data_6XZI # _model_server_result.job_id O4f2y3SIfuZiiSgNBZ--Zw _model_server_result.datetime_utc '2024-11-29 02:29:27' _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 6xzi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 6XZI # _exptl.entry_id 6XZI _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 6XZI _cell.length_a 66.35 _cell.length_b 66.35 _cell.length_c 262.37 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XZI _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,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 # 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 LEU 5 B LEU 690 1_555 B N OUK 6 B OUK 691 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale2 B C OUK 6 B OUK 691 1_555 B N UIL 7 B UIL 692 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale3 B C UIL 7 B UIL 692 1_555 B N URL 8 B URL 693 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? # _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 463 n n O2 HO2 VDX sing 464 n n O3 C25 VDX sing 465 n n O3 HO3 VDX sing 466 n n C1 C2 VDX sing 467 n n C1 C10 VDX sing 468 n n C1 O1 VDX sing 469 n n C1 H11 VDX sing 470 n n C2 C3 VDX sing 471 n n C2 H21 VDX sing 472 n n C2 H22 VDX sing 473 n n C3 C4 VDX sing 474 n n C3 H31 VDX sing 475 n n C4 C5 VDX sing 476 n n C4 H41 VDX sing 477 n n C4 H42 VDX sing 478 n n C5 C6 VDX doub 479 z n C5 C10 VDX sing 480 n n C6 C7 VDX sing 481 n n C6 H61 VDX sing 482 n n C7 C8 VDX doub 483 e n C7 H71 VDX sing 484 n n C8 C9 VDX sing 485 n n C8 C14 VDX sing 486 n n C9 C11 VDX sing 487 n n C9 H91 VDX sing 488 n n C9 H92 VDX sing 489 n n C10 C19 VDX doub 490 n n C11 C12 VDX sing 491 n n C11 H111 VDX sing 492 n n C11 H112 VDX sing 493 n n C12 C13 VDX sing 494 n n C12 H121 VDX sing 495 n n C12 H122 VDX sing 496 n n C13 C14 VDX sing 497 n n C13 C17 VDX sing 498 n n C13 C18 VDX sing 499 n n C14 C15 VDX sing 500 n n C14 H141 VDX sing 501 n n C15 C16 VDX sing 502 n n C15 H151 VDX sing 503 n n C15 H152 VDX sing 504 n n C16 C17 VDX sing 505 n n C16 H161 VDX sing 506 n n C16 H162 VDX sing 507 n n C17 C20 VDX sing 508 n n C17 H171 VDX sing 509 n n C18 H181 VDX sing 510 n n C18 H182 VDX sing 511 n n C18 H183 VDX sing 512 n n C19 H191 VDX sing 513 n n C19 H192 VDX sing 514 n n C20 C21 VDX sing 515 n n C20 C22 VDX sing 516 n n C20 H201 VDX sing 517 n n C21 H211 VDX sing 518 n n C21 H212 VDX sing 519 n n C21 H213 VDX sing 520 n n C22 C23 VDX sing 521 n n C22 H221 VDX sing 522 n n C22 H222 VDX sing 523 n n C23 C24 VDX sing 524 n n C23 H231 VDX sing 525 n