data_2ZL9 # _model_server_result.job_id RwkD-4dAxfF459wWJo1M9g _model_server_result.datetime_utc '2024-10-11 15:16:52' _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 2zl9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":500}' # _entry.id 2ZL9 # _exptl.entry_id 2ZL9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 494.727 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1R,2R,3R,5Z)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethoxy)-9,10-secoestra-5,7,16-triene-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 95.67 _cell.angle_gamma 90 _cell.entry_id 2ZL9 _cell.length_a 153.902 _cell.length_b 42.32 _cell.length_c 42.13 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZL9 _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 PISA _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,E _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C28 H46 O5 S' _chem_comp.formula_weight 494.727 _chem_comp.id VDA _chem_comp.mon_nstd_flag . _chem_comp.name (1R,2R,3R,5Z)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethoxy)-9,10-secoestra-5,7,16-triene-1,3-diol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(20S)-1alpha,25-dihydroxy-2beta-(2-hydroxyethoxy)-16-ene-22-thia-26,27-dimethyl-19,24-dinorvitamin 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 VDA sing 376 n n C1 C2 VDA sing 377 n n C1 C10 VDA sing 378 n n C1 O1 VDA sing 379 n n C2 C3 VDA sing 380 n n C2 O4 VDA sing 381 n n C3 C4 VDA sing 382 n n C4 C5 VDA sing 383 n n C5 C6 VDA doub 384 n n C5 C10 VDA sing 385 n n C6 C7 VDA sing 386 n n C7 C8 VDA doub 387 n n C8 C9 VDA sing 388 n n C8 C14 VDA sing 389 n n C9 C11 VDA sing 390 n n C11 C12 VDA sing 391 n n C12 C13 VDA sing 392 n n C13 C14 VDA sing 393 n n C13 C17 VDA sing 394 e n C13 C18 VDA sing 395 n n C14 C15 VDA sing 396 n n C15 C16 VDA sing 397 n n C16 C17 VDA doub 398 n n C17 C20 VDA sing 399 n n C20 C21 VDA sing 400 n n C20 S22 VDA sing 401 n n S22 C23 VDA sing 402 n n C23 C25 VDA sing 403 n n C25 O3 VDA sing 404 n n C25 C26 VDA sing 405 n n C25 C27 VDA sing 406 n n C26 C29 VDA sing 407 n n C27 C28 VDA sing 408 n n O4 C30 VDA sing 409 n n C30 C31 VDA sing 410 n n C31 O5 VDA sing 411 n n O2 HO2 VDA sing 412 n n C1 H1 VDA sing 413 n n C2 H2 VDA sing 414 n n C3 H3 VDA sing 415 n n C4 H4 VDA sing 416 n n C4 H4A VDA sing 417 n n C6 H6 VDA sing 418 n n C7 H7 VDA sing 419 n n C9 H9 VDA sing 420 n n C9 H9A VDA sing 421 n n C10 H10 VDA sing 