data_1DF7 # _model_server_result.job_id gy4b8ksdIBquHgmYUiIJtA _model_server_result.datetime_utc '2024-11-24 17:01:17' _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 1df7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 1DF7 # _exptl.entry_id 1DF7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 454.439 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description METHOTREXATE _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 1DF7 _cell.length_a 60.51 _cell.length_b 60.51 _cell.length_c 58.83 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DF7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C20 H22 N8 O5' _chem_comp.formula_weight 454.439 _chem_comp.id MTX _chem_comp.mon_nstd_flag . _chem_comp.name METHOTREXATE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 MTX doub 250 n y N1 C8A MTX sing 251 n y C2 NA2 MTX sing 252 n n C2 N3 MTX sing 253 n y NA2 HN21 MTX sing 254 n n NA2 HN22 MTX sing 255 n n N3 C4 MTX doub 256 n y C4 NA4 MTX sing 257 n n C4 C4A MTX sing 258 n y NA4 HN41 MTX sing 259 n n NA4 HN42 MTX sing 260 n n C4A N5 MTX sing 261 n y C4A C8A MTX doub 262 n y N5 C6 MTX doub 263 n y C6 C7 MTX sing 264 n y C6 C9 MTX sing 265 n n C7 N8 MTX doub 266 n y C7 H7 MTX sing 267 n n N8 C8A MTX sing 268 n y C9 N10 MTX sing 269 n n C9 H91 MTX sing 270 n n C9 H92 MTX sing 271 n n N10 CM MTX sing 272 n n N10 C14 MTX sing 273 n n CM HM1 MTX sing 274 n n CM HM2 MTX sing 275 n n CM HM3 MTX sing 276 n n C11 C12 MTX doub 277 n y C11 C16 MTX sing 278 n y C11 C MTX sing 279 n n C12 C13 MTX sing 280 n y C12 H12 MTX sing 281 n n C13 C14 MTX doub 282 n y C13 H13 MTX sing 283 n n C14 C15 MTX sing 284 n y C15 C16 MTX doub 285 n y C15 H15 MTX sing 286 n n C16 H16 MTX sing 287 n n C O MTX doub 288 n n C N MTX sing 289 n n N CA MTX sing 290 n n N HN MTX sing 291 n n CA CT MTX sing 292 n n CA CB MTX sing 293 n n CA HA MTX sing 294 n n CT O1 MTX doub 295 n n CT O2 MTX sing 296 n n O2 HO2 MTX sing 297 n n CB CG MTX sing 298 n n CB HB1 MTX sing 299 n n CB HB2 MTX sing 300 n n CG CD MTX sing 301 n n CG HG1 MTX sing 302 n n CG HG2 MTX sing 303 n n CD OE1 MTX doub 304 n n CD OE2 MTX sing 305 n n OE2 HOE2 MTX sing 306 n n # _atom_sites.entry_id 1DF7 _atom_sites.fract_transf_matrix[1][1] 0.016526 _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] 0.016526 _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] 0.016998 _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 SO4 A 1 506 5 SO4 SO4 . C 3 NDP A 1 500 1 NDP NDP . D 4 MTX A 1 501 2 MTX MTX . E 5 GOL A 1 502 1 GOL GOL . F 5 GOL A 1 503 2 GOL GOL . G 5 GOL A 1 504 3 GOL GOL . H 5 GOL A 1 505 4 GOL GOL . I 6 HOH A 1 507 1 HOH WAT . I 6 HOH A 2 508 2 HOH WAT . I 6 HOH A 3 509 3 HOH WAT . I 6 HOH A 4 510 4 HOH WAT . I 6 HOH A 5 511 5 HOH WAT . I 6 HOH A 6 512 6 HOH WAT . I 6 HOH