data_5B41 # _model_server_result.job_id UartduGxb7pbU8QZMEJOyw _model_server_result.datetime_utc '2024-11-16 19:47:17' _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 5b41 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5B41 # _exptl.entry_id 5B41 _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 '(1R,3R)-5-(2-((1R,3aS,7aR,E)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-2- methylenecyclohexane-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 96.02 _cell.angle_gamma 90 _cell.entry_id 5B41 _cell.length_a 154.17 _cell.length_b 41.75 _cell.length_c 41.77 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5B41 _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 'C27 H44 O3' _chem_comp.formula_weight 416.636 _chem_comp.id YSV _chem_comp.mon_nstd_flag . _chem_comp.name '(1R,3R)-5-(2-((1R,3aS,7aR,E)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-2- methylenecyclohexane-1,3-diol' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '2-methylidene-19-nor-1alpha,25-dihydroxyvitamin 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 C28 C2 YSV doub 376 n n O2 C3 YSV sing 377 n n C2 C3 YSV sing 378 n n C2 C1 YSV sing 379 n n C3 C4 YSV sing 380 n n C1 O1 YSV sing 381 n n C1 C10 YSV sing 382 n n C4 C5 YSV sing 383 n n C10 C5 YSV sing 384 n n C5 C6 YSV doub 385 n n C6 C7 YSV sing 386 n n C7 C8 YSV doub 387 e n C8 C14 YSV sing 388 n n C8 C9 YSV sing 389 n n C15 C14 YSV sing 390 n n C15 C16 YSV sing 391 n n C18 C13 YSV sing 392 n n C14 C13 YSV sing 393 n n C9 C11 YSV sing 394 n n C16 C17 YSV sing 395 n n C13 C17 YSV sing 396 n n C13 C12 YSV sing 397 n n C26 C25 YSV sing 398 n n C24 C25 YSV sing 399 n n C24 C23 YSV sing 400 n n C11 C12 YSV sing 401 n n C22 C23 YSV sing 402 n n C22 C20 YSV sing 403 n n C17 C20 YSV sing 404 n n C25 C27 YSV sing 405 n n C25 O3 YSV sing 406 n n C20 C21 YSV sing 407 n n O3 H1 YSV sing 408 n n C27 H2 YSV sing 409 n n C27 H3 YSV sing 410 n n C27 H4 YSV sing 411 n n C26 H5 YSV sing 412 n n C26 H6 YSV sing 413 n n C26 H7 YSV sing 414 n n C24 H8 YSV sing 415 n n C24 H9 YSV sing 416 n n C23 H10 YSV sing 417 n n C23 H11 YSV sing 418 n n C22 H12 YSV sing 419 n n C22 H13 YSV sing 420 n n C20 H14 YSV sing 421 n n C21 H15 YSV sing 422 n n C21 H16 YSV sing 423 n n C21 H17 YSV sing 424 n n C17 H18 YSV sing 425 n n C16 H19 YSV sing 426 n n C16 H20 YSV sing 427 n n C18 H21 YSV sing 428 n n C18 H22 YSV sing 429 n n C18 H23 YSV sing 430 n n C14 H24 YSV sing 431 n n C15 H25 YSV sing 432 n n C15 H26 YSV sing 433 n n C12 H27 YSV sing 434 n n C12 H28 