422 n n C10 H10A VDA sing 423 n n C11 H11 VDA sing 424 n n C11 H11A VDA sing 425 n n C12 H12 VDA sing 426 n n C12 H12A VDA sing 427 n n C14 H14 VDA sing 428 n n C15 H15 VDA sing 429 n n C15 H15A VDA sing 430 n n C16 H16 VDA sing 431 n n C18 H18 VDA sing 432 n n C18 H18A VDA sing 433 n n C18 H18B VDA sing 434 n n C20 H20 VDA sing 435 n n C21 H21 VDA sing 436 n n C21 H21A VDA sing 437 n n C21 H21B VDA sing 438 n n C23 H23 VDA sing 439 n n C23 H23A VDA sing 440 n n O3 HO3 VDA sing 441 n n C26 H26 VDA sing 442 n n C26 H26A VDA sing 443 n n C27 H27 VDA sing 444 n n C27 H27A VDA sing 445 n n O1 HO1 VDA sing 446 n n C30 H30 VDA sing 447 n n C30 H30A VDA sing 448 n n C31 H31 VDA sing 449 n n C31 H31A VDA sing 450 n n O5 HO5 VDA sing 451 n n C29 H29 VDA sing 452 n n C29 H29A VDA sing 453 n n C29 H29B VDA sing 454 n n C28 H28 VDA sing 455 n n C28 H28A VDA sing 456 n n C28 H28B VDA sing 457 n n # _atom_sites.entry_id 2ZL9 _atom_sites.fract_transf_matrix[1][1] 0.006498 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000645 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023629 _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] 0.023853 _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 C 3 VDA A 1 500 500 VDA VDA . D 4 HOH A 1 59 59 HOH HOH . D 4 HOH A 2 501 1 HOH HOH . D 4 HOH A 3 502 2 HOH HOH . D 4 HOH A 4 503 3 HOH HOH . D 4 HOH A 5 504 4 HOH HOH . D 4 HOH A 6 505 5 HOH HOH . D 4 HOH A 7 506 6 HOH HOH . D 4 HOH A 8 507 7 HOH HOH . D 4 HOH A 9 508 8 HOH HOH . D 4 HOH A 10 509 11 HOH HOH . D 4 HOH A 11 510 12 HOH HOH . D 4 HOH A 12 511 13 HOH HOH . D 4 HOH A 13 512 15 HOH HOH . D 4 HOH A 14 513 17 HOH HOH . D 4 HOH A 15 514 19 HOH HOH . D 4 HOH A 16 515 20 HOH HOH . D 4 HOH A 17 516 21 HOH HOH . D 4 HOH A 18 517 25 HOH HOH . D 4 HOH A 19 518 26 HOH HOH . D 4 HOH A 20 519 27 HOH HOH . D 4 HOH A 21 520 28 HOH HOH . D 4 HOH A 22 521 29 HOH HOH . D 4 HOH A 23 522 30 HOH HOH . D 4 HOH A 24 523 31 HOH HOH . D 4 HOH A 25 524 32 HOH HOH . D 4 HOH A 26 525 33 HOH HOH . D 4 HOH A 27 526 34 HOH HOH . D 4 HOH A 28 527 35 HOH HOH . D 4 HOH A 29 528 36 HOH HOH . D 4 HOH A 30 529 37 HOH HOH . D 4 HOH A 31 530 38 HOH HOH . D 4 HOH A 32 531 39 HOH HOH . D 4 HOH A 33 532 40 HOH HOH . D 4 HOH A 34 533 44 HOH HOH . D 4 HOH A 35 534 45 HOH HOH . D 4 HOH A 36 535 46 HOH HOH . D 4 HOH A 37 536 47 HOH HOH . D 4 HOH A 38 537 48 HOH HOH . D 4 HOH A 39 538 49 HOH HOH . D 4 HOH A 40 539 50 HOH HOH . D 4 HOH