data_1RJK
#
_model_server_result.job_id            wwKmR5DWanKmauPQlUP5AQ 
_model_server_result.datetime_utc      '2024-11-21 21:29:46' 
_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          1rjk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":500}' 
#
_entry.id    1RJK 
#
_exptl.entry_id    1RJK 
_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}-2-METHYLENE-CYCLOHEXANE-1,3-DIO L' 
_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          96.07 
_cell.angle_gamma         90 
_cell.entry_id            1RJK 
_cell.length_a            154.6 
_cell.length_b            43.292 
_cell.length_c            41.848 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1RJK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA tetrameric 4 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E 1 1 
A,B,C,D,E 2 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' 2_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 154.6 0 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 
#
_chem_comp.formula           'C27 H44 O3' 
_chem_comp.formula_weight    416.636 
_chem_comp.id                VDZ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIO L' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '2-METHYLENE-19-NOR-(20S)-1ALPHA,25-DIHYDROXY-VITAMIN D3;2MD' 
#
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
O1 C1 VDZ sing 376 n n 
O1 HO1 VDZ sing 377 n n 
C1 C2 VDZ sing 378 n n 
C1 C10 VDZ sing 379 n n 
C1 H1 VDZ sing 380 n n 
C2 C28 VDZ doub 381 n n 
C2 C3 VDZ sing 382 n n 
C28 H281 VDZ sing 383 n n 
C28 H282 VDZ sing 384 n n 
C3 O2 VDZ sing 385 n n 
C3 C4 VDZ sing 386 n n 
C3 H3 VDZ sing 387 n n 
O2 HO2 VDZ sing 388 n n 
C4 C5 VDZ sing 389 n n 
C4 H41 VDZ sing 390 n n 
C4 H42 VDZ sing 391 n n 
C10 C5 VDZ sing 392 n n 
C10 H101 VDZ sing 393 n n 
C10 H102 VDZ sing 394 n n 
C5 C6 VDZ doub 395 n n 
C6 C7 VDZ sing 396 n n 
C6 H6 VDZ sing 397 n n 
C7 C8 VDZ doub 398 e n 
C7 H7 VDZ sing 399 n n 
C8 C9 VDZ sing 400 n n 
C8 C14 VDZ sing 401 n n 
C9 C11 VDZ sing 402 n n 
C9 H91 VDZ sing 403 n n 
C9 H92 VDZ sing 404 n n 
C11 C12 VDZ sing 405 n n 
C11 H111 VDZ sing 406 n n 
C11 H112 VDZ sing 407 n n 
C14 C13 VDZ sing 408 n n 
C14 C15 VDZ sing 409 n n 
C14 H14 VDZ sing 410 n n 
C13 C12 VDZ sing 411 n n 
C13 C18 VDZ sing 412 n n 
C13 C17 VDZ sing 413 n n 
C12 H121 VDZ sing 414 n n 
C12 H122 VDZ sing 415 n n 
C18 H181 VDZ sing 416 n n 
C18 H182 VDZ sing 417 n n 
C18 H183 VDZ sing 418 n n 
C15 C16 VDZ sing 419 n n 
C15 H151 VDZ sing 420 n n 
C15 H152 VDZ sing 421 n n 
C16 C17 VDZ sing 422 n n 
C16 H161 VDZ sing 423 n n 
C16 H162 VDZ sing 424 n n 
C17 C20 VDZ sing 425 n n 
C17 H17 VDZ sing 426 n n 
C20 C21 VDZ sing 427 n n 
C20 C22 VDZ sing 428 n n 
C20 H20 VDZ sing 429 n n 
C21 H211 VDZ sing 430 n n 
C21 H212 VDZ sing 431 n n 
C21 H213 VDZ sing 432 n n 
C22 C23 VDZ sing 433 n n 
C22 H221 VDZ sing 434 n n 
C22 H222 VDZ sing 435 n n 
C23 C24 VDZ sing 436 n n 
C23 H231 VDZ sing 437 n n 
C23 H232 VDZ sing 438 n n 
C24 C25 VDZ sing 439 n n 
C24 H241 VDZ sing 440 n n 
C24 H242 VDZ sing 441 n n 
C25 C26 VDZ sing 442 n n 
C25 C27 VDZ sing 443 n n 
C25 O3 VDZ sing 444 n n 
C26 H261 VDZ sing 445 n n 
C26 H262 VDZ sing 446 n n 
C26 H263 VDZ sing 447 n n 
C27 H271 VDZ sing 448 n n 
C27 H272 VDZ sing 449 n n 
C27 H273 VDZ sing 450 n n 
O3 HO3 VDZ sing 451 n n 
#
_atom_sites.entry_id                     1RJK 
_atom_sites.fract_transf_matrix[1][1]    0.006468 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000688 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.023099 
_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]    0.024031 
_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 VDZ A 1 500 500 VDZ VDZ . 
