data_6XZH # _model_server_result.job_id BggcFkgsh0OzGPih_QIndw _model_server_result.datetime_utc '2024-10-11 13:24:34' _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 6xzh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":4001}' # _entry.id 6XZH # _exptl.entry_id 6XZH _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 6XZH _cell.length_a 66.09 _cell.length_b 66.09 _cell.length_c 260.14 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XZH _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 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 _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 B C ILE 4 B ILE 3 1_555 B N URL 5 B URL 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? covale ? covale2 B C URL 5 B URL 4 1_555 B N OUK 6 B OUK 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale3 B C OUK 6 B OUK 5 1_555 B N URL 7 B URL 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? covale ? covale4 B C URL 7 B URL 6 1_555 B N LEU 8 B LEU 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? # _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 431 n n O2 HO2 VDX sing 432 n n O3 C25 VDX sing 433 n n O3 HO3 VDX sing 434 n n C1 C2 VDX sing 435 n n C1 C10 VDX sing 436 n n C1 O1 VDX sing 437 n n C1 H11 VDX sing 438 n n C2 C3 VDX sing 439 n n C2 H21 VDX sing 440 n n C2 H22 VDX sing 441 n n C3 C4 VDX sing 442 n n C3 H31 VDX sing 443 n n C4 C5 VDX sing 444 n n C4 H41 VDX sing 445 n n C4 H42 VDX sing 446 n n C5 C6 VDX doub 447 z n C5 C10 VDX sing 448 n n C6 C7 VDX sing 449 n n C6 H61 VDX sing 450 n n C7 C8 VDX doub 451 e n C7 H71 VDX sing 452 n n C8 C9 VDX sing 453 n n C8 C14 VDX sing 454 n n C9 C11 VDX sing 455 n n C9 H91 VDX sing 456 n n C9 H92 VDX sing 457 n n C10 C19 VDX doub 458 n n C11 C12 VDX sing 459 n n C11 H111 VDX sing 460 n n C11 H112 VDX sing 461 n n C12 C13 VDX sing 462 n n C12 H121 VDX sing 463 n n C12 H122 VDX sing 464 n n C13 C14 VDX sing 465 n n C13 C17 VDX sing 466 n n C13 C18 VDX sing 467 n n C14 C15 VDX sing 468 n n C14 H141 VDX sing 469 n n C15 C16 VDX sing 470 n n C15 H151 VDX sing 471 n n C15 H152 VDX sing 472 n n C16 C17 VDX sing 473 n n C16 H161 VDX sing 474 n n C16 H162 VDX sing 475 n n C17 C20 VDX sing 476 n n C17 H171 VDX sing 477 n n C18 H181 VDX sing 478 n n C18 H182 VDX sing 479 n n C18 H183 VDX sing 480 n n C19 H191 VDX sing 481 n n C19 H192 VDX sing 482 n n C20 C21 VDX sing 483 n n C20 C22 VDX sing 484 n n C20 H201 VDX sing 485 n n C21 H211 VDX sing 486 n n C21 H212 VDX sing 487 n n C21 H213 VDX sing 488 n n C22 C23 VDX sing 489 n n C22 H221 VDX sing 490 n n C22 H222 VDX sing 491 n n C23 C24 VDX sing 492 n n C23 H231 VDX sing 493 n n C23 H232 VDX sing 494 n n C24 C25 VDX sing 495 n n C24 H241 VDX sing 496 n n C24 H242 VDX sing 497 n n C25 C26 VDX sing 498 n n C25 C27 VDX sing 499 n n C26 H261 VDX sing 500 n n C26 H262 VDX sing 501 n n C26 H263 VDX sing 502 n n C27 H271 VDX sing 