data_1RKH
#
_model_server_result.job_id            '_jOGPcr4qL3sDzg24BmwbQ' 
_model_server_result.datetime_utc      '2024-11-08 20:02:50' 
_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          1rkh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":500}' 
#
_entry.id    1RKH 
#
_exptl.entry_id    1RKH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              418.652 
_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-METHYL-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          96.15 
_cell.angle_gamma         90 
_cell.entry_id            1RKH 
_cell.length_a            154.8 
_cell.length_b            42.291 
_cell.length_c            41.788 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1RKH 
_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 1 1 
A,B,C,D 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 -1 154.8 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 H46 O3' 
_chem_comp.formula_weight    418.652 
_chem_comp.id                VD2 
_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-METHYL-CYCLOHEXANE-1,3-DIOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '2-ALPHA-METHYL-19-NOR-1,25-DIHYDROXYVITAMIN D3;2AM20R' 
#
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
O3 C25 VD2 sing 376 n n 
O3 HO3 VD2 sing 377 n n 
C25 C27 VD2 sing 378 n n 
C25 C26 VD2 sing 379 n n 
C25 C24 VD2 sing 380 n n 
C27 H271 VD2 sing 381 n n 
C27 H272 VD2 sing 382 n n 
C27 H273 VD2 sing 383 n n 
C26 H261 VD2 sing 384 n n 
C26 H262 VD2 sing 385 n n 
C26 H263 VD2 sing 386 n n 
C24 C23 VD2 sing 387 n n 
C24 H241 VD2 sing 388 n n 
C24 H242 VD2 sing 389 n n 
C23 C22 VD2 sing 390 n n 
C23 H231 VD2 sing 391 n n 
C23 H232 VD2 sing 392 n n 
C22 C20 VD2 sing 393 n n 
C22 H221 VD2 sing 394 n n 
C22 H222 VD2 sing 395 n n 
C20 C21 VD2 sing 396 n n 
C20 C17 VD2 sing 397 n n 
C20 H20 VD2 sing 398 n n 
C21 H211 VD2 sing 399 n n 
C21 H212 VD2 sing 400 n n 
C21 H213 VD2 sing 401 n n 
C17 C16 VD2 sing 402 n n 
C17 C13 VD2 sing 403 n n 
C17 H17 VD2 sing 404 n n 
C16 C15 VD2 sing 405 n n 
C16 H161 VD2 sing 406 n n 
C16 H162 VD2 sing 407 n n 
C13 C18 VD2 sing 408 n n 
C13 C14 VD2 sing 409 n n 
C13 C12 VD2 sing 410 n n 
C18 H181 VD2 sing 411 n n 
C18 H182 VD2 sing 412 n n 
C18 H183 VD2 sing 413 n n 
C14 C15 VD2 sing 414 n n 
C14 C8 VD2 sing 415 n n 
C14 H14 VD2 sing 416 n n 
C15 H151 VD2 sing 417 n n 
C15 H152 VD2 sing 418 n n 
C12 C11 VD2 sing 419 n n 
C12 H121 VD2 sing 420 n n 
C12 H122 VD2 sing 421 n n 
C11 C9 VD2 sing 422 n n 
C11 H111 VD2 sing 423 n n 
C11 H112 VD2 sing 424 n n 
C9 C8 VD2 sing 425 n n 
C9 H91 VD2 sing 426 n n 
C9 H92 VD2 sing 427 n n 
C8 C7 VD2 doub 428 e n 
C7 C6 VD2 sing 429 n n 
C7 H7 VD2 sing 430 n n 
C6 C5 VD2 doub 431 n n 
C6 H6 VD2 sing 432 n n 
C5 C10 VD2 sing 433 n n 
C5 C4 VD2 sing 434 n n 
C10 C1 VD2 sing 435 n n 
C10 H101 VD2 sing 436 n n 
C10 H102 VD2 sing 437 n n 
C4 C3 VD2 sing 438 n n 
C4 H41 VD2 sing 439 n n 
C4 H42 VD2 sing 440 n n 
C3 O2 VD2 sing 441 n n 
C3 C2 VD2 sing 442 n n 
C3 H3 VD2 sing 443 n n 
O2 HO2 VD2 sing 444 n n 
C2 C28 VD2 sing 445 n n 
C2 C1 VD2 sing 446 n n 
C2 H2 VD2 sing 447 n n 
C28 H281 VD2 sing 448 n n 
C28 H282 VD2 sing 449 n n 
C28 H283 VD2 sing 450 n n 
C1 O1 VD2 sing 451 n n 
C1 H1 VD2 sing 452 n n 
O1 HO1 VD2 sing 453 n n 
#
_atom_sites.entry_id                     1RKH 
_atom_sites.fract_transf_matrix[1][1]    0.00646 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000696 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.023646 
_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]    0.024069 
_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 VD2 A 1 500 500 VD2 VD2 . 