YSV sing 435 n n C11 H29 YSV sing 436 n n C11 H30 YSV sing 437 n n C9 H31 YSV sing 438 n n C9 H32 YSV sing 439 n n C7 H33 YSV sing 440 n n C6 H34 YSV sing 441 n n C10 H35 YSV sing 442 n n C10 H36 YSV sing 443 n n C4 H37 YSV sing 444 n n C4 H38 YSV sing 445 n n C3 H39 YSV sing 446 n n O2 H40 YSV sing 447 n n C28 H41 YSV sing 448 n n C28 H42 YSV sing 449 n n C1 H43 YSV sing 450 n n O1 H44 YSV sing 451 n n # _atom_sites.entry_id 5B41 _atom_sites.fract_transf_matrix[1][1] 0.006486 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000684 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023952 _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] 0.024073 _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 YSV A 1 501 1 YSV YSd . D 4 HOH A 1 601 250 HOH HOH . D 4 HOH A 2 602 255 HOH HOH . D 4 HOH A 3 603 52 HOH HOH . D 4 HOH A 4 604 87 HOH HOH . D 4 HOH A 5 605 115 HOH HOH . D 4 HOH A 6 606 4 HOH HOH . D 4 HOH A 7 607 233 HOH HOH . D 4 HOH A 8 608 240 HOH HOH . D 4 HOH A 9 609 254 HOH HOH . D 4 HOH A 10 610 15 HOH HOH . D 4 HOH A 11 611 241 HOH HOH . D 4 HOH A 12 612 23 HOH HOH . D 4 HOH A 13 613 100 HOH HOH . D 4 HOH A 14 614 21 HOH HOH . D 4 HOH A 15 615 194 HOH HOH . D 4 HOH A 16 616 252 HOH HOH . D 4 HOH A 17 617 251 HOH HOH . D 4 HOH A 18 618 182 HOH HOH . D 4 HOH A 19 619 156 HOH HOH . D 4 HOH A 20 620 50 HOH HOH . D 4 HOH A 21 621 34 HOH HOH . D 4 HOH A 22 622 111 HOH HOH . D 4 HOH A 23 623 64 HOH HOH . D 4 HOH A 24 624 44 HOH HOH . D 4 HOH A 25 625 55 HOH HOH . D 4 HOH A 26 626 6 HOH HOH . D 4 HOH A 27 627 95 HOH HOH . D 4 HOH A 28 628 12 HOH HOH . D 4 HOH A 29 629 48 HOH HOH . D 4 HOH A 30 630 61 HOH HOH . D 4 HOH A 31 631 28 HOH HOH . D 4 HOH A 32 632 57 HOH HOH . D 4 HOH A 33 633 162 HOH HOH . D 4 HOH A 34 634 13 HOH HOH . D 4 HOH A 35 635 30 HOH HOH . D 4 HOH A 36 636 235 HOH HOH . D 4 HOH A 37 637 25 HOH HOH . D 4 HOH A 38 638 82 HOH HOH . D 4 HOH A 39 639 253 HOH HOH . D 4 HOH A 40 640 246 HOH HOH . D 4 HOH A 41 641 42 HOH HOH . D 4 HOH A 42 642 198 HOH HOH . D 4 HOH A 43 643 53 HOH HOH . D 4 HOH A 44 644 93 HOH HOH . D 4 HOH A 45 645 37 HOH HOH . D 4 HOH A 46 646 238 HOH HOH . D 4 HOH A 47 647 19 HOH HOH . D 4 HOH A 48 648 54 HOH HOH . D 4 HOH A 49 649 51 HOH HOH . D 4 HOH A 50 650 47 HOH HOH . D 4 HOH A 51 651 163 HOH HOH . D 4 HOH A 52 652 77 HOH HOH . D 4 HOH A 53 653 59 HOH HOH . D 4 HOH A 54 654 102 HOH HOH . D 4 HOH A 55 655 237 HOH HOH . D 4 HOH A 56 656 121 HOH HOH . D 4 HOH A 57 657 234 HOH HOH . D 4 HOH A 58 658 10 HOH HOH . D 4 HOH A 59 659 129 HOH