data_1DB1 # _model_server_result.job_id 4xT4obpmR5lxv4KGUMfE9w _model_server_result.datetime_utc '2024-10-11 05:26:46' _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 1db1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":428}' # _entry.id 1DB1 # _exptl.entry_id 1DB1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 416.636 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL _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 1DB1 _cell.length_a 45.193 _cell.length_b 52.443 _cell.length_c 133.286 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DB1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C27 H44 O3' _chem_comp.formula_weight 416.636 _chem_comp.id VDX _chem_comp.mon_nstd_flag . _chem_comp.name 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '1,25 DIHYDROXY VITAMIN D3' # 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 O2 C3 VDX sing 376 n n O2 HO2 VDX sing 377 n n O3 C25 VDX sing 378 n n O3 HO3 VDX sing 379 n n C1 C2 VDX sing 380 n n C1 C10 VDX sing 381 n n C1 O1 VDX sing 382 n n C1 H11 VDX sing 383 n n C2 C3 VDX sing 384 n n C2 H21 VDX sing 385 n n C2 H22 VDX sing 386 n n C3 C4 VDX sing 387 n n C3 H31 VDX sing 388 n n C4 C5 VDX sing 389 n n C4 H41 VDX sing 390 n n C4 H42 VDX sing 391 n n C5 C6 VDX doub 392 z n C5 C10 VDX sing 393 n n C6 C7 VDX sing 394 n n C6 H61 VDX sing 395 n n C7 C8 VDX doub 396 e n C7 H71 VDX sing 397 n n C8 C9 VDX sing 398 n n C8 C14 VDX sing 399 n n C9 C11 VDX sing 400 n n C9 H91 VDX sing 401 n n C9 H92 VDX sing 402 n n C10 C19 VDX doub 403 n n C11 C12 VDX sing 404 n n C11 H111 VDX sing 405 n n C11 H112 VDX sing 406 n n C12 C13 VDX sing 407 n n C12 H121 VDX sing 408 n n C12 H122 VDX sing 409 n n C13 C14 VDX sing 410 n n C13 C17 VDX sing 411 n n C13 C18 VDX sing 412 n n C14 C15 VDX sing 413 n n C14 H141 VDX sing 414 n n C15 C16 VDX sing 415 n n C15 H151 VDX sing 416 n n C15 H152 VDX sing 417 n n C16 C17 VDX sing 418 n n C16 H161 VDX sing 419 n n C16 H162 VDX sing 420 n n C17 C20 VDX sing 421 n n C17 H171 VDX sing 422 n n C18 H181 VDX sing 423 n n C18 H182 VDX sing 424 n n C18 H183 VDX sing 425 n n C19 H191 VDX sing 426 n n C19 H192 VDX sing 427 n n C20 C21 VDX sing 428 n n C20 C22 VDX sing 429 n n C20 H201 VDX sing 430 n n C21 H211 VDX sing 431 n n C21 H212 VDX sing 432 n n C21 H213 VDX sing 433 n n C22 C23 VDX sing 434 n n C22 H221 VDX sing 435 n n C22 H222 VDX sing 436 n n C23 C24 VDX sing 437 n n C23 H231 VDX sing 438 n n C23 H232 VDX sing 439 n n C24 C25 VDX sing 440 n n C24 H241 VDX sing 441 n n C24 H242 VDX sing 442 n n C25 C26 VDX sing 443 n n C25 C27 VDX sing 444 n n C26 H261 VDX sing 445 n n C26 H262 VDX sing 446 