data_1MDZ # _model_server_result.job_id Vagaar_VFtftnTKh0OaXzw _model_server_result.datetime_utc '2024-10-31 01:17:03' _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 1mdz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":400}' # _entry.id 1MDZ # _exptl.entry_id 1MDZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 333.234 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE _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 1MDZ _cell.length_a 90.904 _cell.length_b 90.904 _cell.length_c 127.71 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1MDZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # 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 PISA,PQS dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D 1 1 A,B,C,D 2 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' 7_555 y,x,-z 0 1 0 1 0 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 188 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 188 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _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 401 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id A _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id A _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 1.471 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C11 H16 N3 O7 P' _chem_comp.formula_weight 333.234 _chem_comp.id DCS _chem_comp.mon_nstd_flag . _chem_comp.name D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms D-PYRIDOXYL-N,O-CYCLOSERYLAMIDE-5-MONOPHOSPHATE # _atom_sites.entry_id 1MDZ _atom_sites.fract_transf_matrix[1][1] 0.011001 _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] 0.011001 _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] 0.00783 _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 DCS A 1 400 400 DCS SCP . C 3 PLP A 1 401 401 PLP PLP . D 4 HOH A 1 402 3 HOH HOH . D 4 HOH A 2 403 4 HOH HOH . D 4 HOH A 3 404 5 HOH HOH . D 4 HOH A 4 405 6 HOH HOH . D 4 HOH A 5 406 7 HOH HOH . D 4 HOH A 6 407 8 HOH HOH . D 4 HOH A 7 408 9 HOH HOH . D 4 HOH A 8 409 10 HOH HOH . D 4 HOH A 9 410 11 HOH HOH . D 4 HOH A 10 411 12 HOH HOH . D 4 HOH A 11 412 13 HOH HOH . D 4 HOH A 12 413 14 HOH HOH . D 4 HOH A 13 414 15 HOH HOH . D 4 HOH A 14 415 16 HOH HOH . D 4 HOH A 15 416 17 HOH HOH . D 4 HOH A 16 417 18 HOH HOH . D 4 HOH A 17 418 19 HOH HOH . D 4 HOH A 18 419 20 HOH HOH . D 4 HOH A 19 420 21 HOH HOH . D 4 HOH A 20 421 22 HOH HOH . D 4 HOH A 21 422 23 HOH HOH . D 4 HOH A 22 423 24 HOH HOH . D 4 HOH A 23 424 25 HOH HOH . D 4 HOH A 24 425 26 HOH HOH . D 4 HOH A 25 426 27 HOH HOH . D 4 HOH A 26 427 28 HOH HOH . D 4 HOH A 27 428 29 HOH HOH . D 4 HOH A 28 429 30 HOH HOH . D 4 HOH A 29 430 31 HOH HOH . D 4 HOH A 30 431 32 HOH HOH . D 4 HOH A 31 432 33 HOH HOH . D 4 HOH A 32 433 34 HOH HOH . D 4 HOH A 33 434 35 HOH HOH . D 4 HOH A 34 435 36 HOH HOH . D 4 HOH A 35 436 37 HOH HOH . D 4 HOH A 