D 4 HOH A 1 501 1 HOH HOH . 
D 4 HOH A 2 502 2 HOH HOH . 
D 4 HOH A 3 503 3 HOH HOH . 
D 4 HOH A 4 504 4 HOH HOH . 
D 4 HOH A 5 505 5 HOH HOH . 
D 4 HOH A 6 506 6 HOH HOH . 
D 4 HOH A 7 507 7 HOH HOH . 
D 4 HOH A 8 508 8 HOH HOH . 
D 4 HOH A 9 509 9 HOH HOH . 
D 4 HOH A 10 510 10 HOH HOH . 
D 4 HOH A 11 511 11 HOH HOH . 
D 4 HOH A 12 512 12 HOH HOH . 
D 4 HOH A 13 513 13 HOH HOH . 
D 4 HOH A 14 514 14 HOH HOH . 
D 4 HOH A 15 515 15 HOH HOH . 
D 4 HOH A 16 516 16 HOH HOH . 
D 4 HOH A 17 517 17 HOH HOH . 
D 4 HOH A 18 518 18 HOH HOH . 
D 4 HOH A 19 519 19 HOH HOH . 
D 4 HOH A 20 520 20 HOH HOH . 
D 4 HOH A 21 521 21 HOH HOH . 
D 4 HOH A 22 522 22 HOH HOH . 
D 4 HOH A 23 523 23 HOH HOH . 
D 4 HOH A 24 524 24 HOH HOH . 
D 4 HOH A 25 525 25 HOH HOH . 
D 4 HOH A 26 526 26 HOH HOH . 
D 4 HOH A 27 527 27 HOH HOH . 
D 4 HOH A 28 528 28 HOH HOH . 
D 4 HOH A 29 529 29 HOH HOH . 
D 4 HOH A 30 530 30 HOH HOH . 
D 4 HOH A 31 531 31 HOH HOH . 
D 4 HOH A 32 532 32 HOH HOH . 
D 4 HOH A 33 533 34 HOH HOH . 
D 4 HOH A 34 534 35 HOH HOH . 
D 4 HOH A 35 535 36 HOH HOH . 
D 4 HOH A 36 536 37 HOH HOH . 
D 4 HOH A 37 537 38 HOH HOH . 
D 4 HOH A 38 538 39 HOH HOH . 
D 4 HOH A 39 539 40 HOH HOH . 
D 4 HOH A 40 540 41 HOH HOH . 
D 4 HOH A 41 541 42 HOH HOH . 
D 4 HOH A 42 542 43 HOH HOH . 
D 4 HOH A 43 543 44 HOH HOH . 
D 4 HOH A 44 544 45 HOH HOH . 
D 4 HOH A 45 545 46 HOH HOH . 
D 4 HOH A 46 546 47 HOH HOH . 
D 4 HOH A 47 547 48 HOH HOH . 
D 4 HOH A 48 548 49 HOH HOH . 
D 4 HOH A 49 549 50 HOH HOH . 
D 4 HOH A 50 550 51 HOH HOH . 
D 4 HOH A 51 551 52 HOH HOH . 
D 4 HOH A 52 552 53 HOH HOH . 
D 4 HOH A 53 553 54 HOH HOH . 
D 4 HOH A 54 554 55 HOH HOH . 
D 4 HOH A 55 555 56 HOH HOH . 
D 4 HOH A 56 556 57 HOH HOH . 
D 4 HOH A 57 557 58 HOH HOH . 
D 4 HOH A 58 558 59 HOH HOH . 
D 4 HOH A 59 559 60 HOH HOH . 
D 4 HOH A 60 560 61 HOH HOH . 
D 4 HOH A 61 561 62 HOH HOH . 
D 4 HOH A 62 562 63 HOH HOH . 