n C23 H232 VDX sing 526 n n C24 C25 VDX sing 527 n n C24 H241 VDX sing 528 n n C24 H242 VDX sing 529 n n C25 C26 VDX sing 530 n n C25 C27 VDX sing 531 n n C26 H261 VDX sing 532 n n C26 H262 VDX sing 533 n n C26 H263 VDX sing 534 n n C27 H271 VDX sing 535 n n C27 H272 VDX sing 536 n n C27 H273 VDX sing 537 n n O1 HO1 VDX sing 538 n n # _atom_sites.entry_id 6XZI _atom_sites.fract_transf_matrix[1][1] 0.015072 _atom_sites.fract_transf_matrix[1][2] 0.008702 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017403 _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] 0.003811 _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 ACT A 1 502 1428 ACT ACT . E 5 HOH A 1 601 65 HOH HOH . E 5 HOH A 2 602 57 HOH HOH . E 5 HOH A 3 603 31 HOH HOH . E 5 HOH A 4 604 54 HOH HOH . E 5 HOH A 5 605 66 HOH HOH . E 5 HOH A 6 606 63 HOH HOH . E 5 HOH A 7 607 11 HOH HOH . E 5 HOH A 8 608 61 HOH HOH . E 5 HOH A 9 609 48 HOH HOH . E 5 HOH A 10 610 62 HOH HOH . E 5 HOH A 11 611 59 HOH HOH . E 5 HOH A 12 612 25 HOH HOH . E 5 HOH A 13 613 29 HOH HOH . E 5 HOH A 14 614 1 HOH HOH . E 5 HOH A 15 615 67 HOH HOH . E 5 HOH A 16 616 4 HOH HOH . E 5 HOH A 17 617 21 HOH HOH . E 5 HOH A 18 618 44 HOH HOH . E 5 HOH A 19 619 26 HOH HOH . E 5 HOH A 20 620 7 HOH HOH . E 5 HOH A 21 621 23 HOH HOH . E 5 HOH A 22 622 39 HOH HOH . E 5 HOH A 23 623 10 HOH HOH . E 5 HOH A 24 624 13 HOH HOH . E 5 HOH A 25 625 2 HOH HOH . E 5 HOH A 26 626 9 HOH HOH . E 5 HOH A 27 627 27 HOH HOH . E 5 HOH A 28 628 16 HOH HOH . E 5 HOH A 29 629 5 HOH HOH . E 5 HOH A 30 630 6 HOH HOH . E 5 HOH A 31 631 64 HOH HOH . E 5 HOH A 32 632 41 HOH HOH . E 5 HOH A 33 633 45 HOH HOH . E 5 HOH A 34 634 22 HOH HOH . E 5 HOH A 35 635 3 HOH HOH . E 5 HOH A 36 636 34 HOH HOH . E 5 HOH A 37 637 32 HOH HOH . E 5 HOH A 38 638 14 HOH HOH . E 5 HOH A 39 639 60 HOH HOH . E 5 HOH A 40 640 28 HOH HOH . E 5 HOH A 41 641 15 HOH HOH . E 5 HOH A 42 642 38 HOH HOH . E 5 HOH A 43 643 37 HOH HOH . E 5 HOH A 44 644 36 HOH HOH . E 5 HOH A 45 645 24 HOH HOH . E 5 HOH A 46 646 18 HOH HOH . E 5 HOH A 47 647 20 HOH HOH . E 5 HOH A 48 648 12 HOH HOH . E 5 HOH A 49 649 17 HOH HOH . E 5 HOH A 50 650 42 HOH HOH . E 5 HOH A 51 651 8 HOH HOH . E 5 HOH A 52 652 56 HOH HOH . E 5 HOH A 53 653 53 HOH HOH . E 5 HOH A 54 654 35 HOH HOH . E 5 HOH A 55 655 49 HOH HOH . E 5 HOH A 56 656 30 HOH HOH . E 5 HOH A 57 657 58 HOH HOH . E 5 HOH A 58 658 46 HOH HOH . E 5 HOH A 59 659 33 HOH HOH . E 5 HOH A 60 660 43 HOH HOH . E 5 HOH A 61 661 40 HOH HOH . E 5 HOH A 62 662 50 HOH HOH . E 5 