36 437 38 HOH HOH . D 4 HOH A 37 438 39 HOH HOH . D 4 HOH A 38 439 40 HOH HOH . D 4 HOH A 39 440 41 HOH HOH . D 4 HOH A 40 441 42 HOH HOH . D 4 HOH A 41 442 43 HOH HOH . D 4 HOH A 42 443 44 HOH HOH . D 4 HOH A 43 444 45 HOH HOH . D 4 HOH A 44 445 46 HOH HOH . D 4 HOH A 45 446 47 HOH HOH . D 4 HOH A 46 447 48 HOH HOH . D 4 HOH A 47 448 49 HOH HOH . D 4 HOH A 48 449 50 HOH HOH . D 4 HOH A 49 450 51 HOH HOH . D 4 HOH A 50 451 52 HOH HOH . D 4 HOH A 51 452 53 HOH HOH . D 4 HOH A 52 453 54 HOH HOH . D 4 HOH A 53 454 55 HOH HOH . D 4 HOH A 54 455 56 HOH HOH . D 4 HOH A 55 456 57 HOH HOH . D 4 HOH A 56 457 58 HOH HOH . D 4 HOH A 57 458 59 HOH HOH . D 4 HOH A 58 459 60 HOH HOH . D 4 HOH A 59 460 61 HOH HOH . D 4 HOH A 60 461 62 HOH HOH . D 4 HOH A 61 462 63 HOH HOH . D 4 HOH A 62 463 64 HOH HOH . D 4 HOH A 63 464 65 HOH HOH . D 4 HOH A 64 465 66 HOH HOH . D 4 HOH A 65 466 67 HOH HOH . D 4 HOH A 66 467 68 HOH HOH . D 4 HOH A 67 468 69 HOH HOH . D 4 HOH A 68 469 70 HOH HOH . D 4 HOH A 69 470 71 HOH HOH . D 4 HOH A 70 471 72 HOH HOH . D 4 HOH A 71 472 73 HOH HOH . D 4 HOH A 72 473 74 HOH HOH . D 4 HOH A 73 474 75 HOH HOH . D 4 HOH A 74 475 76 HOH HOH . D 4 HOH A 75 476 77 HOH HOH . D 4 HOH A 76 477 78 HOH HOH . D 4 HOH A 77 478 79 HOH HOH . D 4 HOH A 78 479 80 HOH HOH . D 4 HOH A 79 480 81 HOH HOH . D 4 HOH A 80 481 82 HOH HOH . D 4 HOH A 81 482 83 HOH HOH . D 4 HOH A 82 483 84 HOH HOH . D 4 HOH A 83 484 85 HOH HOH . D 4 HOH A 84 485 86 HOH HOH . D 4 HOH A 85 486 87 HOH HOH . D 4 HOH A 86 487 88 HOH HOH . D 4 HOH A 87 488 89 HOH HOH . D 4 HOH A 88 489 90 HOH HOH . D 4 HOH A 89 490 91 HOH HOH . D 4 HOH A 90 491 92 HOH HOH . D 4 HOH A 91 492 93 HOH HOH . D 4 HOH A 92 493 94 HOH HOH . D 4 HOH A 93 494 95 HOH HOH . D 4 HOH A 94 495 96 HOH HOH . D 4 HOH A 95 496 97 HOH HOH . D 4 HOH A 96 497 98 HOH HOH . D 4 HOH A 97 498 99 HOH HOH . D 4 HOH A 98 499 100 HOH HOH . D 4 HOH A 99 500 101 HOH HOH . D 4 HOH A 100 501 102 HOH HOH . D 4 HOH A 101 502 103 HOH HOH . D 4 HOH A 102 503 104 HOH HOH . D 4 HOH A 103 504 105 HOH HOH . D 4 HOH A 104 505 106 HOH HOH . D 4 HOH A 105 506 107 HOH HOH . D 4 HOH A 106 507 108 HOH HOH . D 4 HOH A 107 508 109 HOH HOH . D 4 HOH A 108 509 110 HOH HOH . D 4 HOH A 109 510 111 HOH HOH . D 4 HOH A 110 511 112 HOH HOH . D 4 HOH A 111 512 113 HOH HOH . D 4 HOH A 112 513 114 HOH HOH . D 4 HOH A 113 514 115 HOH HOH . D 4 HOH A 114 515 116 HOH HOH . D 4 HOH A 115 516 117 HOH HOH . D 4 HOH A 116 517 118 HOH HOH . D 4 HOH A 117 518 119 HOH HOH . D 4 HOH A 118 519 120 HOH HOH . D 4 HOH A 119 520 121 HOH HOH . D 4 HOH A 120 521 122 HOH HOH . D 4 HOH A 121 522 123 HOH HOH . D 4 HOH A 122 523 124 HOH HOH . D 4 HOH A 123 524 125 HOH HOH . D 4 HOH A 124 525 126 HOH HOH . D 4 HOH A 125 526 127 HOH HOH . D 4 HOH A 126 527 128 HOH HOH . D 4 HOH A 127 528 129 HOH HOH . D 4 HOH A 128 529 130 HOH HOH . D 4 HOH A 129 530 131 HOH HOH . D 4 