data_4RUJ # _model_server_result.job_id GiTvgDvsJaAGSWwDGDmqlA _model_server_result.datetime_utc '2025-06-22 15:56:16' _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 4ruj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 4RUJ # _exptl.entry_id 4RUJ _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 90 _cell.angle_gamma 120 _cell.entry_id 4RUJ _cell.length_a 65.851 _cell.length_b 65.851 _cell.length_c 264.373 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RUJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 32.9255 57.028639 44.062167 # _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 376 n n O2 HO2 VDX sing 377 n n O3 C25 VDX sing 378 n n O3 HO3 VDX sing 379 n n C1 C2 VDX sing 380 n n C1 C10 VDX sing 381 n n C1 O1 VDX sing 382 n n C1 H11 VDX sing 383 n n C2 C3 VDX sing 384 n n C2 H21 VDX sing 385 n n C2 H22 VDX sing 386 n n C3 C4 VDX sing 387 n n C3 H31 VDX sing 388 n n C4 C5 VDX sing 389 n n C4 H41 VDX sing 390 n n C4 H42 VDX sing 391 n n C5 C6 VDX doub 392 z n C5 C10 VDX sing 393 n n C6 C7 VDX sing 394 n n C6 H61 VDX sing 395 n n C7 C8 VDX doub 396 e n C7 H71 VDX sing 397 n n C8 C9 VDX sing 398 n n C8 C14 VDX sing 399 n n C9 C11 VDX sing 400 n n C9 H91 VDX sing 401 n n C9 H92 VDX sing 402 n n C10 C19 VDX doub 403 n n C11 C12 VDX sing 404 n n C11 H111 VDX sing 405 n n C11 H112 VDX sing 406 n n C12 C13 VDX sing 407 n n C12 H121 VDX sing 408 n n C12 H122 VDX sing 409 n n C13 C14 VDX sing 410 n n C13 C17 VDX sing 411 n n C13 C18 VDX sing 412 n n C14 C15 VDX sing 413 n n C14 H141 VDX sing 414 n n C15 C16 VDX sing 415 n n C15 H151 VDX sing 416 n n C15 H152 VDX sing 417 n n C16 C17 VDX sing 418 n n C16 H161 VDX sing 419 n n C16 H162 VDX sing 420 n n C17 C20 VDX sing 421 n n C17 H171 VDX sing 422 n n C18 H181 VDX sing 423 n n C18 H182 VDX sing 424 n n C18 H183 VDX sing 425 n n C19 H191 VDX sing 426 n n C19 H192 VDX sing 427 n n C20 C21 VDX sing 428 n n C20 C22 VDX sing 429 n n C20 H201 VDX sing 430 n n C21 H211 VDX sing 431 n n C21 H212 VDX sing 432 n n C21 H213 VDX sing 433 n n C22 C23 VDX sing 434 n n C22 H221 VDX sing 435 n n C22 H222 VDX sing 436 n n C23 C24 VDX sing 437 n n C23 H231 VDX sing 438 n n C23 H232 VDX sing 439 n n C24 C25 VDX sing 440 n n C24 H241 VDX sing 441 n n C24 H242 VDX sing 442 n n C25 C26 VDX sing 443 n n C25 C27 VDX sing 444 n n C26 H261 VDX sing 445 n n C26 H262 VDX sing 446 n n C26 H263 VDX sing 447 n n C27 H271 VDX sing 448 n n C27 H272 VDX sing 449 n n C27 H273 VDX sing 450 n n O1 HO1 VDX sing 451 n n # _atom_sites.entry_id 4RUJ _atom_sites.fract_transf_matrix[1][1] 0.015186 _atom_sites.fract_transf_matrix[1][2] 0.008768 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017535 _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] 0.003783 _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 1 501 525 VDX VD . D 4 HOH A 1 601 1 HOH HOH . D 4 HOH A 2 602 2 HOH HOH . D 4 HOH A 3 603 3 HOH HOH . D 4 HOH A 4 604 4 HOH HOH . D 4 HOH A 5 605 5 HOH HOH . D 4 HOH A 6 606 6 HOH HOH . D 4 HOH A 7 607 7 HOH HOH . D 4 HOH A 8 608 8 HOH HOH . D 4 HOH A 9 609 9 HOH HOH . D 4 HOH A 10 610 10 HOH HOH . D 4 HOH A 11 611 11 HOH HOH . D 4 HOH A 12 612 12 HOH HOH . D 4 HOH A 13 613 13 HOH HOH . D 4 HOH A 14 614 14 HOH HOH . D 4 HOH A 15 615 15 HOH HOH . D 4 HOH A 16 616 16 HOH HOH . D 4 HOH A 17 617 17 HOH HOH . D 4 HOH A 18 618 18 HOH HOH . D 4 HOH A 19 619 19 HOH