A 41 540 52 HOH HOH . D 4 HOH A 42 541 53 HOH HOH . D 4 HOH A 43 542 54 HOH HOH . D 4 HOH A 44 543 55 HOH HOH . D 4 HOH A 45 544 56 HOH HOH . D 4 HOH A 46 545 57 HOH HOH . D 4 HOH A 47 546 58 HOH HOH . D 4 HOH A 48 547 60 HOH HOH . D 4 HOH A 49 548 62 HOH HOH . D 4 HOH A 50 549 63 HOH HOH . D 4 HOH A 51 550 64 HOH HOH . D 4 HOH A 52 551 65 HOH HOH . D 4 HOH A 53 552 66 HOH HOH . D 4 HOH A 54 553 67 HOH HOH . D 4 HOH A 55 554 68 HOH HOH . D 4 HOH A 56 555 70 HOH HOH . D 4 HOH A 57 556 74 HOH HOH . D 4 HOH A 58 557 75 HOH HOH . D 4 HOH A 59 558 76 HOH HOH . D 4 HOH A 60 559 77 HOH HOH . D 4 HOH A 61 560 78 HOH HOH . D 4 HOH A 62 561 79 HOH HOH . D 4 HOH A 63 562 80 HOH HOH . D 4 HOH A 64 563 81 HOH HOH . D 4 HOH A 65 564 83 HOH HOH . D 4 HOH A 66 565 84 HOH HOH . D 4 HOH A 67 566 85 HOH HOH . D 4 HOH A 68 567 87 HOH HOH . D 4 HOH A 69 568 88 HOH HOH . D 4 HOH A 70 569 90 HOH HOH . D 4 HOH A 71 570 91 HOH HOH . D 4 HOH A 72 571 92 HOH HOH . D 4 HOH A 73 572 93 HOH HOH . D 4 HOH A 74 573 94 HOH HOH . D 4 HOH A 75 574 95 HOH HOH . D 4 HOH A 76 575 96 HOH HOH . D 4 HOH A 77 576 97 HOH HOH . D 4 HOH A 78 577 99 HOH HOH . D 4 HOH A 79 578 100 HOH HOH . D 4 HOH A 80 579 101 HOH HOH . D 4 HOH A 81 580 102 HOH HOH . D 4 HOH A 82 581 103 HOH HOH . D 4 HOH A 83 582 104 HOH HOH . D 4 HOH A 84 583 105 HOH HOH . D 4 HOH A 85 584 106 HOH HOH . D 4 HOH A 86 585 107 HOH HOH . D 4 HOH A 87 586 108 HOH HOH . D 4 HOH A 88 587 109 HOH HOH . D 4 HOH A 89 588 110 HOH HOH . D 4 HOH A 90 589 111 HOH HOH . D 4 HOH A 91 590 112 HOH HOH . D 4 HOH A 92 591 113 HOH HOH . D 4 HOH A 93 592 114 HOH HOH . D 4 HOH A 94 593 115 HOH HOH . D 4 HOH A 95 594 116 HOH HOH . D 4 HOH A 96 595 118 HOH HOH . D 4 HOH A 97 596 119 HOH HOH . D 4 HOH A 98 597 121 HOH HOH . D 4 HOH A 99 598 122 HOH HOH . D 4 HOH A 100 599 123 HOH HOH . D 4 HOH A 101 600 125 HOH HOH . D 4 HOH A 102 601 126 HOH HOH . D 4 HOH A 103 602 127 HOH HOH . D 4 HOH A 104 603 129 HOH HOH . D 4 HOH A 105 604 130 HOH HOH . D 4 HOH A 106 605 132 HOH HOH . D 4 HOH A 107 606 133 HOH HOH . D 4 HOH A 108 607 135 HOH HOH . D 4 HOH A 109 608 136 HOH HOH . D 4 HOH A 110 609 137 HOH HOH . D 4 HOH A 111 610 138 HOH HOH . D 4 HOH A 112 611 139 HOH HOH . D 4 HOH A 113 612 140 HOH HOH . D 4 HOH A 114 613 141 HOH HOH . D 4 HOH A 115 614 143 HOH HOH . D 4 HOH A 116 615 144 HOH HOH . D 4 HOH A 117 616 145 HOH HOH . D 4 HOH A 118 617 147 HOH HOH . D 4 HOH A 119 618 149 HOH HOH . D 4 HOH