n n C26 H263 VDX sing 447 n n C27 H271 VDX sing 448 n n C27 H272 VDX sing 449 n n C27 H273 VDX sing 450 n n O1 HO1 VDX sing 451 n n # _atom_sites.entry_id 1DB1 _atom_sites.fract_transf_matrix[1][1] 0.022127 _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] 0.019068 _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] 0.007503 _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 VDX A 1 428 425 VDX VDX . C 3 HOH A 1 500 500 HOH TIP . C 3 HOH A 2 501 501 HOH TIP . C 3 HOH A 3 502 502 HOH TIP . C 3 HOH A 4 503 503 HOH TIP . C 3 HOH A 5 504 504 HOH TIP . C 3 HOH A 6 505 505 HOH TIP . C 3 HOH A 7 506 506 HOH TIP . C 3 HOH A 8 507 507 HOH TIP . C 3 HOH A 9 508 508 HOH TIP . C 3 HOH A 10 509 509 HOH TIP . C 3 HOH A 11 510 510 HOH TIP . C 3 HOH A 12 511 511 HOH TIP . C 3 HOH A 13 512 512 HOH TIP . C 3 HOH A 14 513 513 HOH TIP . C 3 HOH A 15 514 514 HOH TIP . C 3 HOH A 16 515 515 HOH TIP . C 3 HOH A 17 516 516 HOH TIP . C 3 HOH A 18 517 517 HOH TIP . C 3 HOH A 19 518 518 HOH TIP . C 3 HOH A 20 519 519 HOH TIP . C 3 HOH A 21 520 520 HOH TIP . C 3 HOH A 22 521 521 HOH TIP . C 3 HOH A 23 522 522 HOH TIP . C 3 HOH A 24 523 523 HOH TIP . C 3 HOH A 25 524 524 HOH TIP . C 3 HOH A 26 525 525 HOH TIP . C 3 HOH A 27 526 526 HOH TIP . C 3 HOH A 28 527 527 HOH TIP . C 3 HOH A 29 528 528 HOH TIP . C 3 HOH A 30 529 529 HOH TIP . C 3 HOH A 31 530 530 HOH TIP . C 3 HOH A 32 531 531 HOH TIP . C 3 HOH A 33 532 532 HOH TIP . C 3 HOH A 34 533 533 HOH TIP . C 3 HOH A 35 534 534 HOH TIP . C 3 HOH A 36 535 535 HOH TIP . C 3 HOH A 37 536 536 HOH TIP . C 3 HOH A 38 537 537 HOH TIP . C 3 HOH A 39 538 538 HOH TIP . C 3 HOH A 40 539 539 HOH TIP . C 3 HOH A 41 540 540 HOH TIP . C 3 HOH A 42 541 541 HOH TIP . C 3 HOH A 43 542 542 HOH TIP . C 3 HOH A 44 543 543 HOH TIP . C 3 HOH A 45 544 544 HOH TIP . C 3 HOH A 46 545 545 HOH TIP . C 3 HOH A 47 546 546 HOH TIP . C 3 HOH A 48 547 547 HOH TIP . C 3 HOH A 49 548 548 HOH TIP . C 3 HOH A 50 549 549 HOH TIP . C 3 HOH A 51 550 550 HOH TIP . C 3 HOH A 52 551 551 HOH TIP . C 3 HOH A 53 552 552 HOH TIP . C 3 HOH A 54 553 553 HOH TIP . C 3 HOH A 55 554 554 HOH TIP . C 3 HOH A 56 556 556 HOH TIP . C 3 HOH A 57 557 557 HOH TIP . C 3 HOH A 58 558 558 HOH TIP . C 3 HOH A 59 559 559 HOH TIP . C 3 HOH A 60 560 560 HOH TIP . C 3 HOH A 61 561 561 HOH TIP . C 3 HOH A 62 562 562 HOH TIP . C 3 HOH A 63 563 563 HOH TIP . C 3 HOH A 64 564 564 HOH TIP . C 3 HOH A 65 565 565 HOH TIP . C 3 HOH A 66 566 566 HOH TIP . C 3 HOH A 67 567 567 HOH TIP . C 3 HOH A 68 568 568 HOH TIP . C 3 HOH A 69 569 569 HOH TIP . C 3 HOH A 70 570 570 HOH TIP . C 3 HOH A 71 571 571 HOH TIP . C 3 HOH A 72 572 572 HOH TIP . C 3 HOH A 73 573 573 HOH TIP . C 3 HOH A 74 574 574 HOH TIP . C 3 HOH A 75 575 575 HOH TIP . C 3 HOH A 76 576 576 HOH TIP . C 3 HOH A 77 577 577 HOH TIP . C 3 HOH A 78 578 578 HOH TIP . C 3 HOH A 79 579 579 HOH TIP . C 3 HOH A 80 580 580 HOH TIP . C 3 HOH A 81 581 581 HOH TIP . C 3 HOH A 82 582 582 HOH TIP . C 3 HOH A 83 583 583 HOH TIP . C 3 HOH A 84 584 584 HOH TIP . C 3 HOH A 85 585 585 HOH TIP . C 3 HOH A 86 586 586 HOH TIP . C 3 HOH A 87 587 587 HOH TIP . C 3 HOH A 88 588 588 HOH TIP . C 3 HOH A 89 589 589 HOH TIP . C 3 HOH A 90 590 590 HOH TIP . C 3 HOH A 91 591 591 HOH TIP . C 3 HOH A 92 592 592 HOH TIP . C 3 HOH A 93 593 593 HOH TIP . C 3 HOH A 94 594 594 HOH TIP . C 3 HOH A 95 595 595 HOH TIP . C 3 HOH A 96 596 596 HOH TIP . C 3 HOH A 97 597 597 HOH TIP . C 3 HOH A 98 598 598 HOH TIP . C 3 HOH A 99 599 599 HOH TIP . C 3 HOH A 100 600 600 HOH TIP . C 3 HOH A 101 601 601 HOH TIP . C 3 HOH A 102 602 602 HOH TIP . C 3 HOH A 103 603 603 HOH TIP . C 3 HOH A 104 604 604 HOH TIP . C 3 HOH A 105 605 605 HOH TIP . C 3 HOH A 106 606 606 HOH TIP . C 3 HOH A 107 607 607 HOH TIP . C 3 HOH A 108 608 608 HOH TIP . C 3 HOH A 109 609 609 HOH TIP . C 3 HOH A 110 610 610 HOH TIP . C 3 HOH A 111 611 611 HOH TIP . C 3 HOH A 112 612 612 HOH TIP . C 3 HOH A 113 613 613 HOH TIP . C 3 HOH A 114 614 614 HOH TIP . C 3 HOH A 115 615 615 HOH TIP . C 3 HOH A 116 616 616 HOH TIP . C 3 HOH A 117 617 617 HOH TIP . C 3 HOH A 118 618 618 HOH TIP . C 3 HOH A 119 619 619 HOH TIP . C 3 HOH A 120 620 620 HOH TIP . C 3 HOH A 121 621 621 HOH TIP . C 3 HOH A 122 622 622 HOH TIP . C 3 HOH A 123 623 623 HOH TIP . C 3 HOH A 124 624 624 HOH TIP . C 3 HOH A 125 625 625 HOH TIP . C 3 HOH A 126 626 626 HOH TIP . C 3 HOH A 127 627 627 HOH TIP . C 3 HOH A 128 628 628 HOH TIP . C 3 HOH A 129 629 629 HOH TIP . C 3 HOH A 130 630 630 HOH TIP . C 3 HOH A 131 631 631 HOH TIP . C 3 HOH A 132 632 632 HOH TIP . C 3 HOH A 133 633 633 HOH TIP . C 3 HOH A 134 634 634 HOH TIP . C 3 HOH A 135 635 635 HOH TIP . C 3 HOH A 136 636 636 HOH TIP . C 3 HOH A 137 637 637 HOH TIP . C 3 HOH A 138 638 638 HOH TIP . C 3 HOH A 139 639 639 HOH TIP . C 3 HOH A 140 640 640 HOH TIP . C 3 HOH A 141 641 641 HOH TIP . C 3 HOH A 142 642 642 HOH TIP . C 3 HOH A 143 644 644 HOH TIP . C 3 HOH A 144 645 645 HOH TIP . C 3 HOH A 145 646 646 HOH TIP . C 3 HOH A 146 647 647 HOH TIP . C 3 HOH A 147 648 648 HOH TIP . C 3 HOH A 148 649 649 HOH TIP . C 3 HOH A 149 650 650 HOH TIP . C 3 HOH A 150 651 651 HOH TIP . C 3 HOH A 151 652 652 HOH TIP . C 3 HOH A 152 653 653 HOH TIP . C 3 HOH A 153 654 654 HOH TIP . C 3 HOH A 154 655 655 HOH TIP . C 3 HOH A 155 656 656 HOH TIP . C 3 