D 4 HOH A 63 563 64 HOH HOH . 
D 4 HOH A 64 564 65 HOH HOH . 
D 4 HOH A 65 565 66 HOH HOH . 
D 4 HOH A 66 566 67 HOH HOH . 
D 4 HOH A 67 567 68 HOH HOH . 
D 4 HOH A 68 568 69 HOH HOH . 
D 4 HOH A 69 569 70 HOH HOH . 
D 4 HOH A 70 570 71 HOH HOH . 
D 4 HOH A 71 571 72 HOH HOH . 
D 4 HOH A 72 572 73 HOH HOH . 
D 4 HOH A 73 573 74 HOH HOH . 
D 4 HOH A 74 574 75 HOH HOH . 
D 4 HOH A 75 575 76 HOH HOH . 
D 4 HOH A 76 576 77 HOH HOH . 
D 4 HOH A 77 577 78 HOH HOH . 
D 4 HOH A 78 578 79 HOH HOH . 
D 4 HOH A 79 579 80 HOH HOH . 
D 4 HOH A 80 580 81 HOH HOH . 
D 4 HOH A 81 581 82 HOH HOH . 
D 4 HOH A 82 582 83 HOH HOH . 
D 4 HOH A 83 583 84 HOH HOH . 
D 4 HOH A 84 584 85 HOH HOH . 
D 4 HOH A 85 585 86 HOH HOH . 
D 4 HOH A 86 586 87 HOH HOH . 
D 4 HOH A 87 587 88 HOH HOH . 
D 4 HOH A 88 588 90 HOH HOH . 
D 4 HOH A 89 589 91 HOH HOH . 
D 4 HOH A 90 590 92 HOH HOH . 
D 4 HOH A 91 591 93 HOH HOH . 
D 4 HOH A 92 592 94 HOH HOH . 
D 4 HOH A 93 593 95 HOH HOH . 
D 4 HOH A 94 594 96 HOH HOH . 
D 4 HOH A 95 595 97 HOH HOH . 
D 4 HOH A 96 596 98 HOH HOH . 
D 4 HOH A 97 597 99 HOH HOH . 
D 4 HOH A 98 598 100 HOH HOH . 
D 4 HOH A 99 599 101 HOH HOH . 
D 4 HOH A 100 600 102 HOH HOH . 
D 4 HOH A 101 601 104 HOH HOH . 
D 4 HOH A 102 602 105 HOH HOH . 
D 4 HOH A 103 603 106 HOH HOH . 
D 4 HOH A 104 604 107 HOH HOH . 
D 4 HOH A 105 605 108 HOH HOH . 
D 4 HOH A 106 606 109 HOH HOH . 
D 4 HOH A 107 607 110 HOH HOH . 
D 4 HOH A 108 608 111 HOH HOH . 
D 4 HOH A 109 609 112 HOH HOH . 
D 4 HOH A 110 610 113 HOH HOH . 
D 4 HOH A 111 611 114 HOH HOH . 
D 4 HOH A 112 612 115 HOH HOH . 
D 4 HOH A 113 613 116 HOH HOH . 
D 4 HOH A 114 614 117 HOH HOH . 
D 4 HOH A 115 615 118 HOH HOH . 
D 4 HOH A 116 616 119 HOH HOH . 
D 4 HOH A 117 617 120 HOH HOH . 
D 4 HOH A 118 618 121 HOH HOH . 
D 4 HOH A 119 619 122 HOH HOH . 
D 4 HOH A 120 620 123 HOH HOH . 
D 4 HOH A 121 621 124 HOH HOH . 
D 4 HOH A 122 622 125 HOH HOH . 
D 4 HOH A 123 623 126 HOH HOH . 
D 4 HOH A 124 624 127 HOH HOH . 
D 4 HOH A 125 625 128 HOH HOH . 
D 4 HOH A 126 626 129 HOH HOH . 
D 4 HOH A 127 627 130 HOH HOH . 
D 4 HOH A 128 628 131 HOH HOH . 
E 4 HOH C 1 33 33 HOH HOH . 
E 4 HOH C 2 89 89 HOH HOH . 