A 7 513 7 HOH WAT . I 6 HOH A 8 514 8 HOH WAT . I 6 HOH A 9 515 9 HOH WAT . I 6 HOH A 10 516 10 HOH WAT . I 6 HOH A 11 517 11 HOH WAT . I 6 HOH A 12 518 12 HOH WAT . I 6 HOH A 13 519 13 HOH WAT . I 6 HOH A 14 520 14 HOH WAT . I 6 HOH A 15 521 15 HOH WAT . I 6 HOH A 16 522 16 HOH WAT . I 6 HOH A 17 523 17 HOH WAT . I 6 HOH A 18 524 18 HOH WAT . I 6 HOH A 19 525 19 HOH WAT . I 6 HOH A 20 526 20 HOH WAT . I 6 HOH A 21 527 21 HOH WAT . I 6 HOH A 22 528 22 HOH WAT . I 6 HOH A 23 529 23 HOH WAT . I 6 HOH A 24 530 24 HOH WAT . I 6 HOH A 25 531 25 HOH WAT . I 6 HOH A 26 532 26 HOH WAT . I 6 HOH A 27 533 27 HOH WAT . I 6 HOH A 28 534 28 HOH WAT . I 6 HOH A 29 535 29 HOH WAT . I 6 HOH A 30 536 30 HOH WAT . I 6 HOH A 31 537 31 HOH WAT . I 6 HOH A 32 538 32 HOH WAT . I 6 HOH A 33 539 33 HOH WAT . I 6 HOH A 34 540 34 HOH WAT . I 6 HOH A 35 541 35 HOH WAT . I 6 HOH A 36 542 36 HOH WAT . I 6 HOH A 37 543 37 HOH WAT . I 6 HOH A 38 544 38 HOH WAT . I 6 HOH A 39 545 39 HOH WAT . I 6 HOH A 40 546 40 HOH WAT . I 6 HOH A 41 547 41 HOH WAT . I 6 HOH A 42 548 42 HOH WAT . I 6 HOH A 43 549 43 HOH WAT . I 6 HOH A 44 550 44 HOH WAT . I 6 HOH A 45 551 45 HOH WAT . I 6 HOH A 46 552 46 HOH WAT . I 6 HOH A 47 553 47 HOH WAT . I 6 HOH A 48 554 48 HOH WAT . I 6 HOH A 49 555 49 HOH WAT . I 6 HOH A 50 556 50 HOH WAT . I 6 HOH A 51 557 51 HOH WAT . I 6 HOH A 52 558 52 HOH WAT . I 6 HOH A 53 559 53 HOH WAT . I 6 HOH A 54 560 54 HOH WAT . I 6 HOH A 55 561 55 HOH WAT . I 6 HOH A 56 562 56 HOH WAT . I 6 HOH A 57 563 57 HOH WAT . I 6 HOH A 58 564 58 HOH WAT . I 6 HOH A 59 565 59 HOH WAT . I 6 HOH A 60 566 60 HOH WAT . I 6 HOH A 61 567 61 HOH WAT . I 6 HOH A 62 568 62 HOH WAT . I 6 HOH A 63 569 63 HOH WAT . I 6 HOH A 64 570 64 HOH WAT . I 6 HOH A 65 571 65 HOH WAT . I 6 HOH A 66 572 66 HOH WAT . I 6 HOH A 67 573 67 HOH WAT . I 6 HOH A 68 574 68 HOH WAT . I 6 HOH A 69 575 69 HOH WAT . I 6 HOH A 70 576 70 HOH WAT . I 6 HOH A 71 577 71 HOH WAT . I 6 HOH A 72 578 72 HOH WAT . I 6 HOH A 73 579 73 HOH WAT . I 6 HOH A 74 580 74 HOH WAT . I 6 HOH A 75 581 75 HOH WAT . I 6 HOH A 76 582 76 HOH WAT . I 6 HOH A 77 583 77 HOH WAT . I 6 HOH A 78 584 78 HOH WAT . I 6 HOH A 79 585 79 HOH WAT . I 6 HOH A 80 586 80 HOH WAT . I 6 HOH A 81 587 81 HOH WAT . I 6 HOH A 82 588 82 HOH WAT . I 6 HOH A 83 589 83 HOH WAT . I 6 HOH A 84 590 84 HOH WAT . I 6 HOH A 85 591 85 HOH WAT . I 6 HOH A 86 592 86 HOH WAT . I 6 HOH A 87 593 87 HOH WAT . I 6 HOH A 88 594 88 HOH WAT . I 6 HOH A 89 595 89 HOH WAT . I 6 HOH A 90 596 90 HOH WAT . I 6 HOH A 91 597 91 HOH WAT . I 6 HOH A 92 598 92 HOH WAT . I 6 HOH A 93 599 93 HOH WAT . I 6 HOH A 94 600 94 HOH WAT . I 6 HOH A 95 601 95 HOH WAT . I 6 HOH A 96 602 96 HOH WAT . I 6 HOH A 97 603 97 HOH WAT . I 6 HOH A 98 604 98 HOH WAT . I 6 HOH A 99 605 99 HOH WAT . I 6 HOH A 100 606 