D 4 HOH A 1 1 1 HOH HOH . 
D 4 HOH A 2 2 2 HOH HOH . 
D 4 HOH A 3 3 3 HOH HOH . 
D 4 HOH A 4 4 4 HOH HOH . 
D 4 HOH A 5 5 5 HOH HOH . 
D 4 HOH A 6 6 6 HOH HOH . 
D 4 HOH A 7 7 7 HOH HOH . 
D 4 HOH A 8 8 8 HOH HOH . 
D 4 HOH A 9 9 9 HOH HOH . 
D 4 HOH A 10 10 10 HOH HOH . 
D 4 HOH A 11 11 11 HOH HOH . 
D 4 HOH A 12 12 12 HOH HOH . 
D 4 HOH A 13 13 13 HOH HOH . 
D 4 HOH A 14 14 14 HOH HOH . 
D 4 HOH A 15 15 15 HOH HOH . 
D 4 HOH A 16 16 16 HOH HOH . 
D 4 HOH A 17 17 17 HOH HOH . 
D 4 HOH A 18 18 18 HOH HOH . 
D 4 HOH A 19 19 19 HOH HOH . 
D 4 HOH A 20 20 20 HOH HOH . 
D 4 HOH A 21 21 21 HOH HOH . 
D 4 HOH A 22 22 22 HOH HOH . 
D 4 HOH A 23 23 23 HOH HOH . 
D 4 HOH A 24 24 24 HOH HOH . 
D 4 HOH A 25 25 25 HOH HOH . 
D 4 HOH A 26 26 26 HOH HOH . 
D 4 HOH A 27 27 27 HOH HOH . 
D 4 HOH A 28 28 28 HOH HOH . 
D 4 HOH A 29 29 29 HOH HOH . 
D 4 HOH A 30 30 30 HOH HOH . 
D 4 HOH A 31 31 31 HOH HOH . 
D 4 HOH A 32 32 32 HOH HOH . 
D 4 HOH A 33 33 33 HOH HOH . 
D 4 HOH A 34 34 34 HOH HOH . 
D 4 HOH A 35 35 35 HOH HOH . 
D 4 HOH A 36 36 36 HOH HOH . 
D 4 HOH A 37 37 37 HOH HOH . 
D 4 HOH A 38 38 38 HOH HOH . 
D 4 HOH A 39 39 39 HOH HOH . 
D 4 HOH A 40 40 40 HOH HOH . 
D 4 HOH A 41 41 41 HOH HOH . 
D 4 HOH A 42 42 42 HOH HOH . 
D 4 HOH A 43 43 43 HOH HOH . 
D 4 HOH A 44 44 44 HOH HOH . 
D 4 HOH A 45 45 45 HOH HOH . 
D 4 HOH A 46 46 46 HOH HOH . 
D 4 HOH A 47 47 47 HOH HOH . 
D 4 HOH A 48 48 48 HOH HOH . 
D 4 HOH A 49 49 49 HOH HOH . 
D 4 HOH A 50 50 50 HOH HOH . 
D 4 HOH A 51 51 51 HOH HOH . 
D 4 HOH A 52 52 52 HOH HOH . 
D 4 HOH A 53 53 53 HOH HOH . 
D 4 HOH A 54 54 54 HOH HOH . 
D 4 HOH A 55 55 55 HOH HOH . 
D 4 HOH A 56 56 56 HOH HOH . 
D 4 HOH A 57 57 57 HOH HOH . 
D 4 HOH A 58 58 58 HOH HOH . 
D 4 HOH A 59 59 59 HOH HOH . 
D 4 HOH A 60 60 60 HOH HOH . 
D 4 HOH A 61 61 61 HOH HOH . 
D 4 HOH A 62 62 62 HOH HOH . 
D 4 HOH A 63 63 63 HOH HOH . 
D 4 HOH A 64 64 64 HOH HOH . 
D 4 HOH A 65 65 65 HOH HOH . 