E 4 HOH C 3 103 103 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 O1 VDZ . . . C 3 60.75 4.465 2.321 1 20.24 ? O1 VDZ 500 A 1 
HETATM 2 C C1 VDZ . . . C 3 60.342 5.624 1.55 1 19.82 ? C1 VDZ 500 A 1 
HETATM 3 C C2 VDZ . . . C 3 60.774 6.948 2.031 1 20.51 ? C2 VDZ 500 A 1 
HETATM 4 C C28 VDZ . . . C 3 61.437 7.054 3.164 1 17.49 ? C28 VDZ 500 A 1 
HETATM 5 C C3 VDZ . . . C 3 60.568 8.207 1.231 1 21.2 ? C3 VDZ 500 A 1 
HETATM 6 O O2 VDZ . . . C 3 59.068 8.23 1.261 1 19.87 ? O2 VDZ 500 A 1 
HETATM 7 C C4 VDZ . . . C 3 60.935 8.127 -0.223 1 22.01 ? C4 VDZ 500 A 1 
HETATM 8 C C10 VDZ . . . C 3 60.912 5.543 0.105 1 19.02 ? C10 VDZ 500 A 1 
HETATM 9 C C5 VDZ . . . C 3 60.738 6.773 -0.822 1 21.58 ? C5 VDZ 500 A 1 
HETATM 10 C C6 VDZ . . . C 3 60.373 6.819 -2.186 1 21.39 ? C6 VDZ 500 A 1 
HETATM 11 C C7 VDZ . . . C 3 60.087 5.589 -2.985 1 20.07 ? C7 VDZ 500 A 1 
HETATM 12 C C8 VDZ . . . C 3 60.417 5.432 -4.25 1 20.68 ? C8 VDZ 500 A 1 
HETATM 13 C C9 VDZ . . . C 3 61.209 6.465 -5.004 1 20.21 ? C9 VDZ 500 A 1 
HETATM 14 C C11 VDZ . . . C 3 62.524 5.788 -5.463 1 20.64 ? C11 VDZ 500 A 1 
HETATM 15 C C14 VDZ . . . C 3 60.079 4.108 -4.903 1 19.79 ? C14 VDZ 500 A 1 
HETATM 16 C C13 VDZ . . . C 3 61.472 3.461 -5.335 1 21.37 ? C13 VDZ 500 A 1 
HETATM 17 C C12 VDZ . . . C 3 62.385 4.401 -6.141 1 18.84 ? C12 VDZ 500 A 1 
HETATM 18 C C18 VDZ . . . C 3 62.288 3.114 -3.984 1 16.8 ? C18 VDZ 500 A 1 
HETATM 19 C C15 VDZ . . . C 3 59.198 3.027 -4.321 1 17.58 ? C15 VDZ 500 A 1 
HETATM 20 C C16 VDZ . . . C 3 59.651 1.753 -5.105 1 21.58 ? C16 VDZ 500 A 1 
HETATM 21 C C17 VDZ . . . C 3 60.946 2.14 -5.909 1 21.42 ? C17 VDZ 500 A 1 
HETATM 22 C C20 VDZ . . . C 3 61.84 0.914 -6.008 1 20.09 ? C20 VDZ 500 A 1 
HETATM 23 C C21 VDZ . . . C 3 61.004 -0.108 -6.815 1 22.18 ? C21 VDZ 500 A 1 
HETATM 24 C C22 VDZ . . . C 3 63.271 1.147 -6.557 1 22.28 ? C22 VDZ 500 A 1 
HETATM 25 C C23 VDZ . . . C 3 64.07 -0.151 -6.592 1 19.96 ? C23 VDZ 500 A 1 
HETATM 26 C C24 VDZ . . . C 3 65.574 0.014 -6.804 1 20.13 ? C24 VDZ 500 A 1 
HETATM 27 C C25 VDZ . . . C 3 66.378 -1.318 -6.672 1 23.22 ? C25 VDZ 500 A 1 
HETATM 28 C C26 VDZ . . . C 3 67.692 -1.049 -7.347 1 24.62 ? C26 VDZ 500 A 1 
HETATM 29 C C27 VDZ . . . C 3 66.537 -1.89 -5.234 1 21.5 ? C27 VDZ 500 A 1 
HETATM 30 O O3 VDZ . . . C 3 65.723 -2.313 -7.402 1 23.15 ? O3 VDZ 500 A 1 
#
_model_server_stats.io_time_ms              63 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           376 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           30 
#