data_1RKG
#
_model_server_result.job_id            jSJjgEo8XyEVyfDo-gEUJg 
_model_server_result.datetime_utc      '2024-10-11 13:21:09' 
_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          1rkg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":500}' 
#
_entry.id    1RKG 
#
_exptl.entry_id    1RKG 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              344.531 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               'DRIP 205 NR2 box peptide' 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          96.62 
_cell.angle_gamma         90 
_cell.entry_id            1RKG 
_cell.length_a            154.447 
_cell.length_b            44.114 
_cell.length_c            41.86 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1RKG 
_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 -1 154.447 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           'C23 H36 O2' 
_chem_comp.formula_weight    344.531 
_chem_comp.id                VD1 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     1-ALPHA-HYDROXY-2-METHYLENE-19-NOR-(20S)-BISHOMOPREGNACALCIFEROL;2MBISP 
#
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 VD1 sing 376 n n 
O2 HO2 VD1 sing 377 n n 
C3 C2 VD1 sing 378 n n 
C3 C4 VD1 sing 379 n n 
C3 H3 VD1 sing 380 n n 
C2 C28 VD1 doub 381 n n 
C2 C1 VD1 sing 382 n n 
C28 H281 VD1 sing 383 n n 
C28 H282 VD1 sing 384 n n 
C1 O1 VD1 sing 385 n n 
C1 C10 VD1 sing 386 n n 
C1 H1 VD1 sing 387 n n 
O1 HO1 VD1 sing 388 n n 
C4 C5 VD1 sing 389 n n 
C4 H41 VD1 sing 390 n n 
C4 H42 VD1 sing 391 n n 
C5 C10 VD1 sing 392 n n 
C5 C6 VD1 doub 393 n n 
C10 H101 VD1 sing 394 n n 
C10 H102 VD1 sing 395 n n 
C6 C7 VD1 sing 396 n n 
C6 H6 VD1 sing 397 n n 
C7 C8 VD1 doub 398 e n 
C7 H7 VD1 sing 399 n n 
C8 C9 VD1 sing 400 n n 
C8 C14 VD1 sing 401 n n 
C9 C11 VD1 sing 402 n n 
C9 H91 VD1 sing 403 n n 
C9 H92 VD1 sing 404 n n 
C11 C12 VD1 sing 405 n n 
C11 H111 VD1 sing 406 n n 
C11 H112 VD1 sing 407 n n 
C12 C13 VD1 sing 408 n n 
C12 H121 VD1 sing 409 n n 
C12 H122 VD1 sing 410 n n 
C13 C18 VD1 sing 411 n n 
C13 C14 VD1 sing 412 n n 
C13 C17 VD1 sing 413 n n 
C18 H181 VD1 sing 414 n n 
C18 H182 VD1 sing 415 n n 
C18 H183 VD1 sing 416 n n 
C14 C15 VD1 sing 417 n n 
C14 H14 VD1 sing 418 n n 
C15 C16 VD1 sing 419 n n 
C15 H151 VD1 sing 420 n n 
C15 H152 VD1 sing 421 n n 
C17 C16 VD1 sing 422 n n 
C17 C20 VD1 sing 423 n n 
C17 H17 VD1 sing 424 n n 
C16 H161 VD1 sing 425 n n 
C16 H162 VD1 sing 426 n n 
C20 C21 VD1 sing 427 n n 
C20 C22 VD1 sing 428 n n 
C20 H20 VD1 sing 429 n n 
C21 H211 VD1 sing 430 n n 
C21 H212 VD1 sing 431 n n 
C21 H213 VD1 sing 432 n n 
C22 C23 VD1 sing 433 n n 
C22 H221 VD1 sing 434 n n 
C22 H222 VD1 sing 435 n n 
C23 H231 VD1 sing 436 n n 
C23 H232 VD1 sing 437 n n 
C23 H233 VD1 sing 438 n n 
#
_atom_sites.entry_id                     1RKG 
_atom_sites.fract_transf_matrix[1][1]    0.006475 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000751 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.022669 
_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]    0.024049 
_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 VD1 A 1 500 500 VD1 VD1 . 
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 28 HOH HOH . 
D 4 HOH A 28 528 29 HOH HOH . 
D 4 HOH A 29 529 30 HOH HOH . 
D 4 HOH A 30 530 31 HOH HOH . 
D 4 HOH A 31 531 32 HOH HOH . 
D 4 HOH A 32 532 33 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 89 HOH HOH . 
D 4 HOH A 89 589 90 HOH HOH . 
D 4 HOH A 90 590 91 HOH HOH . 
D 4 HOH A 91 591 92 HOH HOH . 
D 4 HOH A 92 592 93 HOH HOH . 
D 4 HOH A 93 593 94 HOH HOH . 
D 4 HOH A 94 594 95 HOH HOH . 
D 4 HOH A 95 595 96 HOH HOH . 
D 4 HOH A 96 596 97 HOH HOH . 
D 4 HOH A 97 597 98 HOH HOH . 
D 4 HOH A 98 598 99 HOH HOH . 
D 4 HOH A 99 599 100 HOH HOH . 
