data_3VT3 # _model_server_result.job_id fRueh002mVz70kdDvkJsyQ _model_server_result.datetime_utc '2024-10-11 13:26:26' _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 3vt3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":500}' # _entry.id 3VT3 # _exptl.entry_id 3VT3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 416.636 _entity.id 3 _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 96.31 _cell.angle_gamma 90 _cell.entry_id 3VT3 _cell.length_a 153.883 _cell.length_b 41.626 _cell.length_c 41.956 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VT3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 software_defined_assembly 1 ? monomeric 1 author_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,E,F,G,H 1 1 A,C,D,E,F,G 2 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 '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 389 n n O2 HO2 VDX sing 390 n n O3 C25 VDX sing 391 n n O3 HO3 VDX sing 392 n n C1 C2 VDX sing 393 n n C1 C10 VDX sing 394 n n C1 O1 VDX sing 395 n n C1 H11 VDX sing 396 n n C2 C3 VDX sing 397 n n C2 H21 VDX sing 398 n n C2 H22 VDX sing 399 n n C3 C4 VDX sing 400 n n C3 H31 VDX sing 401 n n C4 C5 VDX sing 402 n n C4 H41 VDX sing 403 n n C4 H42 VDX sing 404 n n C5 C6 VDX doub 405 z n C5 C10 VDX sing 406 n n C6 C7 VDX sing 407 n n C6 H61 VDX sing 408 n n C7 C8 VDX doub 409 e n C7 H71 VDX sing 410 n n C8 C9 VDX sing 411 n n C8 C14 VDX sing 412 n n C9 C11 VDX sing 413 n n C9 H91 VDX sing 414 n n C9 H92 VDX sing 415 n n C10 C19 VDX doub 416 n n C11 C12 VDX sing 417 n n C11 H111 VDX sing 418 n n C11 H112 VDX sing 419 n n C12 C13 VDX sing 420 n n C12 H121 VDX sing 421 n n C12 H122 VDX sing 422 n n C13 C14 VDX sing 423 n n C13 C17 VDX sing 424 n n C13 C18 VDX sing 425 n n C14 C15 VDX sing 426 n n C14 H141 VDX sing 427 n n C15 C16 VDX sing 428 n n C15 H151 VDX sing 429 n n C15 H152 VDX sing 430 n n C16 C17 VDX sing 431 n n C16 H161 VDX sing 432 n n C16 H162 VDX sing 433 n n C17 C20 VDX sing 434 n n C17 H171 VDX sing 435 n n C18 H181 VDX sing 436 n n C18 H182 VDX sing 437 n n C18 H183 VDX sing 438 n n C19 H191 VDX sing 439 n n C19 H192 VDX sing 440 n n C20 C21 VDX sing 441 n n C20 C22 VDX sing 442 n n C20 H201 VDX sing 443 n n C21 H211 VDX sing 444 n n C21 H212 VDX sing 445 n n C21 H213 VDX sing 446 n n C22 C23 VDX sing 447 n n C22 H221 VDX sing 448 n n C22 H222 VDX sing 449 n n C23 C24 VDX sing 450 n n C23 H231 VDX sing 451 n n C23 H232 VDX sing 452 n n C24 C25 VDX sing 453 n n C24 H241 VDX sing 454 n n C24 H242 VDX sing 455 n n C25 C26 VDX sing 456 n n C25 C27 VDX sing 457 n n C26 H261 VDX sing 458 n n C26 H262 VDX sing 459 n n C26 H263 VDX sing 460 n n C27 H271 VDX