HOH A 130 531 132 HOH HOH . D 4 HOH A 131 532 133 HOH HOH . D 4 HOH A 132 533 134 HOH HOH . D 4 HOH A 133 534 135 HOH HOH . D 4 HOH A 134 535 136 HOH HOH . D 4 HOH A 135 536 137 HOH HOH . D 4 HOH A 136 537 138 HOH HOH . D 4 HOH A 137 538 139 HOH HOH . D 4 HOH A 138 539 140 HOH HOH . D 4 HOH A 139 540 141 HOH HOH . D 4 HOH A 140 541 142 HOH HOH . D 4 HOH A 141 542 143 HOH HOH . D 4 HOH A 142 543 144 HOH HOH . D 4 HOH A 143 544 145 HOH HOH . D 4 HOH A 144 545 146 HOH HOH . D 4 HOH A 145 546 147 HOH HOH . D 4 HOH A 146 547 148 HOH HOH . D 4 HOH A 147 548 149 HOH HOH . D 4 HOH A 148 549 150 HOH HOH . D 4 HOH A 149 550 151 HOH HOH . D 4 HOH A 150 551 152 HOH HOH . D 4 HOH A 151 552 153 HOH HOH . D 4 HOH A 152 553 154 HOH HOH . D 4 HOH A 153 554 155 HOH HOH . D 4 HOH A 154 555 156 HOH HOH . D 4 HOH A 155 556 157 HOH HOH . D 4 HOH A 156 557 158 HOH HOH . D 4 HOH A 157 558 159 HOH HOH . D 4 HOH A 158 559 160 HOH HOH . D 4 HOH A 159 560 161 HOH HOH . D 4 HOH A 160 561 162 HOH HOH . D 4 HOH A 161 562 163 HOH HOH . D 4 HOH A 162 563 164 HOH HOH . D 4 HOH A 163 564 165 HOH HOH . D 4 HOH A 164 565 166 HOH HOH . D 4 HOH A 165 566 167 HOH HOH . D 4 HOH A 166 567 168 HOH HOH . D 4 HOH A 167 568 169 HOH HOH . D 4 HOH A 168 569 170 HOH HOH . D 4 HOH A 169 570 171 HOH HOH . D 4 HOH A 170 571 172 HOH HOH . D 4 HOH A 171 572 173 HOH HOH . D 4 HOH A 172 573 174 HOH HOH . D 4 HOH A 173 574 175 HOH HOH . D 4 HOH A 174 575 176 HOH HOH . D 4 HOH A 175 576 177 HOH HOH . D 4 HOH A 176 577 178 HOH HOH . D 4 HOH A 177 578 179 HOH HOH . D 4 HOH A 178 579 180 HOH HOH . D 4 HOH A 179 580 181 HOH HOH . D 4 HOH A 180 581 182 HOH HOH . D 4 HOH A 181 582 183 HOH HOH . D 4 HOH A 182 583 184 HOH HOH . D 4 HOH A 183 584 185 HOH HOH . D 4 HOH A 184 585 186 HOH HOH . D 4 HOH A 185 586 187 HOH HOH . D 4 HOH A 186 587 188 HOH HOH . D 4 HOH A 187 588 189 HOH HOH . D 4 HOH A 188 589 190 HOH HOH . D 4 HOH A 189 590 191 HOH HOH . D 4 HOH A 190 591 192 HOH HOH . D 4 HOH A 191 592 193 HOH HOH . D 4 HOH A 192 593 194 HOH HOH . D 4 HOH A 193 594 195 HOH HOH . D 4 HOH A 194 595 196 HOH HOH . D 4 HOH A 195 596 197 HOH HOH . D 4 HOH A 196 597 198 HOH HOH . D 4 HOH A 197 598 199 HOH HOH . D 4 HOH A 198 599 200 HOH HOH . D 4 HOH A 199 600 201 HOH HOH . D 4 HOH A 200 601 202 HOH HOH . D 4 HOH A 201 602 203 HOH HOH . D 4 HOH A 202 603 204 HOH HOH . D 4 HOH A 203 604 205 HOH HOH . D 4 HOH A 204 605 206 HOH HOH . D 4 HOH A 205 606 207 HOH HOH . D 4 HOH A 206 607 208 HOH HOH . D 4 HOH A 207 608 209 HOH HOH . D 4 HOH A 208 609 210 HOH HOH . D 4 HOH A 209 610 211 HOH HOH . D 4 HOH A 210 611 212 HOH HOH . D 4 HOH A 211 612 213 HOH HOH . D 4 HOH A 212 613 214 HOH HOH . D 4 HOH A 213 614 215 HOH HOH . D 4 HOH A 214 615 216 HOH HOH . D 4 HOH A 215 616 217 HOH HOH . D 4 HOH A 216 617 218 HOH HOH . D 4 HOH A 217 618 219 HOH HOH . D 4 HOH A 218 619 220 HOH HOH . D 4 HOH A 219 620 221 HOH HOH . D 4 