data_2ZLA # _model_server_result.job_id YsmBGi-egti5ok-Pbusfdg _model_server_result.datetime_utc '2024-12-04 11:00:15' _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 2zla # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":500}' # _entry.id 2ZLA # _exptl.entry_id 2ZLA _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,2S,3R,5Z,7E)-17-{(1R)-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 95.77 _cell.angle_gamma 90 _cell.entry_id 2ZLA _cell.length_a 153.985 _cell.length_b 42.002 _cell.length_c 42.152 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZLA _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 VDB _chem_comp.mon_nstd_flag . _chem_comp.name (1R,2S,3R,5Z,7E)-17-{(1R)-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 '(20R)-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 C29 C26 VDB sing 376 n n C26 C25 VDB sing 377 n n C25 C27 VDB sing 378 n n C25 O3 VDB sing 379 n n C25 C23 VDB sing 380 n n C27 C28 VDB sing 381 n n C23 S22 VDB sing 382 n n S22 C20 VDB sing 383 n n C20 C21 VDB sing 384 n n C20 C17 VDB sing 385 n n C17 C16 VDB doub 386 n n C17 C13 VDB sing 387 n n C16 C15 VDB sing 388 n n C15 C14 VDB sing 389 n n C14 C13 VDB sing 390 n n C14 C8 VDB sing 391 n n C13 C18 VDB sing 392 n n C13 C12 VDB sing 393 n n C12 C11 VDB sing 394 n n C11 C9 VDB sing 395 n n C9 C8 VDB sing 396 n n C8 C7 VDB doub 397 n n C7 C6 VDB sing 398 n n C6 C5 VDB doub 399 n n C5 C10 VDB sing 400 n n C5 C4 VDB sing 401 n n C10 C1 VDB sing 402 n n C1 O1 VDB sing 403 n n C1 C2 VDB sing 404 n n C4 C3 VDB sing 405 n n C3 O2 VDB sing 406 n n C3 C2 VDB sing 407 n n C2 O4 VDB sing 408 n n O4 C30 VDB sing 409 n n C30 C31 VDB sing 410 n n C31 O5 VDB sing 411 n n C29 H29 VDB sing 412 n n C29 H29A VDB sing 413 n n C29 H29B VDB sing 414 n n C26 H26 VDB sing 415 n n C26 H26A VDB sing 416 n n C27 H27 VDB sing 417 n n C27 H27A VDB sing 418 n n C28 H28 VDB sing 419 n n C28 H28A VDB sing 420 n n C28 H28B VDB sing 421 n n O3 HO3 VDB sing 422 n n C23 H23 VDB sing 423 n n C23 H23A VDB sing 424 n n C20 H20 VDB sing 425 n n C21 H21 VDB sing 426 n n C21 H21A VDB sing 427 e n C21 H21B VDB sing 428 n n C16 H16 VDB sing 429 n n C15 H15 VDB sing 430 n n C15 H15A VDB sing 431 n n C14 H14 VDB sing 432 n n C18 H18 VDB sing 433 n n C18 H18A VDB sing 434 n n C18 H18B VDB sing 435 n n C12 H12 VDB sing 436 n n C12 H12A VDB sing 437 n n C11 H11 VDB sing 438 n n C11 H11A VDB sing 439 n n C9 H9 VDB sing 440 n n C9 H9A VDB sing 441 n n C7 H7 VDB sing 442 n n C6 H6 VDB sing 443 n n C10 H10 VDB sing 444 n n C10 H10A VDB sing 445 n n C1 H1 VDB sing 446 n n O1 HO1 VDB sing 447 n n C4 H4 VDB sing 448 n n C4 H4A VDB sing 449 n n C3 H3 VDB sing 450 n n O2 HO2 VDB sing 451 n n C2 H2 VDB sing 452 n n C30 H30 VDB sing 453 n n C30 H30A VDB sing 454 n n C31 H31 VDB sing 455 n n C31 H31A VDB sing 