HOH . D 4 HOH A 31 445 31 HOH HOH . D 4 HOH A 32 446 32 HOH HOH . D 4 HOH A 33 447 33 HOH HOH . D 4 HOH A 34 448 34 HOH HOH . D 4 HOH A 35 449 35 HOH HOH . D 4 HOH A 36 450 36 HOH HOH . D 4 HOH A 37 451 37 HOH HOH . D 4 HOH A 38 452 38 HOH HOH . D 4 HOH A 39 453 40 HOH HOH . D 4 HOH A 40 454 41 HOH HOH . D 4 HOH A 41 455 42 HOH HOH . D 4 HOH A 42 456 43 HOH HOH . D 4 HOH A 43 457 45 HOH HOH . D 4 HOH A 44 458 46 HOH HOH . D 4 HOH A 45 459 47 HOH HOH . D 4 HOH A 46 460 48 HOH HOH . D 4 HOH A 47 461 49 HOH HOH . D 4 HOH A 48 462 50 HOH HOH . D 4 HOH A 49 463 51 HOH HOH . D 4 HOH A 50 464 52 HOH HOH . D 4 HOH A 51 465 53 HOH HOH . D 4 HOH A 52 466 54 HOH HOH . D 4 HOH A 53 467 55 HOH HOH . D 4 HOH A 54 468 56 HOH HOH . D 4 HOH A 55 469 57 HOH HOH . D 4 HOH A 56 470 58 HOH HOH . D 4 HOH A 57 471 59 HOH HOH . D 4 HOH A 58 472 60 HOH HOH . D 4 HOH A 59 473 61 HOH HOH . D 4 HOH A 60 474 62 HOH HOH . D 4 HOH A 61 475 63 HOH HOH . D 4 HOH A 62 476 64 HOH HOH . D 4 HOH A 63 477 65 HOH HOH . D 4 HOH A 64 478 66 HOH HOH . D 4 HOH A 65 479 67 HOH HOH . D 4 HOH A 66 480 68 HOH HOH . D 4 HOH A 67 481 69 HOH HOH . D 4 HOH A 68 482 70 HOH HOH . D 4 HOH A 69 483 71 HOH HOH . D 4 HOH A 70 484 72 HOH HOH . D 4 HOH A 71 485 73 HOH HOH . D 4 HOH A 72 486 74 HOH HOH . D 4 HOH A 73 487 75 HOH HOH . D 4 HOH A 74 488 76 HOH HOH . D 4 HOH A 75 489 77 HOH HOH . D 4 HOH A 76 490 78 HOH HOH . D 4 HOH A 77 491 79 HOH HOH . D 4 HOH A 78 492 80 HOH HOH . D 4 HOH A 79 493 82 HOH HOH . D 4 HOH A 80 494 83 HOH HOH . D 4 HOH A 81 495 84 HOH HOH . D 4 HOH A 82 496 85 HOH HOH . D 4 HOH A 83 497 86 HOH HOH . D 4 HOH A 84 498 87 HOH HOH . D 4 HOH A 85 499 88 HOH HOH . D 4 HOH A 86 500 89 HOH HOH . D 4 HOH A 87 501 90 HOH HOH . D 4 HOH A 88 502 91 HOH HOH . D 4 HOH A 89 503 92 HOH HOH . D 4 HOH A 90 504 93 HOH HOH . D 4 HOH A 91 505 94 HOH HOH . D 4 HOH A 92 506 95 HOH HOH . D 4 HOH A 93 507 96 HOH HOH . D 4 HOH A 94 508 97 HOH HOH . D 4 HOH A 95 509 98 HOH HOH . D 4 HOH A 96 510 99 HOH HOH . D 4 HOH A 97 511 100 HOH HOH . D 4 HOH A 98 512 102 HOH HOH . D 4 HOH A 99 513 103 HOH HOH . D 4 HOH A 100 514 104 HOH HOH . D 4 HOH A 101 515 105 HOH HOH . D 4 HOH A 102 516 106 HOH HOH . D 4 HOH A 103 517 108 HOH HOH . D 4 HOH A 104 518 109 HOH HOH . D 4 HOH A 105 519 110 HOH HOH . D 4 HOH A 106 520 112 HOH HOH . D 4 HOH A 107 521 113 HOH HOH . D 4 HOH A 108 522 114 HOH HOH . D 4 HOH A 109 523 115 HOH HOH . D 4 HOH A 110 524 117 HOH HOH . D 4 HOH A 111 525 118 HOH HOH . D 4 HOH A 112 526 120 HOH HOH . D 4 HOH A 113 527 121 HOH HOH . D 4 HOH A 114 528 122 HOH HOH . D 4 HOH A 115 529 123 HOH HOH . D 4 HOH A 116 530 124 HOH HOH . D 4 HOH A 117 531 126 HOH HOH . D 4 HOH A 118 532 128 HOH HOH . D 4 HOH A 119 533 129 HOH HOH . D 4 HOH A 120 534 130 HOH HOH . D 4 HOH A 121 535 131 HOH HOH . D 4 HOH A 122 536 133 HOH HOH . D 4 