HOH . D 4 HOH A 60 660 75 HOH HOH . D 4 HOH A 61 661 62 HOH HOH . D 4 HOH A 62 662 106 HOH HOH . D 4 HOH A 63 663 239 HOH HOH . D 4 HOH A 64 664 17 HOH HOH . D 4 HOH A 65 665 249 HOH HOH . D 4 HOH A 66 666 80 HOH HOH . D 4 HOH A 67 667 5 HOH HOH . D 4 HOH A 68 668 45 HOH HOH . D 4 HOH A 69 669 120 HOH HOH . D 4 HOH A 70 670 2 HOH HOH . D 4 HOH A 71 671 258 HOH HOH . D 4 HOH A 72 672 32 HOH HOH . D 4 HOH A 73 673 98 HOH HOH . D 4 HOH A 74 674 166 HOH HOH . D 4 HOH A 75 675 114 HOH HOH . D 4 HOH A 76 676 31 HOH HOH . D 4 HOH A 77 677 135 HOH HOH . D 4 HOH A 78 678 9 HOH HOH . D 4 HOH A 79 679 40 HOH HOH . D 4 HOH A 80 680 20 HOH HOH . D 4 HOH A 81 681 18 HOH HOH . D 4 HOH A 82 682 24 HOH HOH . D 4 HOH A 83 683 243 HOH HOH . D 4 HOH A 84 684 89 HOH HOH . D 4 HOH A 85 685 26 HOH HOH . D 4 HOH A 86 686 63 HOH HOH . D 4 HOH A 87 687 14 HOH HOH . D 4 HOH A 88 688 97 HOH HOH . D 4 HOH A 89 689 138 HOH HOH . D 4 HOH A 90 690 173 HOH HOH . D 4 HOH A 91 691 151 HOH HOH . D 4 HOH A 92 692 242 HOH HOH . D 4 HOH A 93 693 119 HOH HOH . D 4 HOH A 94 694 39 HOH HOH . D 4 HOH A 95 695 41 HOH HOH . D 4 HOH A 96 696 107 HOH HOH . D 4 HOH A 97 697 8 HOH HOH . D 4 HOH A 98 698 22 HOH HOH . D 4 HOH A 99 699 244 HOH HOH . D 4 HOH A 100 700 71 HOH HOH . D 4 HOH A 101 701 1 HOH HOH . D 4 HOH A 102 702 38 HOH HOH . D 4 HOH A 103 703 36 HOH HOH . D 4 HOH A 104 704 245 HOH HOH . D 4 HOH A 105 705 85 HOH HOH . D 4 HOH A 106 706 43 HOH HOH . D 4 HOH A 107 707 70 HOH HOH . D 4 HOH A 108 708 248 HOH HOH . D 4 HOH A 109 709 124 HOH HOH . D 4 HOH A 110 710 215 HOH HOH . D 4 HOH A 111 711 56 HOH HOH . D 4 HOH A 112 712 231 HOH HOH . D 4 HOH A 113 713 218 HOH HOH . D 4 HOH A 114 714 69 HOH HOH . D 4 HOH A 115 715 257 HOH HOH . D 4 HOH A 116 716 27 HOH HOH . D 4 HOH A 117 717 247 HOH HOH . D 4 HOH A 118 718 155 HOH HOH . D 4 HOH A 119 719 236 HOH HOH . D 4 HOH A 120 720 153 HOH HOH . D 4 HOH A 121 721 81 HOH HOH . D 4 HOH A 122 722 210 HOH HOH . D 4 HOH A 123 723 214 HOH HOH . D 4 HOH A 124 724 256 HOH HOH . D 4 HOH A 125 725 223 HOH HOH . D 4 HOH A 126 726 165 HOH HOH . D 4 HOH A 127 727 99 HOH HOH . D 4 HOH A 128 728 117 HOH HOH . D 4 HOH A 129 729 137 HOH HOH . D 4 HOH A 130 730 72 HOH HOH . D 4 HOH A 131 731 101 HOH HOH . D 4 HOH A 132 732 206 HOH HOH . D 4 HOH A 133 733 212 HOH HOH . D 4 HOH A 134 734 209 HOH HOH . D 4 HOH A 135 735 230 HOH HOH . D 4 HOH A 136 736 219 HOH HOH . D 4 HOH A 137 737 148 HOH HOH . D 4 HOH A 138 738 127 HOH HOH . D 4 HOH A 139 739 96 HOH HOH . D 4 HOH A 140 740 134 HOH HOH . D 4 HOH A 