sing 461 n n C27 H272 VDX sing 462 n n C27 H273 VDX sing 463 n n O1 HO1 VDX sing 464 n n # _atom_sites.entry_id 3VT3 _atom_sites.fract_transf_matrix[1][1] 0.006498 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000718 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024023 _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] 0.02398 _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 VDX A 1 500 500 VDX VDX . D 4 EDO A 1 501 501 EDO EDO . E 5 FMT A 1 502 502 FMT FMT . F 5 FMT A 1 503 503 FMT FMT . G 6 HOH A 1 601 1 HOH HOH . G 6 HOH A 2 602 2 HOH HOH . G 6 HOH A 3 603 3 HOH HOH . G 6 HOH A 4 604 4 HOH HOH . G 6 HOH A 5 605 5 HOH HOH . G 6 HOH A 6 606 6 HOH HOH . G 6 HOH A 7 607 7 HOH HOH . G 6 HOH A 8 608 8 HOH HOH . G 6 HOH A 9 609 9 HOH HOH . G 6 HOH A 10 610 10 HOH HOH . G 6 HOH A 11 611 11 HOH HOH . G 6 HOH A 12 612 12 HOH HOH . G 6 HOH A 13 613 13 HOH HOH . G 6 HOH A 14 614 14 HOH HOH . G 6 HOH A 15 615 15 HOH HOH . G 6 HOH A 16 616 16 HOH HOH . G 6 HOH A 17 617 17 HOH HOH . G 6 HOH A 18 618 18 HOH HOH . G 6 HOH A 19 619 19 HOH HOH . G 6 HOH A 20 620 20 HOH HOH . G 6 HOH A 21 621 21 HOH HOH . G 6 HOH A 22 622 22 HOH HOH . G 6 HOH A 23 623 23 HOH HOH . G 6 HOH A 24 624 24 HOH HOH . G 6 HOH A 25 625 25 HOH HOH . G 6 HOH A 26 626 26 HOH HOH . G 6 HOH A 27 627 27 HOH HOH . G 6 HOH A 28 628 28 HOH HOH . G 6 HOH A 29 629 29 HOH HOH . G 6 HOH A 30 630 30 HOH HOH . G 6 HOH A 31 631 31 HOH HOH . G 6 HOH A 32 632 32 HOH HOH . G 6 HOH A 33 633 33 HOH HOH . G 6 HOH A 34 634 34 HOH HOH . G 6 HOH A 35 635 35 HOH HOH . G 6 HOH A 36 636 36 HOH HOH . G 6 HOH A 37 637 37 HOH HOH . G 6 HOH A 38 638 38 HOH HOH . G 6 HOH A 39 639 39 HOH HOH . G 6 HOH A 40 640 40 HOH HOH . G 6 HOH A 41 641 41 HOH HOH . G 6 HOH A 42 642 42 HOH HOH . G 6 HOH A 43 643 43 HOH HOH . G 6 HOH A 44 644 45 HOH HOH . G 6 HOH A 45 645 46 HOH HOH . G 6 HOH A 46 646 47 HOH HOH . G 6 HOH A 47 647 48 HOH HOH . G 6 HOH A 48 648 49 HOH HOH . G 6 HOH A 49 649 50 HOH HOH . G 6 HOH A 50 650 51 HOH HOH . G 6 HOH A 51 651 52 HOH HOH . G 6 HOH A 52 652 53 HOH HOH . G 6 HOH A 53 653 54 HOH HOH . G 6 HOH A 54 654 55 HOH HOH . G 6 HOH A 55 655 56 HOH HOH . G 6 HOH A 56 656 57 HOH HOH . G 6 HOH A 57 657 58 HOH HOH . G 6 HOH A 58 658 59 HOH HOH . G 6 HOH A 59 659 60 HOH HOH . G 6 HOH A 60 660 61 HOH HOH . G 6 HOH A 61 661 62 HOH HOH . G 6 HOH A 62 662 63 HOH HOH . G 6 HOH A 63 663 64 HOH HOH . G 6 HOH A 64 664 65 HOH HOH . G 6 HOH A 65 665 66 HOH HOH . G 6 HOH A 66 666 67 HOH HOH . G 6 HOH A 67 667 68 HOH HOH . G 6 HOH A 68 668 69 HOH HOH . G 6 HOH A 69 669 70 HOH HOH . G 6 HOH A 70 670 71 HOH HOH . G 6 HOH A 71 671 72 HOH HOH . G 6 HOH A 72 672 73 HOH HOH . G 