HOH A 123 537 134 HOH HOH . D 4 HOH A 124 538 135 HOH HOH . D 4 HOH A 125 539 136 HOH HOH . D 4 HOH A 126 540 137 HOH HOH . D 4 HOH A 127 541 141 HOH HOH . D 4 HOH A 128 542 142 HOH HOH . D 4 HOH A 129 543 143 HOH HOH . D 4 HOH A 130 544 145 HOH HOH . D 4 HOH A 131 545 146 HOH HOH . D 4 HOH A 132 546 147 HOH HOH . D 4 HOH A 133 547 149 HOH HOH . D 4 HOH A 134 548 151 HOH HOH . D 4 HOH A 135 549 153 HOH HOH . D 4 HOH A 136 550 154 HOH HOH . D 4 HOH A 137 551 155 HOH HOH . D 4 HOH A 138 552 156 HOH HOH . D 4 HOH A 139 553 158 HOH HOH . D 4 HOH A 140 554 161 HOH HOH . D 4 HOH A 141 555 164 HOH HOH . D 4 HOH A 142 556 165 HOH HOH . D 4 HOH A 143 557 166 HOH HOH . D 4 HOH A 144 558 167 HOH HOH . D 4 HOH A 145 559 171 HOH HOH . D 4 HOH A 146 560 175 HOH HOH . D 4 HOH A 147 561 176 HOH HOH . D 4 HOH A 148 562 177 HOH HOH . D 4 HOH A 149 563 178 HOH HOH . D 4 HOH A 150 564 179 HOH HOH . D 4 HOH A 151 565 182 HOH HOH . D 4 HOH A 152 566 185 HOH HOH . D 4 HOH A 153 567 186 HOH HOH . D 4 HOH A 154 568 187 HOH HOH . D 4 HOH A 155 569 189 HOH HOH . D 4 HOH A 156 570 191 HOH HOH . D 4 HOH A 157 571 194 HOH HOH . D 4 HOH A 158 572 195 HOH HOH . D 4 HOH A 159 573 198 HOH HOH . D 4 HOH A 160 574 199 HOH HOH . D 4 HOH A 161 575 200 HOH HOH . D 4 HOH A 162 576 205 HOH HOH . D 4 HOH A 163 577 209 HOH HOH . D 4 HOH A 164 578 211 HOH HOH . D 4 HOH A 165 579 212 HOH HOH . D 4 HOH A 166 580 219 HOH HOH . D 4 HOH A 167 581 223 HOH HOH . D 4 HOH A 168 582 236 HOH HOH . D 4 HOH A 169 583 240 HOH HOH . D 4 HOH A 170 584 245 HOH HOH . D 4 HOH A 171 585 248 HOH HOH . D 4 HOH A 172 586 251 HOH HOH . D 4 HOH A 173 587 253 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 26.977 4.552 -14.893 1 15.68 ? N1 PLP 413 A 1 HETATM 2 C C2 PLP . . . B 2 26.396 5.507 -15.69 1 17.43 ? C2 PLP 413 A 1 HETATM 3 C C2A PLP . . . B 2 27.213 5.931 -16.91 1 17.75 ? C2A PLP 413 A 1 HETATM 4 C C3 PLP . . . B 2 25.144 5.991 -15.329 1 18.52 ? C3 PLP 413 A 1 HETATM 5 O O3 PLP . . . B 2 24.622 6.933 -16.159 1 17.99 ? O3 PLP 413 A 1 HETATM 6 C C4 PLP . . . B 2 24.446 5.548 -14.191 1 19.2 ? C4 PLP 413 A 1 HETATM 7 C C4A PLP . . . B 2 23.042 6.105 -13.841 1 18.93 ? C4A PLP 413 A 1 HETATM 8 C C5 PLP . . . B 2 25.061 4.553 -13.359 1 18.8 ? C5 PLP 413 A 1 HETATM 9 C C6 PLP . . . B 2 26.311 4.105 -13.767 1 16.59 ? C6 PLP 413 A 1 HETATM 10 C C5A PLP . . . B 2 24.499 3.927 -12.086 1 18.07 ? C5A PLP 413 A 1 HETATM 11 O O4P PLP . . . B 2 23.595 4.71 -11.346 1 17.58 ? O4P PLP 413 A 1 HETATM 12 P P PLP . . . B 2 22.957 4.219 -10.028 1 16.17 ? P PLP 413 A 1 HETATM 13 O O1P PLP . . . B 2 22.081 5.377 -9.671 1 20.92 ? O1P PLP 413 A 1 HETATM 14 O O2P PLP . . . B 2 24.058 4.04 -9.035 1 14.44 ? O2P PLP 413 A 1 HETATM 15 O O3P PLP . . . B 2 22.211 3.003 -10.277 1 14.15 ? O3P PLP 413 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 15 #