A 120 619 150 HOH HOH . D 4 HOH A 121 620 153 HOH HOH . D 4 HOH A 122 621 154 HOH HOH . D 4 HOH A 123 622 155 HOH HOH . D 4 HOH A 124 623 156 HOH HOH . D 4 HOH A 125 624 157 HOH HOH . D 4 HOH A 126 625 158 HOH HOH . D 4 HOH A 127 626 159 HOH HOH . D 4 HOH A 128 627 161 HOH HOH . D 4 HOH A 129 628 163 HOH HOH . D 4 HOH A 130 629 164 HOH HOH . D 4 HOH A 131 630 166 HOH HOH . D 4 HOH A 132 631 167 HOH HOH . D 4 HOH A 133 632 169 HOH HOH . D 4 HOH A 134 633 172 HOH HOH . D 4 HOH A 135 634 174 HOH HOH . D 4 HOH A 136 635 175 HOH HOH . D 4 HOH A 137 636 177 HOH HOH . D 4 HOH A 138 637 178 HOH HOH . D 4 HOH A 139 638 179 HOH HOH . D 4 HOH A 140 639 180 HOH HOH . D 4 HOH A 141 640 183 HOH HOH . D 4 HOH A 142 641 184 HOH HOH . D 4 HOH A 143 642 185 HOH HOH . D 4 HOH A 144 643 186 HOH HOH . D 4 HOH A 145 644 187 HOH HOH . D 4 HOH A 146 645 191 HOH HOH . D 4 HOH A 147 646 192 HOH HOH . D 4 HOH A 148 647 194 HOH HOH . D 4 HOH A 149 648 197 HOH HOH . D 4 HOH A 150 649 198 HOH HOH . D 4 HOH A 151 650 199 HOH HOH . D 4 HOH A 152 651 201 HOH HOH . D 4 HOH A 153 652 202 HOH HOH . D 4 HOH A 154 653 204 HOH HOH . D 4 HOH A 155 654 205 HOH HOH . D 4 HOH A 156 655 206 HOH HOH . D 4 HOH A 157 656 207 HOH HOH . D 4 HOH A 158 657 208 HOH HOH . D 4 HOH A 159 658 210 HOH HOH . D 4 HOH A 160 659 211 HOH HOH . D 4 HOH A 161 660 212 HOH HOH . D 4 HOH A 162 661 213 HOH HOH . D 4 HOH A 163 662 214 HOH HOH . D 4 HOH A 164 663 215 HOH HOH . D 4 HOH A 165 664 216 HOH HOH . D 4 HOH A 166 665 217 HOH HOH . D 4 HOH A 167 666 220 HOH HOH . D 4 HOH A 168 667 221 HOH HOH . D 4 HOH A 169 668 223 HOH HOH . D 4 HOH A 170 669 224 HOH HOH . D 4 HOH A 171 670 227 HOH HOH . D 4 HOH A 172 671 228 HOH HOH . D 4 HOH A 173 672 230 HOH HOH . D 4 HOH A 174 673 234 HOH HOH . D 4 HOH A 175 674 236 HOH HOH . D 4 HOH A 176 675 240 HOH HOH . D 4 HOH A 177 676 242 HOH HOH . D 4 HOH A 178 677 243 HOH HOH . D 4 HOH A 179 678 244 HOH HOH . D 4 HOH A 180 679 245 HOH HOH . D 4 HOH A 181 680 246 HOH HOH . E 4 HOH C 1 51 51 HOH HOH . E 4 HOH C 2 71 71 HOH HOH . E 4 HOH C 3 73 73 HOH HOH . E 4 HOH C 4 86 86 HOH HOH . E 4 HOH C 5 128 128 HOH HOH . E 4 HOH C 6 134 134 HOH HOH . E 4 HOH C 7 148 148 HOH HOH . E 4 HOH C 8 193 193 HOH HOH . E 4 HOH C 9 203 203 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 O O2 VDA . . . C 3 16.341 8.598 19.342 1 25.61 ? O2 VDA 500 A 1 HETATM 2 C C1 VDA . . . C 3 14.808 6.038 19.069 1 28.21 ? C1 VDA 500 A 1 HETATM 3 C