456 n n O5 HO5 VDB sing 457 n n # _atom_sites.entry_id 2ZLA _atom_sites.fract_transf_matrix[1][1] 0.006494 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000656 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023808 _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] 0.023844 _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 VDB A 1 500 500 VDB VDB . D 4 HOH A 1 501 2 HOH HOH . D 4 HOH A 2 502 3 HOH HOH . D 4 HOH A 3 503 4 HOH HOH . D 4 HOH A 4 504 5 HOH HOH . D 4 HOH A 5 505 6 HOH HOH . D 4 HOH A 6 506 7 HOH HOH . D 4 HOH A 7 507 8 HOH HOH . D 4 HOH A 8 508 9 HOH HOH . D 4 HOH A 9 509 10 HOH HOH . D 4 HOH A 10 510 11 HOH HOH . D 4 HOH A 11 511 12 HOH HOH . D 4 HOH A 12 512 13 HOH HOH . D 4 HOH A 13 513 14 HOH HOH . D 4 HOH A 14 514 15 HOH HOH . D 4 HOH A 15 515 16 HOH HOH . D 4 HOH A 16 516 17 HOH HOH . D 4 HOH A 17 517 18 HOH HOH . D 4 HOH A 18 518 19 HOH HOH . D 4 HOH A 19 519 20 HOH HOH . D 4 HOH A 20 520 21 HOH HOH . D 4 HOH A 21 521 22 HOH HOH . D 4 HOH A 22 522 23 HOH HOH . D 4 HOH A 23 523 24 HOH HOH . D 4 HOH A 24 524 25 HOH HOH . D 4 HOH A 25 525 26 HOH HOH . D 4 HOH A 26 526 27 HOH HOH . D 4 HOH A 27 527 28 HOH HOH . D 4 HOH A 28 528 29 HOH HOH . D 4 HOH A 29 529 30 HOH HOH . D 4 HOH A 30 530 31 HOH HOH . D 4 HOH A 31 531 32 HOH HOH . D 4 HOH A 32 532 33 HOH HOH . D 4 HOH A 33 533 35 HOH HOH . D 4 HOH A 34 534 37 HOH HOH . D 4 HOH A 35 535 39 HOH HOH . D 4 HOH A 36 536 40 HOH HOH . D 4 HOH A 37 537 41 HOH HOH . D 4 HOH A 38 538 42 HOH HOH . D 4 HOH A 39 539 43 HOH HOH . D 4 HOH A 40 540 44 HOH HOH . D 4 HOH A 41 541 45 HOH HOH . D 4 HOH A 42 542 47 HOH HOH . D 4 HOH A 43 543 48 HOH HOH . D 4 HOH A 44 544 50 HOH HOH . D 4 HOH A 45 545 51 HOH HOH . D 4 HOH A 46 546 52 HOH HOH . D 4 HOH A 47 547 53 HOH HOH . D 4 HOH A 48 548 54 HOH HOH . D 4 HOH A 49 549 55 HOH HOH . D 4 HOH A 50 550 56 HOH HOH . D 4 HOH A 51 551 57 HOH HOH . D 4 HOH A 52 552 58 HOH HOH . D 4 HOH A 53 553 59 HOH HOH . D 4 HOH A 54 554 60 HOH HOH . D 4 HOH A 55 555 61 HOH HOH . D 4 HOH A 56 556 64 HOH HOH . D 4 HOH A 57 557 65 HOH HOH . D 4 HOH A 58 558 66 HOH HOH . D 4 HOH A 59 559 67 HOH HOH . D 4 HOH A 60 560 68 HOH HOH . D 4 HOH A 61 561 69 HOH HOH . D 4 HOH A 62 562 70 HOH HOH . D 4 HOH A 63 563 71 HOH HOH . D 4 HOH A 64 564 72 HOH HOH . D 4 HOH A 65 565 73 HOH HOH . D 4 HOH A 66 566 74 HOH HOH . D 4 HOH A 67 567 75 HOH HOH . D 4 HOH A 68 568 76 HOH HOH . D 4 HOH A 69 569 77 HOH HOH . D 4 HOH A 70 570 78 HOH HOH . D 4 HOH A 71 571 79 HOH HOH . D 4 HOH A 72 572 80 HOH HOH . D 4 HOH A 73 573 82 HOH HOH . D 4 HOH A 74 574 83 HOH HOH . D 4 HOH A 75 575 84 HOH HOH . D 4 HOH A 76 576 87 HOH HOH . D 4 HOH A 77 577 88 HOH HOH . D 4 HOH A 78 578 89 HOH HOH . D 4 HOH A 79 579 90 HOH HOH . D 4 HOH A 80 580 92 HOH HOH . D 4 HOH A 81 581 93 HOH HOH . D 4 HOH A 82 582 94 HOH HOH . D 4 HOH A 83 583 95 HOH HOH . D 4 HOH A 84 584 96 HOH HOH . D 4 HOH A 85 585 97 HOH HOH . D 4 HOH A 86 586 102 HOH HOH . D 4 HOH A 87 587 103 HOH HOH . D 4 HOH A 88 588 104 HOH HOH . D 4 HOH A 89 589 105 HOH HOH . D 4 HOH A 90 590 106 HOH HOH . D 4 HOH A 91 591 107 HOH HOH . D 4 HOH A 92 592 108 HOH HOH . D 4 HOH A 93 593 109 HOH HOH . D 4 HOH A 94 594 110 HOH HOH . D 4 HOH A 95 595 112 HOH HOH . D 4 HOH A 96 596 114 HOH HOH . D 4 HOH A 97 597 115 HOH HOH . D 4 HOH A 98 598 117 HOH HOH . D 4 HOH A 99 599 119 HOH HOH . D 4 HOH A 100 600 120 HOH HOH . D 4 HOH A 101 601 122 HOH HOH . D 4 HOH A 102 602 124 HOH HOH . D 4 HOH A 103 603 125 HOH HOH . D 4 HOH A 104 604 127 HOH HOH . D 4 HOH A 105 605 128 HOH HOH . D 4 HOH A 106 606 129 HOH HOH . D 4 HOH A 107 607 130 HOH HOH . D 4 HOH A 108 608 131 HOH HOH . D 4 HOH A 109 609 132 HOH HOH . D 4 HOH A 110 610 133 HOH HOH . D 4 HOH A 111 611 136 HOH HOH . D 4 HOH A 112 612 137 HOH HOH . D 4 HOH A 113 613 138 HOH HOH . D 4 HOH A 114 614 139 HOH HOH . D 4 HOH A 115 615 141 HOH HOH . D 4 HOH A 116 616 142 HOH HOH . D 4 HOH A 117 617 143 HOH HOH . D 4 HOH A 118 618 145 HOH HOH . D 4 HOH A 119 619 146 HOH HOH . D 4 HOH A 120 620 147 HOH HOH . D 4 HOH A 121 622 150 HOH HOH . D 4 HOH A 122 623 152 HOH HOH . D 4 HOH A 123 624 153 HOH HOH . D 4 HOH A 124 625 156 HOH HOH . D 4 HOH A 125 626 157 HOH HOH . D 4 HOH A 126 627 160 HOH HOH . D 4 HOH A 127 628 162 HOH HOH . D 4 HOH A 128 629 163 HOH HOH . D 4 HOH A 129 630 164 HOH HOH . D 4 HOH A 130 631 165 HOH HOH . D 4 HOH A 131 632 167 HOH HOH . D 4 HOH A 132 633 168 HOH HOH . D 4 HOH A 133 634 169 HOH HOH . D 4 HOH A 134 635 170 HOH HOH . D 4 HOH A 135 636 177 HOH HOH . D 4 HOH A 136 637 178 HOH HOH . D 4 HOH A 137 638 179 HOH HOH . D 4 HOH A 138 639 181 HOH HOH . D 4 HOH A 139 640 182 HOH HOH . D 4 HOH A 140 641 183 HOH HOH . D 4 HOH A 141 642 184 HOH HOH . D 4 HOH A 142 643 186 HOH HOH . D 4 HOH A 143 644 187 HOH HOH . D 4 HOH A 144 645 188 HOH HOH . D 4 HOH A 145 646 190 HOH HOH . D 4 HOH A 146 647 191 HOH HOH . D 4 HOH A 147 648 192 HOH HOH . D 4 HOH A 148 649 193 HOH HOH . D 4 HOH A 149 650 194 HOH HOH . D 4 HOH A 150 651 197 HOH HOH . D 4 HOH A 151 652 199 HOH HOH . D 4 HOH A 152 653 200 HOH HOH . D 4 HOH A 153 654 201 HOH HOH . D 4 HOH A 154 655 202 HOH HOH . D 4 HOH A 155 656 203 HOH HOH . D 4 HOH A 156 657 204 HOH HOH . D 4 HOH A 157 658 207 HOH HOH . D 4 HOH A 158 659 208 HOH HOH . D 4 HOH A 159 660 211 HOH HOH . D 4 HOH A 160 661 212 HOH HOH . D 4 HOH A 161 662 216 HOH HOH . D 4 HOH A 162 663 218 HOH HOH . D 4 HOH A 163 664 220 HOH HOH . D 4 HOH A 164 665 221 HOH HOH . D 4 HOH A 165 666 222 HOH HOH . D 4 HOH A 166 667 223 HOH HOH . D 4 HOH A 167 668 224 HOH HOH . E 4 HOH C 1 38 38 HOH HOH . E 4 HOH C 2 99 99 HOH HOH . E 4 HOH C 3 101 101 HOH HOH . E 4 HOH C 4 118 118 HOH