data_6XZV # _model_server_result.job_id OpvJpB1kqhONnXV4YpV5dg _model_server_result.datetime_utc '2024-11-25 11:46:04' _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 6xzv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 6XZV # _exptl.entry_id 6XZV _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 6XZV _cell.length_a 66.244 _cell.length_b 66.244 _cell.length_c 252.522 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XZV _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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 G2Z 1 B G2Z 1 1_555 B N UIA 2 B UIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.35 ? covale ? covale2 B C UIA 2 B UIA 2 1_555 B N URL 3 B URL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.354 ? covale ? covale3 B C URL 3 B URL 3 1_555 B N MFH 4 B MFH 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale4 B C MFH 4 B MFH 4 1_555 B N URV 5 B URV 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale5 B C URV 5 B URV 5 1_555 B N UZN 6 B UZN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale6 B C UZN 6 B UZN 6 1_555 B N LYS 7 B LYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? # _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 514 n n O2 HO2 VDX sing 515 n n O3 C25 VDX sing 516 n n O3 HO3 VDX sing 517 n n C1 C2 VDX sing 518 n n C1 C10 VDX sing 519 n n C1 O1 VDX sing 520 n n C1 H11 VDX sing 521 n n C2 C3 VDX sing 522 n n C2 H21 VDX sing 523 n n C2 H22 VDX sing 524 n n C3 C4 VDX sing 525 n n C3 H31 VDX sing 526 n n C4 C5 VDX sing 527 n n C4 H41 VDX sing 528 n n C4 H42 VDX sing 529 n n C5 C6 VDX doub 530 z n C5 C10 VDX sing 531 n n C6 C7 VDX sing 532 n n C6 H61 VDX sing 533 n n C7 C8 VDX doub 534 e n C7 H71 VDX sing 535 n n C8 C9 VDX sing 536 n n C8 C14 VDX sing 537 n n C9 C11 VDX sing 538 n n C9 H91 VDX sing 539 n n C9 H92 VDX sing 540 n n C10 C19 VDX doub 541 n n C11 C12 VDX sing 542 n n C11 H111 VDX sing 543 n n C11 H112 VDX sing 544 n n C12 C13 VDX sing 545 n n C12 H121 VDX sing 546 n n C12 H122 VDX sing 547 n n C13 C14 VDX sing 548 n n C13 C17 VDX sing 549 n n C13 C18 VDX sing 550 n n C14 C15 VDX sing 551 n n C14 H141 VDX sing 552 n n C15 C16 VDX sing 553 n n C15 H151 VDX sing 554 n n C15 H152 VDX sing 555 n n C16 C17 VDX sing 556 n n C16 H161 VDX sing 557 n n C16 H162 VDX sing 558 n n C17 C20 VDX sing 559 n n C17 H171 VDX sing 560 n n C18 H181 VDX sing 561 n n C18 H182 VDX sing 562 n n C18 H183 VDX sing 563 n n C19 H191 VDX sing 564 n n C19 H192 VDX sing 565 n n C20 C21 VDX sing 566 n n C20 C22 VDX sing 567 n n C20 H201 VDX sing 568 n n C21 H211 VDX sing 569 n n C21 H212 VDX sing 570 n n C21 H213 VDX sing 571 n n C22 C23 VDX sing 572 n n C22 H221 VDX sing 573 n n C22 H222 VDX sing 574 n n C23 C24 VDX sing 575 n n C23 H231 VDX sing 576 n n C23 H232 VDX sing 577 n n C24 C25 VDX sing 578 n n C24 H241 VDX sing 579 n n C24 H242 VDX sing 580 n n C25 C26 VDX sing 581 n n C25 C27 VDX sing 582 n n C26 H261 VDX sing 583 n n C26 H262 VDX sing 584 n n C26 H263 VDX sing 585 n n C27 H271 VDX sing 586 n n C27 H272 VDX sing 587 n n C27 H273 VDX sing 588 n n O1 HO1 VDX sing 589 n n # _atom_sites.entry_id 6XZV _atom_sites.fract_transf_matrix[1][1] 0.015096 _atom_sites.fract_transf_matrix[1][2] 0.008716 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017431 _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] 0.00396 _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 VDX . D 4 HOH A 1 601 29 HOH HOH . D 4 HOH A 2 602 33 HOH HOH . D 4 HOH A 3 603 31 HOH HOH . D 4 HOH A 4 604 25 HOH HOH . D 4 HOH A 5 605 2 HOH HOH . D 4 HOH A 6 606 9 HOH HOH . D 4 HOH A 7 607 30 HOH HOH . D 4 HOH A 8 608 38 HOH HOH . D 4 HOH A 9 609 6 HOH HOH . D 4 HOH A 10 610 1 HOH HOH . D 4 HOH A 11 611 10 HOH HOH . D 4 HOH A 12 612 3 HOH HOH . D 4 HOH A 13 613 7 HOH HOH . D 4 HOH A 14 614 23 HOH HOH . D 4 HOH A 15 615 11 HOH HOH . D 4 HOH A 16 616 21 HOH HOH . D 4 HOH A 17 617 5 HOH HOH . D 4 HOH A 18 618 4 HOH HOH . D 4 HOH A 19 619 44 HOH HOH . D 4 HOH A 20 620 15 HOH HOH . D 4 HOH A 21 621 14 HOH HOH . D 4 HOH A 22 622 13 HOH HOH . D 4 HOH A 23 623 18 HOH HOH . D 4 HOH A 24 624 8 HOH HOH . D 4 HOH A 25 625 32 HOH HOH . D 4 HOH A 26 626 26 HOH HOH . D 4 HOH A 27 627 45 HOH HOH . D 4 HOH A 28 628 12 HOH HOH . D 4 HOH A 29 629 24 HOH HOH . D 4 HOH A 30 630 42 HOH HOH . D 4 HOH A 31 631 39 HOH HOH . D 4 HOH A 32 632 19 HOH HOH . D 4 HOH A 33 633 34 HOH HOH . D 4 HOH A 34 634 35 HOH HOH . D 4 HOH A 35 635 37 HOH HOH . D 4 HOH A 36 636 22 HOH HOH . D 4 HOH A 37 637 41 HOH HOH . D 4 HOH A 38 638 16 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 -39.164 20.751 -3.162 1 56.99 ? O2 VDX 501 A 1 HETATM 2 O O3 VDX . . . C 3 -25.3 17.442 -8.601 1 59.23 ? O3 VDX 501 A 1 HETATM 3 C C1 VDX . . . C 3 -37.06 22.103 -4.571 1 61.84 ? C1 VDX 501 A 1 HETATM 4 C C2 VDX . . . C 3 -38.521 21.934 -5.09 1 50.17 ? C2 VDX 501 A 1 HETATM 5 C C3 VDX . . . C 3 -39.107 20.702 -4.602 1 63.09 ? C3 VDX 501 A 1 HETATM 6 C C4 VDX . . . C 3 -38.275 19.443 -5.035 1 51.86 ? C4 VDX 501 A 1 HETATM 7 C C5 VDX . . . C 3 -36.839 19.513 -4.606 1 51.77 ? C5 VDX 501 A 1 HETATM 8 C C6 VDX . . . C 3 -36.13 18.392 -4.251 1 52.29 ? C6 VDX 501 A 1 HETATM 9 C C7 VDX . . . C 3 -34.622 18.458 -3.837 1 52.14 ? C7 VDX 501 A 1 HETATM 10 C C8 VDX . . . C 3 -33.911 17.297 -3.835 1 53.03 ? C8 VDX 501 A 1 HETATM 11 C C9 VDX . . . C 3 -34.51 15.949 -4.139 1 61.04 ? C9 VDX 501 A 1 HETATM 12 C C10 VDX . . . C 3 -36.167 20.945 -4.962 1 59.52 ? C10 VDX 501 A 1 HETATM 13 C C11 VDX . . . C 3 -33.705 15.181 -5.168 1 61.48 ? C11 VDX 501 A 1 HETATM 14 C C12 VDX . . . C 3 -32.279 15.142 -4.918 1 58.45 ? C12 VDX 501 A 1 HETATM 15 C C13 VDX . . . C 3 -31.692 16.612 -4.589 1 51.77 ? C13 VDX 501 A 1 HETATM 16 C C14 VDX . . . C 3 -32.392 17.152 -3.494 1 60.99 ? C14 VDX 501 A 1 HETATM 17 C C15 VDX . . . C 3 -31.722 18.573 -3.341 1 61.67 ? C15 VDX 501 A 1 HETATM 18 C C16 VDX . . . C 3 -30.164 18.252 -3.779 1 66.09 ? C16 VDX 501 A 1 HETATM 19 C C17 VDX . . . C 3 -30.151 16.888 -4.088 1 63.94 ? C17 VDX 501 A 1 HETATM 20 C C18 VDX . . . C 3 -31.963 17.467 -5.839 1 48.91 ? C18 VDX 501 A 1 HETATM 21 C C19 VDX . . . C 3 -35.184 21.066 -5.842 1 68.43 ? C19 VDX 501 A 1 HETATM 22 C C20 VDX . . . C 3 -29.067 16.482 -5.118 1 62.94 ? C20 VDX 501 A 1 HETATM 23 C C21 VDX . . . C 3 -27.861 15.963 -4.353 1 53.9 ? C21 VDX 501 A 1 HETATM 24 C C22 VDX . . . C 3 -28.584 17.634 -6.024 1 61.58 ? C22 VDX 501 A 1 HETATM 25 C C23 VDX . . . C 3 -27.772 17.004 -7.207 1 54.49 ? C23 VDX 501 A 1 HETATM 26 C C24 VDX . . . C 3 -27.655 18.006 -8.399 1 56.8 ? C24 VDX 501 A 1 HETATM 27 C C25 VDX . . . C 3 -26.487 17.562 -9.339 1 63.33 ? C25 VDX 501 A 1 HETATM 28 C C26 VDX . . . C 3 -26.818 16.201 -9.988 1 50.52 ? C26 VDX 501 A 1 HETATM 29 C C27 VDX . . . C 3 -26.293 18.603 -10.448 1 54.88 ? C27 VDX 501 A 1 HETATM 30 O O1 VDX . . . C 3 -36.515 23.296 -5.106 1 63.71 ? O1 VDX 501 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 30 #