HOH A 63 663 55 HOH HOH . E 5 HOH A 64 664 47 HOH HOH . E 5 HOH A 65 665 19 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 36.317 -21.429 -3.775 1 36.97 ? O2 VDX 501 A 1 HETATM 2 O O3 VDX . . . C 3 22.652 -18.234 -9.517 1 39.33 ? O3 VDX 501 A 1 HETATM 3 C C1 VDX . . . C 3 34.088 -22.666 -5.175 1 36.63 ? C1 VDX 501 A 1 HETATM 4 C C2 VDX . . . C 3 35.577 -22.657 -5.632 1 33.39 ? C2 VDX 501 A 1 HETATM 5 C C3 VDX . . . C 3 36.265 -21.453 -5.214 1 39.01 ? C3 VDX 501 A 1 HETATM 6 C C4 VDX . . . C 3 35.554 -20.146 -5.717 1 35.38 ? C4 VDX 501 A 1 HETATM 7 C C5 VDX . . . C 3 34.092 -20.089 -5.379 1 33.46 ? C5 VDX 501 A 1 HETATM 8 C C6 VDX . . . C 3 33.459 -18.934 -4.998 1 34.64 ? C6 VDX 501 A 1 HETATM 9 C C7 VDX . . . C 3 31.935 -18.937 -4.65 1 38.67 ? C7 VDX 501 A 1 HETATM 10 C C8 VDX . . . C 3 31.227 -17.775 -4.707 1 38.18 ? C8 VDX 501 A 1 HETATM 11 C C9 VDX . . . C 3 31.805 -16.443 -5.102 1 41.31 ? C9 VDX 501 A 1 HETATM 12 C C10 VDX . . . C 3 33.319 -21.476 -5.699 1 34.77 ? C10 VDX 501 A 1 HETATM 13 C C11 VDX . . . C 3 31.024 -15.789 -6.224 1 43.85 ? C11 VDX 501 A 1 HETATM 14 C C12 VDX . . . C 3 29.591 -15.753 -6.022 1 40.77 ? C12 VDX 501 A 1 HETATM 15 C C13 VDX . . . C 3 29.017 -17.191 -5.561 1 39.02 ? C13 VDX 501 A 1 HETATM 16 C C14 VDX . . . C 3 29.701 -17.624 -4.411 1 43.24 ? C14 VDX 501 A 1 HETATM 17 C C15 VDX . . . C 3 29.04 -19.034 -4.153 1 41.65 ? C15 VDX 501 A 1 HETATM 18 C C16 VDX . . . C 3 27.484 -18.753 -4.625 1 45.61 ? C16 VDX 501 A 1 HETATM 19 C C17 VDX . . . C 3 27.472 -17.425 -5.064 1 42.39 ? C17 VDX 501 A 1 HETATM 20 C C18 VDX . . . C 3 29.286 -18.154 -6.728 1 34.44 ? C18 VDX 501 A 1 HETATM 21 C C19 VDX . . . C 3 32.415 -21.581 -6.66 1 37.89 ? C19 VDX 501 A 1 HETATM 22 C C20 VDX . . . C 3 26.445 -17.123 -6.18 1 46.2 ? C20 VDX 501 A 1 HETATM 23 C C21 VDX . . . C 3 25.34 -16.273 -5.582 1 45.8 ? C21 VDX 501 A 1 HETATM 24 C C22 VDX . . . C 3 25.811 -18.388 -6.795 1 45.89 ? C22 VDX 501 A 1 HETATM 25 C C23 VDX . . . C 3 24.775 -17.956 -7.891 1 42.71 ? C23 VDX 501 A 1 HETATM 26 C C24 VDX . . . C 3 25.014 -18.744 -9.22 1 32.56 ? C24 VDX 501 A 1 HETATM 27 C C25 VDX . . . C 3 23.844 -18.465 -10.22 1 42 ? C25 VDX 501 A 1 HETATM 28 C C26 VDX . . . C 3 24.18 -17.218 -11.064 1 41.57 ? C26 VDX 501 A 1 HETATM 29 C C27 VDX . . . C 3 23.659 -19.669 -11.152 1 42.43 ? C27 VDX 501 A 1 HETATM 30 O O1 VDX . . . C 3 33.478 -23.861 -5.632 1 38.21 ? O1 VDX 501 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 389 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 30 #