141 741 222 HOH HOH . D 4 HOH A 142 742 232 HOH HOH . D 4 HOH A 143 743 226 HOH HOH . D 4 HOH A 144 744 90 HOH HOH . E 4 HOH C 1 701 7 HOH HOH . E 4 HOH C 2 702 260 HOH HOH . E 4 HOH C 3 703 225 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 O3 YSV . . . C 3 9.144 -1.571 28.319 1 31.99 ? O3 YSV 501 A 1 HETATM 2 C C25 YSV . . . C 3 8.605 -0.597 27.43 1 35.23 ? C25 YSV 501 A 1 HETATM 3 C C27 YSV . . . C 3 7.853 0.446 28.254 1 37.78 ? C27 YSV 501 A 1 HETATM 4 C C26 YSV . . . C 3 7.639 -1.31 26.476 1 32.04 ? C26 YSV 501 A 1 HETATM 5 C C24 YSV . . . C 3 9.772 0.021 26.65 1 30.45 ? C24 YSV 501 A 1 HETATM 6 C C23 YSV . . . C 3 10.654 0.914 27.539 1 30.88 ? C23 YSV 501 A 1 HETATM 7 C C22 YSV . . . C 3 11.855 1.459 26.753 1 29.18 ? C22 YSV 501 A 1 HETATM 8 C C20 YSV . . . C 3 12.757 2.279 27.657 1 27.21 ? C20 YSV 501 A 1 HETATM 9 C C21 YSV . . . C 3 13.334 1.414 28.751 1 29.47 ? C21 YSV 501 A 1 HETATM 10 C C17 YSV . . . C 3 13.894 3.029 26.919 1 25.08 ? C17 YSV 501 A 1 HETATM 11 C C16 YSV . . . C 3 14.564 2.298 25.742 1 23.56 ? C16 YSV 501 A 1 HETATM 12 C C13 YSV . . . C 3 13.53 4.399 26.389 1 23.39 ? C13 YSV 501 A 1 HETATM 13 C C18 YSV . . . C 3 12.271 4.331 25.495 1 24.09 ? C18 YSV 501 A 1 HETATM 14 C C14 YSV . . . C 3 14.776 4.69 25.539 1 25.07 ? C14 YSV 501 A 1 HETATM 15 C C15 YSV . . . C 3 15.105 3.374 24.78 1 23.74 ? C15 YSV 501 A 1 HETATM 16 C C12 YSV . . . C 3 13.378 5.498 27.398 1 30.15 ? C12 YSV 501 A 1 HETATM 17 C C11 YSV . . . C 3 13.123 6.872 26.674 1 26.21 ? C11 YSV 501 A 1 HETATM 18 C C9 YSV . . . C 3 14.226 7.176 25.63 1 24.46 ? C9 YSV 501 A 1 HETATM 19 C C8 YSV . . . C 3 14.576 5.963 24.776 1 24.53 ? C8 YSV 501 A 1 HETATM 20 C C7 YSV . . . C 3 14.714 6.028 23.436 1 22.15 ? C7 YSV 501 A 1 HETATM 21 C C6 YSV . . . C 3 14.488 7.291 22.716 1 22.91 ? C6 YSV 501 A 1 HETATM 22 C C5 YSV . . . C 3 14.276 7.354 21.382 1 22.46 ? C5 YSV 501 A 1 HETATM 23 C C10 YSV . . . C 3 14.039 8.715 20.771 1 23.3 ? C10 YSV 501 A 1 HETATM 24 C C4 YSV . . . C 3 14.208 6.105 20.542 1 21.04 ? C4 YSV 501 A 1 HETATM 25 C C3 YSV . . . C 3 14.701 6.267 19.108 1 21.48 ? C3 YSV 501 A 1 HETATM 26 O O2 YSV . . . C 3 14.22 5.235 18.249 1 21.7 ? O2 YSV 501 A 1 HETATM 27 C C2 YSV . . . C 3 14.33 7.606 18.558 1 22.25 ? C2 YSV 501 A 1 HETATM 28 C C28 YSV . . . C 3 13.743 7.758 17.385 1 20.78 ? C28 YSV 501 A 1 HETATM 29 C C1 YSV . . . C 3 14.71 8.817 19.393 1 21.92 ? C1 YSV 501 A 1 HETATM 30 O O1 YSV . . . C 3 16.119 8.829 19.512 1 20.92 ? O1 YSV 501 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 30 #