6 HOH A 73 673 74 HOH HOH . G 6 HOH A 74 674 75 HOH HOH . G 6 HOH A 75 675 76 HOH HOH . G 6 HOH A 76 676 77 HOH HOH . G 6 HOH A 77 677 78 HOH HOH . G 6 HOH A 78 678 79 HOH HOH . G 6 HOH A 79 679 80 HOH HOH . G 6 HOH A 80 680 81 HOH HOH . G 6 HOH A 81 681 82 HOH HOH . G 6 HOH A 82 682 83 HOH HOH . G 6 HOH A 83 683 84 HOH HOH . G 6 HOH A 84 684 85 HOH HOH . G 6 HOH A 85 685 88 HOH HOH . G 6 HOH A 86 686 89 HOH HOH . G 6 HOH A 87 687 90 HOH HOH . G 6 HOH A 88 688 91 HOH HOH . G 6 HOH A 89 689 92 HOH HOH . G 6 HOH A 90 690 93 HOH HOH . G 6 HOH A 91 691 94 HOH HOH . G 6 HOH A 92 692 95 HOH HOH . G 6 HOH A 93 693 96 HOH HOH . G 6 HOH A 94 694 97 HOH HOH . G 6 HOH A 95 695 98 HOH HOH . G 6 HOH A 96 696 99 HOH HOH . G 6 HOH A 97 697 100 HOH HOH . G 6 HOH A 98 698 101 HOH HOH . G 6 HOH A 99 699 102 HOH HOH . G 6 HOH A 100 700 103 HOH HOH . G 6 HOH A 101 701 104 HOH HOH . G 6 HOH A 102 702 105 HOH HOH . G 6 HOH A 103 703 106 HOH HOH . G 6 HOH A 104 704 107 HOH HOH . G 6 HOH A 105 705 108 HOH HOH . G 6 HOH A 106 706 109 HOH HOH . G 6 HOH A 107 707 110 HOH HOH . G 6 HOH A 108 708 112 HOH HOH . G 6 HOH A 109 709 113 HOH HOH . G 6 HOH A 110 710 114 HOH HOH . G 6 HOH A 111 711 115 HOH HOH . G 6 HOH A 112 712 116 HOH HOH . G 6 HOH A 113 713 117 HOH HOH . G 6 HOH A 114 714 118 HOH HOH . G 6 HOH A 115 715 119 HOH HOH . G 6 HOH A 116 716 120 HOH HOH . G 6 HOH A 117 717 122 HOH HOH . G 6 HOH A 118 718 123 HOH HOH . G 6 HOH A 119 719 124 HOH HOH . G 6 HOH A 120 720 125 HOH HOH . G 6 HOH A 121 721 126 HOH HOH . G 6 HOH A 122 722 127 HOH HOH . G 6 HOH A 123 723 129 HOH HOH . G 6 HOH A 124 724 130 HOH HOH . G 6 HOH A 125 725 131 HOH HOH . G 6 HOH A 126 726 132 HOH HOH . G 6 HOH A 127 727 133 HOH HOH . G 6 HOH A 128 728 134 HOH HOH . G 6 HOH A 129 729 135 HOH HOH . G 6 HOH A 130 730 136 HOH HOH . G 6 HOH A 131 731 137 HOH HOH . G 6 HOH A 132 732 138 HOH HOH . G 6 HOH A 133 733 139 HOH HOH . G 6 HOH A 134 734 140 HOH HOH . G 6 HOH A 135 735 141 HOH HOH . G 6 HOH A 136 736 142 HOH HOH . G 6 HOH A 137 737 143 HOH HOH . G 6 HOH A 138 738 144 HOH HOH . G 6 HOH A 139 739 145 HOH HOH . G 6 HOH A 140 740 146 HOH HOH . G 6 HOH A 141 741 147 HOH HOH . G 6 HOH A 142 742 148 HOH HOH . G 6 HOH A 143 743 149 HOH HOH . G 6 HOH A 144 744 150 HOH HOH . G 6 HOH A 145 745 151 HOH HOH . G 6 HOH A 146 746 152 HOH HOH . G 6 HOH A 147 747 153 HOH HOH . G 6 HOH A 148 748 154 HOH HOH . G 6 HOH A 149 749 155 HOH HOH . G 6 HOH A 150 750 156 HOH HOH . G 6 HOH A 151 751 157 HOH HOH . G 6 HOH A 152 752 158 HOH HOH . G 6 HOH A 153 753 159 HOH HOH . G 6 HOH A 154 754 160 HOH HOH . G 6 HOH A 155 755 161 HOH HOH . G 6 HOH A 156 756 162 HOH HOH . G 6 HOH A 157 757 163 HOH