D 4 HOH A 100 600 101 HOH HOH . 
D 4 HOH A 101 601 102 HOH HOH . 
D 4 HOH A 102 602 103 HOH HOH . 
D 4 HOH A 103 603 104 HOH HOH . 
D 4 HOH A 104 604 105 HOH HOH . 
D 4 HOH A 105 605 106 HOH HOH . 
D 4 HOH A 106 606 107 HOH HOH . 
D 4 HOH A 107 607 108 HOH HOH . 
D 4 HOH A 108 608 109 HOH HOH . 
D 4 HOH A 109 609 110 HOH HOH . 
D 4 HOH A 110 610 111 HOH HOH . 
D 4 HOH A 111 611 112 HOH HOH . 
D 4 HOH A 112 612 113 HOH HOH . 
D 4 HOH A 113 613 114 HOH HOH . 
D 4 HOH A 114 614 115 HOH HOH . 
D 4 HOH A 115 615 116 HOH HOH . 
D 4 HOH A 116 616 117 HOH HOH . 
D 4 HOH A 117 617 118 HOH HOH . 
D 4 HOH A 118 618 119 HOH HOH . 
D 4 HOH A 119 619 120 HOH HOH . 
D 4 HOH A 120 620 121 HOH HOH . 
D 4 HOH A 121 621 122 HOH HOH . 
D 4 HOH A 122 622 123 HOH HOH . 
D 4 HOH A 123 623 124 HOH HOH . 
D 4 HOH A 124 624 125 HOH HOH . 
E 4 HOH C 1 27 27 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 VD1 . . . C 3 58.937 8.128 1.083 1 21.14 ? O2 VD1 500 A 1 
HETATM 2 C C3 VD1 . . . C 3 60.437 8.098 1.175 1 22.15 ? C3 VD1 500 A 1 
HETATM 3 C C2 VD1 . . . C 3 60.695 6.869 2.009 1 19.89 ? C2 VD1 500 A 1 
HETATM 4 C C28 VD1 . . . C 3 61.359 7.021 3.137 1 18.64 ? C28 VD1 500 A 1 
HETATM 5 C C1 VD1 . . . C 3 60.264 5.525 1.564 1 21.26 ? C1 VD1 500 A 1 
HETATM 6 O O1 VD1 . . . C 3 60.781 4.4 2.318 1 19.4 ? O1 VD1 500 A 1 
HETATM 7 C C4 VD1 . . . C 3 60.939 7.994 -0.229 1 21.03 ? C4 VD1 500 A 1 
HETATM 8 C C5 VD1 . . . C 3 60.753 6.639 -0.805 1 22.79 ? C5 VD1 500 A 1 
HETATM 9 C C10 VD1 . . . C 3 60.857 5.418 0.138 1 18.49 ? C10 VD1 500 A 1 
HETATM 10 C C6 VD1 . . . C 3 60.486 6.662 -2.189 1 21.97 ? C6 VD1 500 A 1 
HETATM 11 C C7 VD1 . . . C 3 60.284 5.418 -2.984 1 22.89 ? C7 VD1 500 A 1 
HETATM 12 C C8 VD1 . . . C 3 60.492 5.312 -4.296 1 22.65 ? C8 VD1 500 A 1 
HETATM 13 C C9 VD1 . . . C 3 61.001 6.426 -5.17 1 21.06 ? C9 VD1 500 A 1 
HETATM 14 C C11 VD1 . . . C 3 62.36 5.999 -5.733 1 21.06 ? C11 VD1 500 A 1 
HETATM 15 C C12 VD1 . . . C 3 62.297 4.645 -6.496 1 22.78 ? C12 VD1 500 A 1 
HETATM 16 C C13 VD1 . . . C 3 61.727 3.566 -5.556 1 22.85 ? C13 VD1 500 A 1 
HETATM 17 C C18 VD1 . . . C 3 62.812 3.32 -4.368 1 23.05 ? C18 VD1 500 A 1 
HETATM 18 C C14 VD1 . . . C 3 60.288 3.958 -4.964 1 23.28 ? C14 VD1 500 A 1 
HETATM 19 C C15 VD1 . . . C 3 59.665 2.729 -4.352 1 20.07 ? C15 VD1 500 A 1 
HETATM 20 C C17 VD1 . . . C 3 61.383 2.179 -6.139 1 26.08 ? C17 VD1 500 A 1 
HETATM 21 C C16 VD1 . . . C 3 60.269 1.576 -5.213 1 24.06 ? C16 VD1 500 A 1 
HETATM 22 C C20 VD1 . . . C 3 62.497 1.217 -6.581 1 28.73 ? C20 VD1 500 A 1 
HETATM 23 C C21 VD1 . . . C 3 61.749 0.165 -7.432 1 31.37 ? C21 VD1 500 A 1 
HETATM 24 C C22 VD1 . . . C 3 63.631 1.891 -7.406 1 35.04 ? C22 VD1 500 A 1 
HETATM 25 C C23 VD1 . . . C 3 65.026 1.668 -6.831 1 37.61 ? C23 VD1 500 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           25 
#