C2 VDA . . . C 3 14.284 7.441 18.444 1 24.83 ? C2 VDA 500 A 1 HETATM 4 C C3 VDA . . . C 3 14.911 8.713 19.348 1 25.52 ? C3 VDA 500 A 1 HETATM 5 C C4 VDA . . . C 3 14.394 8.548 20.899 1 26.51 ? C4 VDA 500 A 1 HETATM 6 C C5 VDA . . . C 3 14.551 7.136 21.544 1 30.93 ? C5 VDA 500 A 1 HETATM 7 C C6 VDA . . . C 3 14.434 6.93 22.87 1 30.2 ? C6 VDA 500 A 1 HETATM 8 C C7 VDA . . . C 3 14.95 5.82 23.721 1 31.18 ? C7 VDA 500 A 1 HETATM 9 C C8 VDA . . . C 3 14.727 5.701 24.946 1 32.82 ? C8 VDA 500 A 1 HETATM 10 C C9 VDA . . . C 3 14.513 6.971 26.034 1 31.1 ? C9 VDA 500 A 1 HETATM 11 C C10 VDA . . . C 3 14.254 5.919 20.542 1 25.82 ? C10 VDA 500 A 1 HETATM 12 C C11 VDA . . . C 3 13.256 6.821 27.019 1 31.83 ? C11 VDA 500 A 1 HETATM 13 C C12 VDA . . . C 3 13.092 5.25 27.577 1 33.6 ? C12 VDA 500 A 1 HETATM 14 C C13 VDA . . . C 3 13.302 4.041 26.408 1 32.52 ? C13 VDA 500 A 1 HETATM 15 C C14 VDA . . . C 3 14.728 4.352 25.728 1 33.15 ? C14 VDA 500 A 1 HETATM 16 C C15 VDA . . . C 3 15.217 2.898 25.026 1 32.76 ? C15 VDA 500 A 1 HETATM 17 C C16 VDA . . . C 3 14.366 1.844 25.787 1 34.74 ? C16 VDA 500 A 1 HETATM 18 C C17 VDA . . . C 3 13.624 2.598 26.944 1 34.37 ? C17 VDA 500 A 1 HETATM 19 C C18 VDA . . . C 3 11.938 4.196 25.417 1 32.22 ? C18 VDA 500 A 1 HETATM 20 C C20 VDA . . . C 3 12.798 2.164 28.343 1 34.67 ? C20 VDA 500 A 1 HETATM 21 C C21 VDA . . . C 3 13.549 0.791 28.732 1 35.32 ? C21 VDA 500 A 1 HETATM 22 S S22 VDA . . . C 3 11.124 2.228 28.324 1 40.58 ? S22 VDA 500 A 1 HETATM 23 C C23 VDA . . . C 3 10.551 1.217 27.346 1 38.11 ? C23 VDA 500 A 1 HETATM 24 C C25 VDA . . . C 3 9.335 0.372 27.818 1 38.24 ? C25 VDA 500 A 1 HETATM 25 O O3 VDA . . . C 3 10.242 -0.752 28.394 1 37.07 ? O3 VDA 500 A 1 HETATM 26 C C26 VDA . . . C 3 8.236 0.757 28.508 1 39.3 ? C26 VDA 500 A 1 HETATM 27 C C27 VDA . . . C 3 9.195 -0.373 26.391 1 36.53 ? C27 VDA 500 A 1 HETATM 28 O O1 VDA . . . C 3 14.389 4.919 18.298 1 25.09 ? O1 VDA 500 A 1 HETATM 29 O O4 VDA . . . C 3 14.625 7.62 17.08 1 23.73 ? O4 VDA 500 A 1 HETATM 30 C C30 VDA . . . C 3 13.538 8.121 16.456 1 24.39 ? C30 VDA 500 A 1 HETATM 31 C C31 VDA . . . C 3 14.128 8.244 14.878 1 25.25 ? C31 VDA 500 A 1 HETATM 32 O O5 VDA . . . C 3 13.768 6.985 14.292 1 28.08 ? O5 VDA 500 A 1 HETATM 33 C C29 VDA . . . C 3 7.387 1.974 27.706 1 39.57 ? C29 VDA 500 A 1 HETATM 34 C C28 VDA . . . C 3 8.167 -1.624 26.236 1 38.34 ? C28 VDA 500 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 34 #