100 HOH WAT . I 6 HOH A 101 607 101 HOH WAT . I 6 HOH A 102 608 102 HOH WAT . I 6 HOH A 103 609 103 HOH WAT . I 6 HOH A 104 610 104 HOH WAT . I 6 HOH A 105 611 105 HOH WAT . I 6 HOH A 106 612 106 HOH WAT . I 6 HOH A 107 613 107 HOH WAT . I 6 HOH A 108 614 108 HOH WAT . I 6 HOH A 109 615 109 HOH WAT . I 6 HOH A 110 616 110 HOH WAT . I 6 HOH A 111 617 111 HOH WAT . I 6 HOH A 112 618 112 HOH WAT . I 6 HOH A 113 619 113 HOH WAT . I 6 HOH A 114 620 114 HOH WAT . I 6 HOH A 115 621 115 HOH WAT . I 6 HOH A 116 622 116 HOH WAT . I 6 HOH A 117 623 117 HOH WAT . I 6 HOH A 118 624 118 HOH WAT . I 6 HOH A 119 625 119 HOH WAT . I 6 HOH A 120 626 120 HOH WAT . I 6 HOH A 121 627 121 HOH WAT . I 6 HOH A 122 628 122 HOH WAT . I 6 HOH A 123 629 123 HOH WAT . I 6 HOH A 124 630 124 HOH WAT . I 6 HOH A 125 631 125 HOH WAT . I 6 HOH A 126 632 126 HOH WAT . I 6 HOH A 127 633 127 HOH WAT . I 6 HOH A 128 634 128 HOH WAT . I 6 HOH A 129 635 129 HOH WAT . I 6 HOH A 130 636 130 HOH WAT . I 6 HOH A 131 637 131 HOH WAT . I 6 HOH A 132 638 132 HOH WAT . I 6 HOH A 133 639 133 HOH WAT . I 6 HOH A 134 640 134 HOH WAT . I 6 HOH A 135 641 135 HOH WAT . I 6 HOH A 136 642 136 HOH WAT . I 6 HOH A 137 643 137 HOH WAT . I 6 HOH A 138 644 138 HOH WAT . I 6 HOH A 139 645 139 HOH WAT . I 6 HOH A 140 646 140 HOH WAT . I 6 HOH A 141 647 141 HOH WAT . I 6 HOH A 142 648 142 HOH WAT . I 6 HOH A 143 649 143 HOH WAT . I 6 HOH A 144 650 144 HOH WAT . I 6 HOH A 145 651 145 HOH WAT . I 6 HOH A 146 652 146 HOH WAT . I 6 HOH A 147 653 147 HOH WAT . I 6 HOH A 148 654 148 HOH WAT . I 6 HOH A 149 655 149 HOH WAT . I 6 HOH A 150 656 150 HOH WAT . I 6 HOH A 151 657 151 HOH WAT . I 6 HOH A 152 658 152 HOH WAT . I 6 HOH A 153 659 153 HOH WAT . I 6 HOH A 154 660 154 HOH WAT . I 6 HOH A 155 661 155 HOH WAT . I 6 HOH A 156 662 156 HOH WAT . I 6 HOH A 157 663 157 HOH WAT . I 6 HOH A 158 664 158 HOH WAT . I 6 HOH A 159 665 159 HOH WAT . I 6 HOH A 160 666 160 HOH WAT . I 6 HOH A 161 667 161 HOH WAT . I 6 HOH A 162 668 162 HOH WAT . I 6 HOH A 163 669 163 HOH WAT . I 6 HOH A 164 670 164 HOH WAT . I 6 HOH A 165 671 165 HOH WAT . I 6 HOH A 166 672 166 HOH WAT . I 6 HOH A 167 673 167 HOH WAT . I 6 HOH A 168 674 168 HOH WAT . I 6 HOH A 169 675 169 HOH WAT . I 6 HOH A 170 676 170 HOH WAT . I 6 HOH A 171 677 171 HOH WAT . I 6 HOH A 172 678 172 HOH WAT . I 6 HOH A 173 679 173 HOH WAT . I 6 HOH A 174 680 174 HOH WAT . I 6 HOH A 175 681 175 HOH WAT . I 6 HOH A 176 682 176 HOH WAT . I 6 HOH A 177 683 177 HOH WAT . I 6 HOH A 178 684 178 HOH WAT . I 6 HOH A 179 685 179 HOH WAT . I 6 HOH A 180 686 180 HOH WAT . I 6 HOH A 181 687 181 HOH WAT . I 6 HOH A 182 688 182 HOH WAT . I 6 HOH A 183 689 183 HOH WAT . I 6 HOH A 184 690 184 HOH WAT . I 6 HOH A 185 691 185 HOH WAT . I 6 HOH A 186 692 186 HOH WAT . I 6 HOH A 187 693 187 HOH WAT . I 6 HOH A 188 694 188 HOH WAT . I 6 HOH A 189 695 189 HOH WAT . I 6 HOH A 190 696 190 HOH WAT . I 6 HOH A 191 697 191 HOH WAT . I 6 HOH A 192 698 192 HOH WAT . I 6 HOH A 193 699 193 HOH WAT . I 6 HOH A 194 700 194 HOH WAT . I 6 HOH A 195 701 195 HOH WAT . # 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 MTX . . . D 4 6.712 26.351 8.444 1 13.6 ? N1 MTX 501 A 1 HETATM 2 C C2 MTX . . . D 4 6.825 25.299 7.533 1 13.35 ? C2 MTX 501 A 1 HETATM 3 N NA2 MTX . . . D 4 6.95 25.656 6.227 1 11.98 ? NA2 MTX 501 A 1 HETATM 4 N N3 MTX . . . D 4 6.813 24.025 7.944 1 12.36 ? N3 MTX 501 A 1 HETATM 5 C C4 MTX . . . D 4 6.675 23.571 9.204 1 11.71 ? C4 MTX 501 A 1 HETATM 6 N NA4 MTX . . . D 4 6.644 22.319 9.545 1 10.3 ? NA4 MTX 501 A 1 HETATM 7 C C4A MTX . . . D 4 6.52 24.663 10.18 1 12.66 ? C4A MTX 501 A 1 HETATM 8 N N5 MTX . . . D 4 6.286 24.391 11.488 1 13.25 ? N5 MTX 501 A 1 HETATM 9 C C6 MTX . . . D 4 6.187 25.422 12.322 1 13.66 ? C6 MTX 501 A 1 HETATM 10 C C7 MTX . . . D 4 6.37 26.698 11.794 1 12.84 ? C7 MTX 501 A 1 HETATM 11 N N8 MTX . . . D 4 6.482 27.063 10.627 1 13.97 ? N8 MTX 501 A 1 HETATM 12 C C8A MTX . . . D 4 6.598 26.012 9.752 1 12.81 ? C8A MTX 501 A 1 HETATM 13 C C9 MTX . . . D 4 6.057 25.028 13.799 1 14.78 ? C9 MTX 501 A 1 HETATM 14 N N10 MTX . . . D 4 5.474 26.096 14.525 1 16.64 ? N10 MTX 501 A 1 HETATM 15 C CM MTX . . . D 4 6.329 26.547 15.689 1 16.27 ? CM MTX 501 A 1 HETATM 16 C C11 MTX . . . D 4 1.793 27.915 13.8 1 18.83 ? C11 MTX 501 A 1 HETATM 17 C C12 MTX . . . D 4 2.687 28.449 14.755 1 19.02 ? C12 MTX 501 A 1 HETATM 18 C C13 MTX . . . D 4 3.888 28.012 15.187 1 18.03 ? C13 MTX 501 A 1 HETATM 19 C C14 MTX . . . D 4 4.272 26.72 14.437 1 15.62 ? C14 MTX 501 A 1 HETATM 20 C C15 MTX . . . D 4 3.317 26.196 13.418 1 16.01 ? C15 MTX 501 A 1 HETATM 21 C C16 MTX . . . D 4 2.211 26.771 13.064 1 18.12 ? C16 MTX 501 A 1 HETATM 22 C C MTX . . . D 4 0.673 28.608 13.592 1 20.82 ? C MTX 501 A 1 HETATM 23 O O MTX . . . D 4 0.09 29.583 14.106 1 20.58 ? O MTX 501 A 1 HETATM 24 N N MTX . . . D 4 -0.167 28.416 12.627 1 20.64 ? N MTX 501 A 1 HETATM 25 C CA MTX . . . D 4 -1.406 28.661 12.194 1 21.8 ? CA MTX 501 A 1 HETATM 26 C CT MTX . . . D 4 -1.929 27.421 11.482 1 22.59 ? CT MTX 501 A 1 HETATM 27 O O1 MTX . . . D 4 -1.399 26.537 10.84 1 22.5 ? O1 MTX 501 A 1 HETATM 28 O O2 MTX . . . D 4 -3.296 27.352 11.644 1 21.55 ? O2 MTX 501 A 1 HETATM 29 C CB MTX . . . D 4 -1.724 29.729 11.074 1 23.75 ? CB MTX 501 A 1 HETATM 30 C CG MTX . . . D 4 -1.197 31.118 11.171 1 25.09 ? CG MTX 501 A 1 HETATM 31 C CD MTX . . . D 4 -0.819 32.304 10.06 1 27.15 ? CD MTX 501 A 1 HETATM 32 O OE1 MTX . . . D 4 0.136 33.268 10.223 1 32.99 ? OE1 MTX 501 A 1 HETATM 33 O OE2 MTX . . . D 4 -1.75 31.785 9.287 1 28.59 ? OE2 MTX 501 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 33 #