data_6JEZ # _model_server_result.job_id -q3blUlSZmFzkKZr-V7vcw _model_server_result.datetime_utc '2024-11-15 05:39:18' _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 6jez # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 6JEZ # _exptl.entry_id 6JEZ _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 95.3 _cell.angle_gamma 90 _cell.entry_id 6JEZ _cell.length_a 153.93 _cell.length_b 43.39 _cell.length_c 42 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JEZ _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 software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 408 n n O2 C3 YSV sing 409 n n C2 C3 YSV sing 410 n n C2 C1 YSV sing 411 n n C3 C4 YSV sing 412 n n C1 O1 YSV sing 413 n n C1 C10 YSV sing 414 n n C4 C5 YSV sing 415 n n C10 C5 YSV sing 416 n n C5 C6 YSV doub 417 n n C6 C7 YSV sing 418 n n C7 C8 YSV doub 419 e n C8 C14 YSV sing 420 n n C8 C9 YSV sing 421 n n C15 C14 YSV sing 422 n n C15 C16 YSV sing 423 n n C18 C13 YSV sing 424 n n C14 C13 YSV sing 425 n n C9 C11 YSV sing 426 n n C16 C17 YSV sing 427 n n C13 C17 YSV sing 428 n n C13 C12 YSV sing 429 n n C26 C25 YSV sing 430 n n C24 C25 YSV sing 431 n n C24 C23 YSV sing 432 n n C11 C12 YSV sing 433 n n C22 C23 YSV sing 434 n n C22 C20 YSV sing 435 n n C17 C20 YSV sing 436 n n C25 C27 YSV sing 437 n n C25 O3 YSV sing 438 n n C20 C21 YSV sing 439 n n O3 H1 YSV sing 440 n n C27 H2 YSV sing 441 n n C27 H3 YSV sing 442 n n C27 H4 YSV sing 443 n n C26 H5 YSV sing 444 n n C26 H6 YSV sing 445 n n C26 H7 YSV sing 446 n n C24 H8 YSV sing 447 n n C24 H9 YSV sing 448 n n C23 H10 YSV sing 449 n n C23 H11 YSV sing 450 n n C22 H12 YSV sing 451 n n C22 H13 YSV sing 452 n n C20 H14 YSV sing 453 n n C21 H15 YSV sing 454 n n C21 H16 YSV sing 455 n n C21 H17 YSV sing 456 n n C17 H18 YSV sing 457 n n C16 H19 YSV sing 458 n n C16 H20 YSV sing 459 n n C18 H21 YSV sing 460 n n C18 H22 YSV sing 461 n n C18 H23 YSV sing 462 n n C14 H24 YSV sing 463 n n C15 H25 YSV sing 464 n n C15 H26 YSV sing 465 n n C12 H27 YSV sing 466 n n C12 H28 YSV sing 467 n n C11 H29 YSV sing 468 n n C11 H30 YSV sing 469 n n C9 H31 YSV sing 470 n n C9 H32 YSV sing 471 n n C7 H33 YSV sing 472 n n C6 H34 YSV sing 473 n n C10 H35 YSV sing 474 n n C10 H36 YSV sing 475 n n C4 H37 YSV sing 476 n n C4 H38 YSV sing 477 n n C3 H39 YSV sing 478 n n O2 H40 YSV sing 479 n n C28 H41 YSV sing 480 n n C28 H42 YSV sing 481 n n C1 H43 YSV sing 482 n n O1 H44 YSV sing 483 n n # _atom_sites.entry_id 6JEZ _atom_sites.fract_transf_matrix[1][1] 0.006496 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000603 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023047 _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] 0.023912 _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 2MD . D 4 EJO A 1 502 1 EJO NET . E 5 HOH A 1 601 100 HOH HOH . E 5 HOH A 2 602 146 HOH HOH . E 5 HOH A 3 603 6 HOH HOH . E 5 HOH A 4 604 55 HOH HOH . E 5 HOH A 5 605 103 HOH HOH . E 5 HOH A 6 606 92 HOH HOH . E 5 HOH A 7 607 125 HOH HOH . E 5 HOH A 8 608 11 HOH HOH . E 5 HOH A 9 609 9 HOH HOH . E 5 HOH A 10 610 76 HOH HOH . E 5 HOH A 11 611 19 HOH HOH . E 5 HOH A 12 612 7 HOH HOH . E 5 HOH A 13 613 3 HOH HOH . E 5 HOH A 14 614 90 HOH HOH . E 5 HOH A 15 615 20 HOH HOH . E 5 HOH A 16 616 15 HOH HOH . E 5 HOH A 17 617 56 HOH HOH . E 5 HOH A 18 618 98 HOH HOH . E 5 HOH A 19 619 110 HOH HOH . E 5 HOH A 20 620 4 HOH HOH . E 5 HOH A 21 621 86 HOH HOH . E 5 HOH A 22 622 111 HOH HOH . E 5 HOH A 23 623 8 