HOH . E 4 HOH C 5 158 158 HOH HOH . E 4 HOH C 6 166 166 HOH HOH . E 4 HOH C 7 174 174 HOH HOH . E 4 HOH C 8 206 206 HOH HOH . E 4 HOH C 9 621 149 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 C C29 VDB . . . C 3 7.708 -0.703 29.648 1 34.4 ? C29 VDB 500 A 1 HETATM 2 C C26 VDB . . . C 3 8.339 0.463 28.866 1 32.32 ? C26 VDB 500 A 1 HETATM 3 C C25 VDB . . . C 3 9.388 0.108 27.776 1 30.83 ? C25 VDB 500 A 1 HETATM 4 C C27 VDB . . . C 3 8.728 -0.677 26.603 1 31.64 ? C27 VDB 500 A 1 HETATM 5 C C28 VDB . . . C 3 7.597 0.012 25.814 1 32.15 ? C28 VDB 500 A 1 HETATM 6 O O3 VDB . . . C 3 10.417 -0.676 28.379 1 30.48 ? O3 VDB 500 A 1 HETATM 7 C C23 VDB . . . C 3 9.931 1.47 27.326 1 31.31 ? C23 VDB 500 A 1 HETATM 8 S S22 VDB . . . C 3 11.054 2.4 28.436 1 31.5 ? S22 VDB 500 A 1 HETATM 9 C C20 VDB . . . C 3 12.751 1.734 28.102 1 30.34 ? C20 VDB 500 A 1 HETATM 10 C C21 VDB . . . C 3 13.702 1.898 29.302 1 27.98 ? C21 VDB 500 A 1 HETATM 11 C C17 VDB . . . C 3 13.39 2.429 26.839 1 29.63 ? C17 VDB 500 A 1 HETATM 12 C C16 VDB . . . C 3 14.169 1.796 25.931 1 31.76 ? C16 VDB 500 A 1 HETATM 13 C C15 VDB . . . C 3 14.642 2.781 24.837 1 31.18 ? C15 VDB 500 A 1 HETATM 14 C C14 VDB . . . C 3 14.617 4.042 25.705 1 28.45 ? C14 VDB 500 A 1 HETATM 15 C C13 VDB . . . C 3 13.25 3.933 26.458 1 28.39 ? C13 VDB 500 A 1 HETATM 16 C C18 VDB . . . C 3 11.906 4.076 25.632 1 27.51 ? C18 VDB 500 A 1 HETATM 17 C C12 VDB . . . C 3 13.304 5.002 27.607 1 29.14 ? C12 VDB 500 A 1 HETATM 18 C C11 VDB . . . C 3 13.539 6.466 27.087 1 29.73 ? C11 VDB 500 A 1 HETATM 19 C C9 VDB . . . C 3 14.702 6.58 26.065 1 27.44 ? C9 VDB 500 A 1 HETATM 20 C C8 VDB . . . C 3 14.626 5.461 25.014 1 28.89 ? C8 VDB 500 A 1 HETATM 21 C C7 VDB . . . C 3 14.518 5.646 23.647 1 25.98 ? C7 VDB 500 A 1 HETATM 22 C C6 VDB . . . C 3 14.459 6.736 22.779 1 28.08 ? C6 VDB 500 A 1 HETATM 23 C C5 VDB . . . C 3 14.323 6.903 21.417 1 27.52 ? C5 VDB 500 A 1 HETATM 24 C C10 VDB . . . C 3 14.186 5.726 20.443 1 24.29 ? C10 VDB 500 A 1 HETATM 25 C C1 VDB . . . C 3 14.76 6.002 19.046 1 23.7 ? C1 VDB 500 A 1 HETATM 26 O O1 VDB . . . C 3 14.386 4.9 18.223 1 23.34 ? O1 VDB 500 A 1 HETATM 27 C C4 VDB . . . C 3 14.288 8.357 20.884 1 24.42 ? C4 VDB 500 A 1 HETATM 28 C C3 VDB . . . C 3 14.718 8.509 19.398 1 23.73 ? C3 VDB 500 A 1 HETATM 29 O O2 VDB . . . C 3 16.142 8.523 19.425 1 24.46 ? O2 VDB 500 A 1 HETATM 30 C C2 VDB . . . C 3 14.195 7.341 18.473 1 23.66 ? C2 VDB 500 A 1 HETATM 31 O O4 VDB . . . C 3 14.566 7.624 17.089 1 22.01 ? O4 VDB 500 A 1 HETATM 32 C C30 VDB . . . C 3 13.449 8.187 16.359 1 25.27 ? C30 VDB 500 A 1 HETATM 33 C C31 VDB . . . C 3 13.967 8.152 14.915 1 27.39 ? C31 VDB 500 A 1 HETATM 34 O O5 VDB . . . C 3 13.713 6.899 14.286 1 26.2 ? O5 VDB 500 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 21 _model_server_stats.element_count 34 #