503 n n C27 H272 VDX sing 504 n n C27 H273 VDX sing 505 n n O1 HO1 VDX sing 506 n n # _atom_sites.entry_id 6XZH _atom_sites.fract_transf_matrix[1][1] 0.015131 _atom_sites.fract_transf_matrix[1][2] 0.008736 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017472 _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] 0.003844 _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 4001 4001 VDX VDX . D 4 HOH A 1 4101 7 HOH HOH . D 4 HOH A 2 4102 6 HOH HOH . D 4 HOH A 3 4103 1 HOH HOH . D 4 HOH A 4 4104 3 HOH HOH . D 4 HOH A 5 4105 2 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 0.622 41.664 39.621 1 61.15 ? O2 VDX 4001 A 1 HETATM 2 O O3 VDX . . . C 3 4.731 28.562 33.544 1 62.47 ? O3 VDX 4001 A 1 HETATM 3 C C1 VDX . . . C 3 2.568 40.669 38.185 1 52.2 ? C1 VDX 4001 A 1 HETATM 4 C C2 VDX . . . C 3 1.754 41.841 37.574 1 50.73 ? C2 VDX 4001 A 1 HETATM 5 C C3 VDX . . . C 3 0.448 41.828 38.192 1 57.19 ? C3 VDX 4001 A 1 HETATM 6 C C4 VDX . . . C 3 -0.357 40.567 37.757 1 56.67 ? C4 VDX 4001 A 1 HETATM 7 C C5 VDX . . . C 3 0.395 39.299 38.091 1 53.74 ? C5 VDX 4001 A 1 HETATM 8 C C6 VDX . . . C 3 -0.215 38.17 38.524 1 52.79 ? C6 VDX 4001 A 1 HETATM 9 C C7 VDX . . . C 3 0.627 36.898 38.822 1 53.74 ? C7 VDX 4001 A 1 HETATM 10 C C8 VDX . . . C 3 -0.083 35.766 38.74 1 56.51 ? C8 VDX 4001 A 1 HETATM 11 C C9 VDX . . . C 3 -1.514 35.738 38.27 1 61.06 ? C9 VDX 4001 A 1 HETATM 12 C C10 VDX . . . C 3 1.98 39.335 37.844 1 54.46 ? C10 VDX 4001 A 1 HETATM 13 C C11 VDX . . . C 3 -1.81 34.701 37.197 1 57.76 ? C11 VDX 4001 A 1 HETATM 14 C C12 VDX . . . C 3 -1.204 33.397 37.399 1 56.11 ? C12 VDX 4001 A 1 HETATM 15 C C13 VDX . . . C 3 0.349 33.542 37.836 1 57.11 ? C13 VDX 4001 A 1 HETATM 16 C C14 VDX . . . C 3 0.438 34.335 39.029 1 55.29 ? C14 VDX 4001 A 1 HETATM 17 C C15 VDX . . . C 3 1.979 34.394 39.382 1 52.9 ? C15 VDX 4001 A 1 HETATM 18 C C16 VDX . . . C 3 2.421 32.869 38.874 1 58.53 ? C16 VDX 4001 A 1 HETATM 19 C C17 VDX . . . C 3 1.267 32.273 38.3 1 59.05 ? C17 VDX 4001 A 1 HETATM 20 C C18 VDX . . . C 3 1.066 34.261 36.686 1 52.72 ? C18 VDX 4001 A 1 HETATM 21 C C19 VDX . . . C 3 2.634 38.436 37.12 1 63.27 ? C19 VDX 4001 A 1 HETATM 22 C C20 VDX . . . C 3 1.491 31.22 37.197 1 60.66 ? C20 VDX 4001 A 1 HETATM 23 C C21 VDX . . . C 3 1.695 29.906 37.922 1 59.95 ? C21 VDX 4001 A 1 HETATM 24 C C22 VDX . . . C 3 2.727 31.491 36.312 1 64.03 ? C22 VDX 4001 A 1 HETATM 25 C C23 VDX . . . C 3 2.89 30.359 35.239 1 63.55 ? C23 VDX 4001 A 1 HETATM 26 C C24 VDX . . . C 3 4.006 30.761 34.211 1 60.98 ? C24 VDX 4001 A 1 HETATM 27 C C25 VDX . . . C 3 4.067 29.703 33.073 1 59.95 ? C25 VDX 4001 A 1 HETATM 28 C C26 VDX . . . C 3 2.655 29.305 32.588 1 53.84 ? C26 VDX 4001 A 1 HETATM 29 C C27 VDX . . . C 3 4.849 30.342 31.913 1 64.4 ? C27 VDX 4001 A 1 HETATM 30 O O1 VDX . . . C 3 3.959 40.691 37.843 1 53.43 ? O1 VDX 4001 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 30 #