HOH HOH . E 5 HOH A 24 624 77 HOH HOH . E 5 HOH A 25 625 2 HOH HOH . E 5 HOH A 26 626 65 HOH HOH . E 5 HOH A 27 627 40 HOH HOH . E 5 HOH A 28 628 58 HOH HOH . E 5 HOH A 29 629 120 HOH HOH . E 5 HOH A 30 630 32 HOH HOH . E 5 HOH A 31 631 13 HOH HOH . E 5 HOH A 32 632 12 HOH HOH . E 5 HOH A 33 633 26 HOH HOH . E 5 HOH A 34 634 1 HOH HOH . E 5 HOH A 35 635 83 HOH HOH . E 5 HOH A 36 636 16 HOH HOH . E 5 HOH A 37 637 14 HOH HOH . E 5 HOH A 38 638 43 HOH HOH . E 5 HOH A 39 639 38 HOH HOH . E 5 HOH A 40 640 10 HOH HOH . E 5 HOH A 41 641 46 HOH HOH . E 5 HOH A 42 642 5 HOH HOH . E 5 HOH A 43 643 114 HOH HOH . E 5 HOH A 44 644 80 HOH HOH . E 5 HOH A 45 645 82 HOH HOH . E 5 HOH A 46 646 85 HOH HOH . E 5 HOH A 47 647 74 HOH HOH . E 5 HOH A 48 648 37 HOH HOH . E 5 HOH A 49 649 17 HOH HOH . E 5 HOH A 50 650 109 HOH HOH . E 5 HOH A 51 651 71 HOH HOH . E 5 HOH A 52 652 53 HOH HOH . E 5 HOH A 53 653 75 HOH HOH . E 5 HOH A 54 654 42 HOH HOH . E 5 HOH A 55 655 127 HOH HOH . E 5 HOH A 56 656 70 HOH HOH . E 5 HOH A 57 657 69 HOH HOH . E 5 HOH A 58 658 154 HOH HOH . F 5 HOH C 1 701 18 HOH HOH . F 5 HOH C 2 702 23 HOH HOH . F 5 HOH C 3 703 102 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 9.593 -1.693 28.107 1 31.08 ? O3 YSV 501 A 1 HETATM 2 C C25 YSV . . . C 3 9.031 -0.637 27.324 1 28.55 ? C25 YSV 501 A 1 HETATM 3 C C27 YSV . . . C 3 8.358 0.355 28.264 1 30.28 ? C27 YSV 501 A 1 HETATM 4 C C26 YSV . . . C 3 7.993 -1.24 26.392 1 29.27 ? C26 YSV 501 A 1 HETATM 5 C C24 YSV . . . C 3 10.137 0.042 26.52 1 25.99 ? C24 YSV 501 A 1 HETATM 6 C C23 YSV . . . C 3 11.012 0.939 27.388 1 25.22 ? C23 YSV 501 A 1 HETATM 7 C C22 YSV . . . C 3 12.227 1.478 26.636 1 23.11 ? C22 YSV 501 A 1 HETATM 8 C C20 YSV . . . C 3 13.059 2.357 27.563 1 23.1 ? C20 YSV 501 A 1 HETATM 9 C C21 YSV . . . C 3 13.581 1.551 28.744 1 24.76 ? C21 YSV 501 A 1 HETATM 10 C C17 YSV . . . C 3 14.219 3.09 26.897 1 21.98 ? C17 YSV 501 A 1 HETATM 11 C C16 YSV . . . C 3 14.94 2.354 25.768 1 20.94 ? C16 YSV 501 A 1 HETATM 12 C C13 YSV . . . C 3 13.904 4.462 26.329 1 21.43 ? C13 YSV 501 A 1 HETATM 13 C C18 YSV . . . C 3 12.732 4.386 25.359 1 22.23 ? C18 YSV 501 A 1 HETATM 14 C C14 YSV . . . C 3 15.186 4.742 25.585 1 20.83 ? C14 YSV 501 A 1 HETATM 15 C C15 YSV . . . C 3 15.524 3.445 24.864 1 20.62 ? C15 YSV 501 A 1 HETATM 16 C C12 YSV . . . C 3 13.679 5.579 27.331 1 21.73 ? C12 YSV 501 A 1 HETATM 17 C C11 YSV . . . C 3 13.481 6.896 26.581 1 21.63 ? C11 YSV 501 A 1 HETATM 18 C C9 YSV . . . C 3 14.592 7.222 25.578 1 21.68 ? C9 YSV 501 A 1 HETATM 19 C C8 YSV . . . C 3 15.02 5.999 24.796 1 20.34 ? C8 YSV 501 A 1 HETATM 20 C C7 YSV . . . C 3 15.236 6.055 23.472 1 20.46 ? C7 YSV 501 A 1 HETATM 21 C C6 YSV . . . C 3 15.06 7.322 22.764 1 20.18 ? C6 YSV 501 A 1 HETATM 22 C C5 YSV . . . C 3 14.742 7.395 21.464 1 20.46 ? C5 YSV 501 A 1 HETATM 23 C C10 YSV . . . C 3 14.536 6.147 20.631 1 20.69 ? C10 YSV 501 A 1 HETATM 24 C C4 YSV . . . C 3 14.576 8.76 20.822 1 21.52 ? C4 YSV 501 A 1 HETATM 25 C C3 YSV . . . C 3 15.152 8.838 19.407 1 22.82 ? C3 YSV 501 A 1 HETATM 26 O O2 YSV . . . C 3 16.575 8.93 19.462 1 23.32 ? O2 YSV 501 A 1 HETATM 27 C C2 YSV . . . C 3 14.782 7.618 18.624 1 22.42 ? C2 YSV 501 A 1 HETATM 28 C C28 YSV . . . C 3 14.169 7.723 17.461 1 22.64 ? C28 YSV 501 A 1 HETATM 29 C C1 YSV . . . C 3 15.128 6.287 19.226 1 21.65 ? C1 YSV 501 A 1 HETATM 30 O O1 YSV . . . C 3 14.666 5.231 18.383 1 22.21 ? O1 YSV 501 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 30 #