HOH A 156 657 657 HOH TIP . C 3 HOH A 157 658 658 HOH TIP . C 3 HOH A 158 659 659 HOH TIP . C 3 HOH A 159 660 660 HOH TIP . C 3 HOH A 160 661 661 HOH TIP . C 3 HOH A 161 662 662 HOH TIP . C 3 HOH A 162 663 663 HOH TIP . C 3 HOH A 163 664 664 HOH TIP . C 3 HOH A 164 665 665 HOH TIP . # 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 O O2 VDX . . . B 2 17.029 18.071 34.819 1 21.73 ? O2 VDX 428 A 1 HETATM 2 O O3 VDX . . . B 2 4.489 26.946 35.054 1 24.67 ? O3 VDX 428 A 1 HETATM 3 C C1 VDX . . . B 2 14.139 17.953 35.755 1 20.8 ? C1 VDX 428 A 1 HETATM 4 C C2 VDX . . . B 2 14.879 16.893 34.895 1 21.02 ? C2 VDX 428 A 1 HETATM 5 C C3 VDX . . . B 2 15.992 17.534 33.962 1 21.41 ? C3 VDX 428 A 1 HETATM 6 C C4 VDX . . . B 2 15.368 18.672 33.049 1 21.29 ? C4 VDX 428 A 1 HETATM 7 C C5 VDX . . . B 2 14.622 19.724 33.864 1 21 ? C5 VDX 428 A 1 HETATM 8 C C6 VDX . . . B 2 14.797 21.12 33.792 1 20.95 ? C6 VDX 428 A 1 HETATM 9 C C7 VDX . . . B 2 14.174 22.286 34.514 1 21.23 ? C7 VDX 428 A 1 HETATM 10 C C8 VDX . . . B 2 13.966 23.488 34.042 1 21.54 ? C8 VDX 428 A 1 HETATM 11 C C9 VDX . . . B 2 14.354 23.927 32.544 1 21.77 ? C9 VDX 428 A 1 HETATM 12 C C10 VDX . . . B 2 13.602 19.075 34.828 1 20.74 ? C10 VDX 428 A 1 HETATM 13 C C11 VDX . . . B 2 13.088 24.49 31.671 1 21.66 ? C11 VDX 428 A 1 HETATM 14 C C12 VDX . . . B 2 12.147 25.443 32.564 1 22.04 ? C12 VDX 428 A 1 HETATM 15 C C13 VDX . . . B 2 11.753 24.897 34.07 1 22.01 ? C13 VDX 428 A 1 HETATM 16 C C14 VDX . . . B 2 13.148 24.538 34.777 1 21.8 ? C14 VDX 428 A 1 HETATM 17 C C15 VDX . . . B 2 12.661 24.266 36.35 1 22.22 ? C15 VDX 428 A 1 HETATM 18 C C16 VDX . . . B 2 11.429 25.231 36.497 1 22.39 ? C16 VDX 428 A 1 HETATM 19 C C17 VDX . . . B 2 11.276 25.934 35.106 1 22.31 ? C17 VDX 428 A 1 HETATM 20 C C18 VDX . . . B 2 10.769 23.57 33.779 1 21.5 ? C18 VDX 428 A 1 HETATM 21 C C19 VDX . . . B 2 12.291 19.455 34.852 1 20.77 ? C19 VDX 428 A 1 HETATM 22 C C20 VDX . . . B 2 9.849 26.546 34.726 1 22.9 ? C20 VDX 428 A 1 HETATM 23 C C21 VDX . . . B 2 9.804 27.956 35.482 1 23.65 ? C21 VDX 428 A 1 HETATM 24 C C22 VDX . . . B 2 8.575 25.824 35.268 1 23.16 ? C22 VDX 428 A 1 HETATM 25 C C23 VDX . . . B 2 7.331 26.06 34.405 1 23.73 ? C23 VDX 428 A 1 HETATM 26 C C24 VDX . . . B 2 6.152 25.266 34.672 1 24.36 ? C24 VDX 428 A 1 HETATM 27 C C25 VDX . . . B 2 4.775 25.776 34.336 1 24.75 ? C25 VDX 428 A 1 HETATM 28 C C26 VDX . . . B 2 4.701 26.01 32.842 1 25.41 ? C26 VDX 428 A 1 HETATM 29 C C27 VDX . . . B 2 3.668 24.73 34.723 1 25.39 ? C27 VDX 428 A 1 HETATM 30 O O1 VDX . . . B 2 13.119 17.359 36.62 1 20.68 ? O1 VDX 428 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 30 #