HOH . G 6 HOH A 158 758 164 HOH HOH . G 6 HOH A 159 759 165 HOH HOH . G 6 HOH A 160 760 166 HOH HOH . G 6 HOH A 161 761 167 HOH HOH . G 6 HOH A 162 762 168 HOH HOH . H 6 HOH C 1 701 44 HOH HOH . H 6 HOH C 2 702 86 HOH HOH . H 6 HOH C 3 703 87 HOH HOH . H 6 HOH C 4 704 111 HOH HOH . H 6 HOH C 5 705 121 HOH HOH . H 6 HOH C 6 706 128 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 VDX . . . C 3 16.199 9.021 19.425 1 20.01 ? O2 VDX 500 A 1 HETATM 2 O O3 VDX . . . C 3 9.211 -1.565 28.152 1 22.69 ? O3 VDX 500 A 1 HETATM 3 C C1 VDX . . . C 3 14.531 6.519 18.955 1 24.76 ? C1 VDX 500 A 1 HETATM 4 C C2 VDX . . . C 3 14.313 7.92 18.308 1 22.96 ? C2 VDX 500 A 1 HETATM 5 C C3 VDX . . . C 3 14.791 9.067 19.26 1 18.63 ? C3 VDX 500 A 1 HETATM 6 C C4 VDX . . . C 3 14.114 8.964 20.669 1 22.3 ? C4 VDX 500 A 1 HETATM 7 C C5 VDX . . . C 3 14.189 7.519 21.228 1 22.23 ? C5 VDX 500 A 1 HETATM 8 C C6 VDX . . . C 3 14.579 7.447 22.58 1 20.56 ? C6 VDX 500 A 1 HETATM 9 C C7 VDX . . . C 3 14.736 6.299 23.355 1 19.81 ? C7 VDX 500 A 1 HETATM 10 C C8 VDX . . . C 3 14.587 6.19 24.736 1 18.83 ? C8 VDX 500 A 1 HETATM 11 C C9 VDX . . . C 3 14.206 7.387 25.672 1 25.22 ? C9 VDX 500 A 1 HETATM 12 C C10 VDX . . . C 3 13.868 6.441 20.34 1 23.45 ? C10 VDX 500 A 1 HETATM 13 C C11 VDX . . . C 3 13.005 7.031 26.592 1 21.76 ? C11 VDX 500 A 1 HETATM 14 C C12 VDX . . . C 3 13.113 5.604 27.233 1 23.3 ? C12 VDX 500 A 1 HETATM 15 C C13 VDX . . . C 3 13.408 4.458 26.21 1 21.69 ? C13 VDX 500 A 1 HETATM 16 C C14 VDX . . . C 3 14.752 4.845 25.504 1 20.19 ? C14 VDX 500 A 1 HETATM 17 C C15 VDX . . . C 3 15.154 3.55 24.719 1 22.99 ? C15 VDX 500 A 1 HETATM 18 C C16 VDX . . . C 3 14.605 2.434 25.633 1 23.77 ? C16 VDX 500 A 1 HETATM 19 C C17 VDX . . . C 3 13.971 3.151 26.839 1 19.46 ? C17 VDX 500 A 1 HETATM 20 C C18 VDX . . . C 3 12.161 4.319 25.244 1 19.82 ? C18 VDX 500 A 1 HETATM 21 C C19 VDX . . . C 3 13.002 5.375 20.655 1 22.6 ? C19 VDX 500 A 1 HETATM 22 C C20 VDX . . . C 3 12.946 2.231 27.646 1 19.97 ? C20 VDX 500 A 1 HETATM 23 C C21 VDX . . . C 3 13.637 1.306 28.668 1 21.52 ? C21 VDX 500 A 1 HETATM 24 C C22 VDX . . . C 3 12.035 1.299 26.779 1 21.18 ? C22 VDX 500 A 1 HETATM 25 C C23 VDX . . . C 3 10.641 1.11 27.389 1 20.73 ? C23 VDX 500 A 1 HETATM 26 C C24 VDX . . . C 3 9.735 0.193 26.516 1 22.52 ? C24 VDX 500 A 1 HETATM 27 C C25 VDX . . . C 3 8.619 -0.597 27.256 1 25.44 ? C25 VDX 500 A 1 HETATM 28 C C26 VDX . . . C 3 7.755 0.357 28.081 1 28.01 ? C26 VDX 500 A 1 HETATM 29 C C27 VDX . . . C 3 7.709 -1.333 26.261 1 25.94 ? C27 VDX 500 A 1 HETATM 30 O O1 VDX . . . C 3 14.024 5.526 18.044 1 26.87 ? O1 VDX 500 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 30 #