HOH . D 4 HOH A 20 620 20 HOH HOH . D 4 HOH A 21 621 21 HOH HOH . D 4 HOH A 22 622 22 HOH HOH . D 4 HOH A 23 623 23 HOH HOH . D 4 HOH A 24 624 24 HOH HOH . D 4 HOH A 25 625 25 HOH HOH . D 4 HOH A 26 626 26 HOH HOH . D 4 HOH A 27 627 27 HOH HOH . D 4 HOH A 28 628 28 HOH HOH . D 4 HOH A 29 629 29 HOH HOH . D 4 HOH A 30 630 30 HOH HOH . D 4 HOH A 31 631 31 HOH HOH . D 4 HOH A 32 632 32 HOH HOH . D 4 HOH A 33 633 33 HOH HOH . D 4 HOH A 34 634 34 HOH HOH . D 4 HOH A 35 635 35 HOH HOH . D 4 HOH A 36 636 36 HOH HOH . D 4 HOH A 37 637 37 HOH HOH . D 4 HOH A 38 638 38 HOH HOH . D 4 HOH A 39 639 39 HOH HOH . D 4 HOH A 40 640 40 HOH HOH . D 4 HOH A 41 641 41 HOH HOH . D 4 HOH A 42 642 42 HOH HOH . D 4 HOH A 43 643 43 HOH HOH . D 4 HOH A 44 644 44 HOH HOH . D 4 HOH A 45 645 45 HOH HOH . D 4 HOH A 46 646 46 HOH HOH . D 4 HOH A 47 647 48 HOH HOH . D 4 HOH A 48 648 49 HOH HOH . D 4 HOH A 49 649 50 HOH HOH . D 4 HOH A 50 650 51 HOH HOH . D 4 HOH A 51 651 52 HOH HOH . D 4 HOH A 52 652 53 HOH HOH . D 4 HOH A 53 653 54 HOH HOH . E 4 HOH B 1 801 47 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 0.289 40.544 40.249 1 50.49 ? O2 VDX 501 A 1 HETATM 2 O O3 VDX . . . C 3 5.28 27.297 33.751 1 55.9 ? O3 VDX 501 A 1 HETATM 3 C C1 VDX . . . C 3 2.688 39.642 38.852 1 46.28 ? C1 VDX 501 A 1 HETATM 4 C C2 VDX . . . C 3 1.807 40.788 38.369 1 45.48 ? C2 VDX 501 A 1 HETATM 5 C C3 VDX . . . C 3 0.357 40.611 38.812 1 51.86 ? C3 VDX 501 A 1 HETATM 6 C C4 VDX . . . C 3 -0.238 39.354 38.182 1 43.15 ? C4 VDX 501 A 1 HETATM 7 C C5 VDX . . . C 3 0.641 38.157 38.453 1 42.6 ? C5 VDX 501 A 1 HETATM 8 C C6 VDX . . . C 3 0.06 36.961 38.679 1 46.58 ? C6 VDX 501 A 1 HETATM 9 C C7 VDX . . . C 3 0.791 35.723 38.96 1 46.84 ? C7 VDX 501 A 1 HETATM 10 C C8 VDX . . . C 3 0.144 34.546 38.94 1 49.45 ? C8 VDX 501 A 1 HETATM 11 C C9 VDX . . . C 3 -1.322 34.455 38.597 1 52.01 ? C9 VDX 501 A 1 HETATM 12 C C10 VDX . . . C 3 2.09 38.337 38.415 1 47.63 ? C10 VDX 501 A 1 HETATM 13 C C11 VDX . . . C 3 -1.545 33.401 37.504 1 58.17 ? C11 VDX 501 A 1 HETATM 14 C C12 VDX . . . C 3 -0.763 32.094 37.688 1 56.66 ? C12 VDX 501 A 1 HETATM 15 C C13 VDX . . . C 3 0.704 32.358 37.987 1 51.19 ? C13 VDX 501 A 1 HETATM 16 C C14 VDX . . . C 3 0.809 33.233 39.216 1 50.56 ? C14 VDX 501 A 1 HETATM 17 C C15 VDX . . . C 3 2.286 33.213 39.595 1 47.1 ? C15 VDX 501 A 1 HETATM 18 C C16 VDX . . . C 3 2.722 31.793 39.204 1 49.12 ? C16 VDX 501 A 1 HETATM 19 C C17 VDX . . . C 3 1.528 31.171 38.467 1 50.83 ? C17 VDX 501 A 1 HETATM 20 C C18 VDX . . . C 3 1.365 33.054 36.802 1 46.38 ? C18 VDX 501 A 1 HETATM 21 C C19 VDX . . . C 3 2.879 37.382 37.961 1 47.38 ? C19 VDX 501 A 1 HETATM 22 C C20 VDX . . . C 3 1.857 30.087 37.437 1 57.1 ? C20 VDX 501 A 1 HETATM 23 C C21 VDX . . . C 3 1.915 28.722 38.117 1 45.99 ? C21 VDX 501 A 1 HETATM 24 C C22 VDX . . . C 3 3.141 30.341 36.651 1 54.31 ? C22 VDX 501 A 1 HETATM 25 C C23 VDX . . . C 3 3.136 29.539 35.352 1 52.23 ? C23 VDX 501 A 1 HETATM 26 C C24 VDX . . . C 3 4.551 29.307 34.831 1 52.43 ? C24 VDX 501 A 1 HETATM 27 C C25 VDX . . . C 3 4.589 28.527 33.516 1 53.85 ? C25 VDX 501 A 1 HETATM 28 C C26 VDX . . . C 3 5.374 29.311 32.467 1 50.95 ? C26 VDX 501 A 1 HETATM 29 C C27 VDX . . . C 3 3.195 28.212 32.985 1 41.23 ? C27 VDX 501 A 1 HETATM 30 O O1 VDX . . . C 3 3.996 39.779 38.283 1 43.76 ? O1 VDX 501 A 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 30 #