HOH A 220 621 222 HOH HOH . D 4 HOH A 221 622 223 HOH HOH . D 4 HOH A 222 623 224 HOH HOH . D 4 HOH A 223 624 225 HOH HOH . D 4 HOH A 224 625 226 HOH HOH . D 4 HOH A 225 626 227 HOH HOH . D 4 HOH A 226 627 228 HOH HOH . D 4 HOH A 227 628 229 HOH HOH . D 4 HOH A 228 629 230 HOH HOH . D 4 HOH A 229 630 231 HOH HOH . D 4 HOH A 230 631 232 HOH HOH . D 4 HOH A 231 632 233 HOH HOH . D 4 HOH A 232 633 234 HOH HOH . D 4 HOH A 233 634 235 HOH HOH . D 4 HOH A 234 635 236 HOH HOH . D 4 HOH A 235 636 237 HOH HOH . D 4 HOH A 236 637 238 HOH HOH . D 4 HOH A 237 638 239 HOH HOH . D 4 HOH A 238 639 240 HOH HOH . D 4 HOH A 239 640 241 HOH HOH . D 4 HOH A 240 641 242 HOH HOH . D 4 HOH A 241 642 243 HOH HOH . D 4 HOH A 242 643 244 HOH HOH . D 4 HOH A 243 644 245 HOH HOH . D 4 HOH A 244 645 246 HOH HOH . D 4 HOH A 245 646 247 HOH HOH . D 4 HOH A 246 647 248 HOH HOH . D 4 HOH A 247 648 249 HOH HOH . D 4 HOH A 248 649 250 HOH HOH . D 4 HOH A 249 650 251 HOH HOH . D 4 HOH A 250 651 252 HOH HOH . D 4 HOH A 251 652 253 HOH HOH . D 4 HOH A 252 653 254 HOH HOH . D 4 HOH A 253 654 255 HOH HOH . D 4 HOH A 254 655 256 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 DCS . B . B 2 27.927 25.668 14.991 0.5 23.6 ? N1 DCS 400 A 1 HETATM 2 C C2 DCS . B . B 2 27.923 26.594 15.963 0.5 24.26 ? C2 DCS 400 A 1 HETATM 3 C C2A DCS . B . B 2 27.927 26.069 17.377 0.5 24.74 ? C2A DCS 400 A 1 HETATM 4 C C3 DCS . B . B 2 27.907 27.964 15.698 0.5 25.38 ? C3 DCS 400 A 1 HETATM 5 O O3 DCS . B . B 2 27.894 28.833 16.771 0.5 25.85 ? O3 DCS 400 A 1 HETATM 6 C C4 DCS . B . B 2 27.896 28.431 14.351 0.5 25.77 ? C4 DCS 400 A 1 HETATM 7 C C4A DCS . B . B 2 27.875 29.906 13.98 0.5 26.97 ? C4A DCS 400 A 1 HETATM 8 C C5 DCS . B . B 2 27.895 27.445 13.352 0.5 24.04 ? C5 DCS 400 A 1 HETATM 9 C C6 DCS . B . B 2 27.923 26.092 13.721 0.5 23.58 ? C6 DCS 400 A 1 HETATM 10 C C5A DCS . B . B 2 27.887 27.801 11.903 0.5 23.37 ? C5A DCS 400 A 1 HETATM 11 O O4P DCS . B . B 2 29.197 28.186 11.538 0.5 22.1 ? O4P DCS 400 A 1 HETATM 12 P P DCS . B . B 2 29.395 28.875 10.164 0.5 21.12 ? P DCS 400 A 1 HETATM 13 O O1P DCS . B . B 2 30.831 28.783 9.808 0.5 21.13 ? O1P DCS 400 A 1 HETATM 14 O O2P DCS . B . B 2 28.982 30.3 10.322 0.5 21.46 ? O2P DCS 400 A 1 HETATM 15 O O3P DCS . B . B 2 28.581 28.166 9.138 0.5 20.17 ? O3P DCS 400 A 1 HETATM 16 N N DCS . B . B 2 29.007 30.687 14.353 0.5 29.69 ? N DCS 400 A 1 HETATM 17 C CA DCS . B . B 2 29.02 31.642 15.285 0.5 30.58 ? CA DCS 400 A 1 HETATM 18 C C DCS . B . B 2 27.908 31.898 16.242 0.5 31.56 ? C DCS 400 A 1 HETATM 19 O O DCS . B . B 2 27.036 31.083 16.492 0.5 32.26 ? O DCS 400 A 1 HETATM 20 N ND DCS . B . B 2 28.282 32.921 17.014 0.5 31.59 ? ND DCS 400 A 1 HETATM 21 O OG DCS . B . B 2 29.228 33.704 16.313 0.5 31.67 ? OG DCS 400 A 1 HETATM 22 C CB DCS . B . B 2 29.966 32.818 15.469 0.5 30.93 ? CB DCS 400 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #