data_6XZK
#
_model_server_result.job_id            -y0xNosMBZovdkf6Hd-PPA 
_model_server_result.datetime_utc      '2024-10-11 11:13:39' 
_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          6xzk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":501}' 
#
_entry.id    6XZK 
#
_exptl.entry_id    6XZK 
_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            6XZK 
_cell.length_a            66.112 
_cell.length_b            66.112 
_cell.length_c            262.488 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6XZK 
_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,F,G 
_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 ALA 3 B ALA 3 1_555 B N UIA 4 B UIA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? 
covale ? covale2 B C UIA 4 B UIA 4 1_555 B N URL 5 B URL 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? 
covale ? covale3 B C URL 5 B URL 5 1_555 B N MFH 6 B MFH 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale4 B C MFH 6 B MFH 6 1_555 B N URV 7 B URV 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? 
covale ? covale5 B C URV 7 B URV 7 1_555 B N UZN 8 B UZN 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? 
covale ? covale6 B C UZN 8 B UZN 8 1_555 B N LYS 9 B LYS 9 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 503 n n 
O2 HO2 VDX sing 504 n n 
O3 C25 VDX sing 505 n n 
O3 HO3 VDX sing 506 n n 
C1 C2 VDX sing 507 n n 
C1 C10 VDX sing 508 n n 
C1 O1 VDX sing 509 n n 
C1 H11 VDX sing 510 n n 
C2 C3 VDX sing 511 n n 
C2 H21 VDX sing 512 n n 
C2 H22 VDX sing 513 n n 
C3 C4 VDX sing 514 n n 
C3 H31 VDX sing 515 n n 
C4 C5 VDX sing 516 n n 
C4 H41 VDX sing 517 n n 
C4 H42 VDX sing 518 n n 
C5 C6 VDX doub 519 z n 
C5 C10 VDX sing 520 n n 
C6 C7 VDX sing 521 n n 
C6 H61 VDX sing 522 n n 
C7 C8 VDX doub 523 e n 
C7 H71 VDX sing 524 n n 
C8 C9 VDX sing 525 n n 
C8 C14 VDX sing 526 n n 
C9 C11 VDX sing 527 n n 
C9 H91 VDX sing 528 n n 
C9 H92 VDX sing 529 n n 
C10 C19 VDX doub 530 n n 
C11 C12 VDX sing 531 n n 
C11 H111 VDX sing 532 n n 
C11 H112 VDX sing 533 n n 
C12 C13 VDX sing 534 n n 
C12 H121 VDX sing 535 n n 
C12 H122 VDX sing 536 n n 
C13 C14 VDX sing 537 n n 
C13 C17 VDX sing 538 n n 
C13 C18 VDX sing 539 n n 
C14 C15 VDX sing 540 n n 
C14 H141 VDX sing 541 n n 
C15 C16 VDX sing 542 n n 
C15 H151 VDX sing 543 n n 
C15 H152 VDX sing 544 n n 
C16 C17 VDX sing 545 n n 
C16 H161 VDX sing 546 n n 
C16 H162 VDX sing 547 n n 
C17 C20 VDX sing 548 n n 
C17 H171 VDX sing 549 n n 
C18 H181 VDX sing 550 n n 
C18 H182 VDX sing 551 n n 
C18 H183 VDX sing 552 n n 
C19 H191 VDX sing 553 n n 
C19 H192 VDX sing 554 n n 
C20 C21 VDX sing 555 n n 
C20 C22 VDX sing 556 n n 
C20 H201 VDX sing 557 n n 
C21 H211 VDX sing 558 n n 
C21 H212 VDX sing 559 n n 
C21 H213 VDX sing 560 n n 
C22 C23 VDX sing 561 n n 
C22 H221 VDX sing 562 n n 
C22 H222 VDX sing 563 n n 
C23 C24 VDX sing 564 n n 
C23 H231 VDX sing 565 n n 
C23 H232 VDX sing 566 n n 
C24 C25 VDX sing 567 n n 
C24 H241 VDX sing 568 n n 
C24 H242 VDX sing 569 n n 
C25 C26 VDX sing 570 n n 
C25 C27 VDX sing 571 n n 
C26 H261 VDX sing 572 n n 
C26 H262 VDX sing 573 n n 
C26 H263 VDX sing 574 n n 
C27 H271 VDX sing 575 n n 
C27 H272 VDX sing 576 n n 
C27 H273 VDX sing 577 n n 
O1 HO1 VDX sing 578 n n 
#
_atom_sites.entry_id                     6XZK 
_atom_sites.fract_transf_matrix[1][1]    0.015126 
_atom_sites.fract_transf_matrix[1][2]    0.008733 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.017466 
_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]    0.00381 
_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 1 VDX VDX . 
D 4 ACT A 1 502 1428 ACT ACT . 
E 4 ACT A 1 503 1429 ACT ACT . 
F 5 HOH A 1 601 97 HOH HOH . 
F 5 HOH A 2 602 26 HOH HOH . 
F 5 HOH A 3 603 32 HOH HOH . 
F 5 HOH A 4 604 98 HOH HOH . 
F 5 HOH A 5 605 19 HOH HOH . 
F 5 HOH A 6 606 95 HOH HOH . 
F 5 HOH A 7 607 90 HOH HOH . 
F 5 HOH A 8 608 31 HOH HOH . 
F 5 HOH A 9 609 36 HOH HOH . 
F 5 HOH A 10 610 29 HOH HOH . 
F 5 HOH A 11 611 48 HOH HOH . 
F 5 HOH A 12 612 10 HOH HOH . 
F 5 HOH A 13 613 61 HOH HOH . 
F 5 HOH A 14 614 75 HOH HOH . 
F 5 HOH A 15 615 8 HOH HOH . 
F 5 HOH A 16 616 28 HOH HOH . 
F 5 HOH A 17 617 103 HOH HOH . 
F 5 HOH A 18 618 66 HOH HOH . 
F 5 HOH A 19 619 96 HOH HOH . 
F 5 HOH A 20 620 43 HOH HOH . 
F 5 HOH A 21 621 70 HOH HOH . 
F 5 HOH A 22 622 51 HOH HOH . 
F 5 HOH A 23 623 12 HOH HOH . 
F 5 HOH A 24 624 69 HOH HOH . 
F 5 HOH A 25 625 2 HOH HOH . 
F 5 HOH A 26 626 35 HOH HOH . 
F 5 HOH A 27 627 62 HOH HOH . 
F 5 HOH A 28 628 42 HOH HOH . 
F 5 HOH A 29 629 67 HOH HOH . 
F 5 HOH A 30 630 84 HOH HOH . 
F 5 HOH A 31 631 74 HOH HOH . 
F 5 HOH A 32 632 100 HOH HOH . 
F 5 HOH A 33 633 6 HOH HOH . 
F 5 HOH A 34 634 7 HOH HOH . 
F 5 HOH A 35 635 18 HOH HOH . 
F 5 HOH A 36 636 9 HOH HOH . 
F 5 HOH A 37 637 40 HOH HOH . 
F 5 HOH A 38 638 21 HOH HOH . 
F 5 HOH A 39 639 1 HOH HOH . 
F 5 HOH A 40 640 56 HOH HOH . 
F 5 HOH A 41 641 82 HOH HOH . 
F 5 HOH A 42 642 39 HOH HOH . 
F 5 HOH A 43 643 5 HOH HOH . 
F 5 HOH A 44 644 25 HOH HOH . 
F 5 HOH A 45 645 11 HOH HOH . 
F 5 HOH A 46 646 4 HOH HOH . 
F 5 HOH A 47 647 16 HOH HOH . 
F 5 HOH A 48 648 50 HOH HOH . 
F 5 HOH A 49 649 24 HOH HOH . 
F 5 HOH A 50 650 22 HOH HOH . 
F 5 HOH A 51 651 94 HOH HOH . 
F 5 HOH A 52 652 27 HOH HOH . 
F 5 HOH A 53 653 85 HOH HOH . 
F 5 HOH A 54 654 53 HOH HOH . 
F 5 HOH A 55 655 37 HOH HOH . 
F 5 HOH A 56 656 81 HOH HOH . 
F 5 HOH A 57 657 72 HOH HOH . 
F 5 HOH A 58 658 92 HOH HOH . 
F 5 HOH A 59 659 83 HOH HOH . 
F 5 HOH A 60 660 104 HOH HOH . 
F 5 HOH A 61 661 45 HOH HOH . 
F 5 HOH A 62 662 76 HOH HOH . 
F 5 HOH A 63 663 30 HOH HOH . 
F 5 HOH A 64 664 20 HOH HOH . 
F 5 HOH A 65 665 78 HOH HOH . 
F 5 HOH A 66 666 63 HOH HOH . 
F 5 HOH A 67 667 60 HOH HOH . 
F 5 HOH A 68 668 87 HOH HOH . 
F 5 HOH A 69 669 3 HOH HOH . 
F 5 HOH A 70 670 34 HOH HOH . 
F 5 HOH A 71 671 77 HOH HOH . 
F 5 HOH A 72 672 41 HOH HOH . 
F 5 HOH A 73 673 71 HOH HOH . 
F 5 HOH A 74 674 46 HOH HOH . 
F 5 HOH A 75 675 33 HOH HOH . 
F 5 HOH A 76 676 57 HOH HOH . 
F 5 HOH A 77 677 88 HOH HOH . 
F 5 HOH A 78 678 55 HOH HOH . 
F 5 HOH A 79 679 23 HOH HOH . 
F 5 HOH A 80 680 91 HOH HOH . 
F 5 HOH A 81 681 68 HOH HOH . 
F 5 HOH A 82 682 102 HOH HOH . 
F 5 HOH A 83 683 38 HOH HOH . 
F 5 HOH A 84 684 99 HOH HOH . 
F 5 HOH A 85 685 105 HOH HOH . 
F 5 HOH A 86 686 14 HOH HOH . 
F 5 HOH A 87 687 101 HOH HOH . 
F 5 HOH A 88 688 59 HOH HOH . 
F 5 HOH A 89 689 58 HOH HOH . 
F 5 HOH A 90 690 52 HOH HOH . 
F 5 HOH A 91 691 49 HOH HOH . 
F 5 HOH A 92 692 73 HOH HOH . 
F 5 HOH A 93 693 89 HOH HOH . 
F 5 HOH A 94 694 106 HOH HOH . 
F 5 HOH A 95 695 93 HOH HOH . 
G 5 HOH B 1 101 15 HOH HOH . 
G 5 HOH B 2 102 13 HOH HOH . 
G 5 HOH B 3 103 64 HOH HOH . 
G 5 HOH B 4 104 65 HOH HOH . 
G 5 HOH B 5 105 54 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 -36.966 21.505 -3.776 1 32.4 ? O2 VDX 501 A 1 
HETATM 2 O O3 VDX . . . C 3 -23.328 17.936 -9.493 1 36.27 ? O3 VDX 501 A 1 
HETATM 3 C C1 VDX . . . C 3 -34.771 22.639 -5.27 1 33.15 ? C1 VDX 501 A 1 
HETATM 4 C C2 VDX . . . C 3 -36.263 22.631 -5.715 1 33.46 ? C2 VDX 501 A 1 
HETATM 5 C C3 VDX . . . C 3 -36.959 21.462 -5.216 1 36.79 ? C3 VDX 501 A 1 
HETATM 6 C C4 VDX . . . C 3 -36.282 20.123 -5.681 1 38.09 ? C4 VDX 501 A 1 
HETATM 7 C C5 VDX . . . C 3 -34.805 20.061 -5.41 1 30.24 ? C5 VDX 501 A 1 
HETATM 8 C C6 VDX . . . C 3 -34.186 18.908 -5.008 1 29.54 ? C6 VDX 501 A 1 
HETATM 9 C C7 VDX . . . C 3 -32.677 18.896 -4.599 1 28.91 ? C7 VDX 501 A 1 
HETATM 10 C C8 VDX . . . C 3 -32.005 17.714 -4.647 1 34.03 ? C8 VDX 501 A 1 
HETATM 11 C C9 VDX . . . C 3 -32.64 16.423 -5.088 1 39.14 ? C9 VDX 501 A 1 
HETATM 12 C C10 VDX . . . C 3 -34.025 21.428 -5.782 1 34.63 ? C10 VDX 501 A 1 
HETATM 13 C C11 VDX . . . C 3 -31.824 15.615 -6.084 1 36.64 ? C11 VDX 501 A 1 
HETATM 14 C C12 VDX . . . C 3 -30.384 15.629 -5.926 1 34.39 ? C12 VDX 501 A 1 
HETATM 15 C C13 VDX . . . C 3 -29.8 17.071 -5.5 1 35.94 ? C13 VDX 501 A 1 
HETATM 16 C C14 VDX . . . C 3 -30.483 17.527 -4.359 1 40.26 ? C14 VDX 501 A 1 
HETATM 17 C C15 VDX . . . C 3 -29.808 18.932 -4.112 1 42.73 ? C15 VDX 501 A 1 
HETATM 18 C C16 VDX . . . C 3 -28.249 18.623 -4.555 1 42 ? C16 VDX 501 A 1 
HETATM 19 C C17 VDX . . . C 3 -28.257 17.29 -4.983 1 41.09 ? C17 VDX 501 A 1 
HETATM 20 C C18 VDX . . . C 3 -30.066 18.016 -6.684 1 34.28 ? C18 VDX 501 A 1 
HETATM 21 C C19 VDX . . . C 3 -33.122 21.5 -6.753 1 32.35 ? C19 VDX 501 A 1 
HETATM 22 C C20 VDX . . . C 3 -27.167 16.926 -6.025 1 35.15 ? C20 VDX 501 A 1 
HETATM 23 C C21 VDX . . . C 3 -25.961 16.422 -5.249 1 34.52 ? C21 VDX 501 A 1 
HETATM 24 C C22 VDX . . . C 3 -26.701 18.097 -6.917 1 29.7 ? C22 VDX 501 A 1 
HETATM 25 C C23 VDX . . . C 3 -25.751 17.538 -8.038 1 31.51 ? C23 VDX 501 A 1 
HETATM 26 C C24 VDX . . . C 3 -25.661 18.532 -9.245 1 30.65 ? C24 VDX 501 A 1 
HETATM 27 C C25 VDX . . . C 3 -24.513 18.112 -10.224 1 36.91 ? C25 VDX 501 A 1 
HETATM 28 C C26 VDX . . . C 3 -24.881 16.799 -10.947 1 33.58 ? C26 VDX 501 A 1 
HETATM 29 C C27 VDX . . . C 3 -24.3 19.198 -11.291 1 28.09 ? C27 VDX 501 A 1 
HETATM 30 O O1 VDX . . . C 3 -34.163 23.826 -5.747 1 36.79 ? O1 VDX 501 A 1 
#
_model_server_stats.io_time_ms              53 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           352 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           30 
#