D 4 HOH A 66 66 66 HOH HOH . 
D 4 HOH A 67 67 67 HOH HOH . 
D 4 HOH A 68 68 68 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 O3 VD2 . . . C 3 65.992 -2.504 -7.436 1 24.51 ? O3 VD2 500 A 1 
HETATM 2 C C25 VD2 . . . C 3 66.517 -1.403 -6.745 1 24.39 ? C25 VD2 500 A 1 
HETATM 3 C C27 VD2 . . . C 3 67.388 -1.955 -5.566 1 21.64 ? C27 VD2 500 A 1 
HETATM 4 C C26 VD2 . . . C 3 67.346 -0.512 -7.646 1 22.28 ? C26 VD2 500 A 1 
HETATM 5 C C24 VD2 . . . C 3 65.403 -0.624 -6.123 1 24.9 ? C24 VD2 500 A 1 
HETATM 6 C C23 VD2 . . . C 3 64.551 0.217 -6.903 1 23.9 ? C23 VD2 500 A 1 
HETATM 7 C C22 VD2 . . . C 3 63.254 0.521 -6.194 1 21.6 ? C22 VD2 500 A 1 
HETATM 8 C C20 VD2 . . . C 3 62.358 1.504 -7.004 1 22.08 ? C20 VD2 500 A 1 
HETATM 9 C C21 VD2 . . . C 3 61.534 0.61 -8.071 1 22.22 ? C21 VD2 500 A 1 
HETATM 10 C C17 VD2 . . . C 3 61.215 2.259 -6.168 1 22.24 ? C17 VD2 500 A 1 
HETATM 11 C C16 VD2 . . . C 3 60.443 1.519 -4.989 1 19.93 ? C16 VD2 500 A 1 
HETATM 12 C C13 VD2 . . . C 3 61.754 3.544 -5.519 1 19.02 ? C13 VD2 500 A 1 
HETATM 13 C C18 VD2 . . . C 3 63.027 3.423 -4.433 1 19.51 ? C18 VD2 500 A 1 
HETATM 14 C C14 VD2 . . . C 3 60.329 4.037 -4.916 1 20.37 ? C14 VD2 500 A 1 
HETATM 15 C C15 VD2 . . . C 3 59.708 2.67 -4.206 1 18.3 ? C15 VD2 500 A 1 
HETATM 16 C C12 VD2 . . . C 3 62.226 4.755 -6.478 1 18.05 ? C12 VD2 500 A 1 
HETATM 17 C C11 VD2 . . . C 3 62.357 6.179 -5.721 1 14.85 ? C11 VD2 500 A 1 
HETATM 18 C C9 VD2 . . . C 3 60.94 6.542 -5.122 1 15.96 ? C9 VD2 500 A 1 
HETATM 19 C C8 VD2 . . . C 3 60.562 5.32 -4.139 1 19.18 ? C8 VD2 500 A 1 
HETATM 20 C C7 VD2 . . . C 3 60.498 5.405 -2.852 1 19.18 ? C7 VD2 500 A 1 
HETATM 21 C C6 VD2 . . . C 3 60.719 6.664 -2.073 1 18.19 ? C6 VD2 500 A 1 
HETATM 22 C C5 VD2 . . . C 3 60.883 6.793 -0.703 1 20.6 ? C5 VD2 500 A 1 
HETATM 23 C C10 VD2 . . . C 3 60.942 5.589 0.25 1 18.08 ? C10 VD2 500 A 1 
HETATM 24 C C4 VD2 . . . C 3 61.058 8.144 -0.027 1 18.99 ? C4 VD2 500 A 1 
HETATM 25 C C3 VD2 . . . C 3 60.288 8.237 1.332 1 17.47 ? C3 VD2 500 A 1 
HETATM 26 O O2 VD2 . . . C 3 58.869 8.117 1.108 1 15.01 ? O2 VD2 500 A 1 
HETATM 27 C C2 VD2 . . . C 3 60.773 7.042 2.281 1 18.22 ? C2 VD2 500 A 1 
HETATM 28 C C28 VD2 . . . C 3 62.136 6.947 2.988 1 16.43 ? C28 VD2 500 A 1 
HETATM 29 C C1 VD2 . . . C 3 60.331 5.684 1.679 1 17.13 ? C1 VD2 500 A 1 
HETATM 30 O O1 VD2 . . . C 3 60.813 4.594 2.524 1 17.86 ? O1 VD2 500 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           30 
#