data_1RK3
#
_model_server_result.job_id            JoGk6FuZbPMaeZ9KN3zoXw 
_model_server_result.datetime_utc      '2024-10-11 11:22:16' 
_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          1rk3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":500}' 
#
_entry.id    1RK3 
#
_exptl.entry_id    1RK3 
_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          96.13 
_cell.angle_gamma         90 
_cell.entry_id            1RK3 
_cell.length_a            154.726 
_cell.length_b            44.154 
_cell.length_c            42.072 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1RK3 
_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 -1 154.726 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                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 376 n n 
O2 HO2 VDX sing 377 n n 
O3 C25 VDX sing 378 n n 
O3 HO3 VDX sing 379 n n 
C1 C2 VDX sing 380 n n 
C1 C10 VDX sing 381 n n 
C1 O1 VDX sing 382 n n 
C1 H11 VDX sing 383 n n 
C2 C3 VDX sing 384 n n 
C2 H21 VDX sing 385 n n 
C2 H22 VDX sing 386 n n 
C3 C4 VDX sing 387 n n 
C3 H31 VDX sing 388 n n 
C4 C5 VDX sing 389 n n 
C4 H41 VDX sing 390 n n 
C4 H42 VDX sing 391 n n 
C5 C6 VDX doub 392 z n 
C5 C10 VDX sing 393 n n 
C6 C7 VDX sing 394 n n 
C6 H61 VDX sing 395 n n 
C7 C8 VDX doub 396 e n 
C7 H71 VDX sing 397 n n 
C8 C9 VDX sing 398 n n 
C8 C14 VDX sing 399 n n 
C9 C11 VDX sing 400 n n 
C9 H91 VDX sing 401 n n 
C9 H92 VDX sing 402 n n 
C10 C19 VDX doub 403 n n 
C11 C12 VDX sing 404 n n 
C11 H111 VDX sing 405 n n 
C11 H112 VDX sing 406 n n 
C12 C13 VDX sing 407 n n 
C12 H121 VDX sing 408 n n 
C12 H122 VDX sing 409 n n 
C13 C14 VDX sing 410 n n 
C13 C17 VDX sing 411 n n 
C13 C18 VDX sing 412 n n 
C14 C15 VDX sing 413 n n 
C14 H141 VDX sing 414 n n 
C15 C16 VDX sing 415 n n 
C15 H151 VDX sing 416 n n 
C15 H152 VDX sing 417 n n 
C16 C17 VDX sing 418 n n 
C16 H161 VDX sing 419 n n 
C16 H162 VDX sing 420 n n 
C17 C20 VDX sing 421 n n 
C17 H171 VDX sing 422 n n 
C18 H181 VDX sing 423 n n 
C18 H182 VDX sing 424 n n 
C18 H183 VDX sing 425 n n 
C19 H191 VDX sing 426 n n 
C19 H192 VDX sing 427 n n 
C20 C21 VDX sing 428 n n 
C20 C22 VDX sing 429 n n 
C20 H201 VDX sing 430 n n 
C21 H211 VDX sing 431 n n 
C21 H212 VDX sing 432 n n 
C21 H213 VDX sing 433 n n 
C22 C23 VDX sing 434 n n 
C22 H221 VDX sing 435 n n 
C22 H222 VDX sing 436 n n 
C23 C24 VDX sing 437 n n 
C23 H231 VDX sing 438 n n 
C23 H232 VDX sing 439 n n 
C24 C25 VDX sing 440 n n 
C24 H241 VDX sing 441 n n 
C24 H242 VDX sing 442 n n 
C25 C26 VDX sing 443 n n 
C25 C27 VDX sing 444 n n 
C26 H261 VDX sing 445 n n 
C26 H262 VDX sing 446 n n 
C26 H263 VDX sing 447 n n 
C27 H271 VDX sing 448 n n 
C27 H272 VDX sing 449 n n 
C27 H273 VDX sing 450 n n 
O1 HO1 VDX sing 451 n n 
#
_atom_sites.entry_id                     1RK3 
_atom_sites.fract_transf_matrix[1][1]    0.006463 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000694 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.022648 
_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]    0.023905 
_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 1 500 500 VDX VDX . 
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 37 37 HOH HOH . 
D 4 HOH A 37 38 38 HOH HOH . 
D 4 HOH A 38 39 39 HOH HOH . 
D 4 HOH A 39 40 40 HOH HOH . 
D 4 HOH A 40 41 41 HOH HOH . 
D 4 HOH A 41 42 42 HOH HOH . 
D 4 HOH A 42 43 43 HOH HOH . 
D 4 HOH A 43 44 44 HOH HOH . 
D 4 HOH A 44 45 45 HOH HOH . 
D 4 HOH A 45 46 46 HOH HOH . 
D 4 HOH A 46 47 47 HOH HOH . 
D 4 HOH A 47 48 48 HOH HOH . 
D 4 HOH A 48 49 49 HOH HOH . 
D 4 HOH A 49 50 50 HOH HOH . 
D 4 HOH A 50 51 51 HOH HOH . 
D 4 HOH A 51 52 52 HOH HOH . 
D 4 HOH A 52 53 53 HOH HOH . 
D 4 HOH A 53 54 54 HOH HOH . 
D 4 HOH A 54 57 57 HOH HOH . 
D 4 HOH A 55 58 58 HOH HOH . 
D 4 HOH A 56 59 59 HOH HOH . 
D 4 HOH A 57 60 60 HOH HOH . 
D 4 HOH A 58 61 61 HOH HOH . 
D 4 HOH A 59 62 62 HOH HOH . 
D 4 HOH A 60 63 63 HOH HOH . 
D 4 HOH A 61 64 64 HOH HOH . 
D 4 HOH A 62 65 65 HOH HOH . 
D 4 HOH A 63 66 66 HOH HOH . 
D 4 HOH A 64 67 67 HOH HOH . 
D 4 HOH A 65 68 68 HOH HOH . 
D 4 HOH A 66 69 69 HOH HOH . 
D 4 HOH A 67 70 70 HOH HOH . 
D 4 HOH A 68 71 71 HOH HOH . 
D 4 HOH A 69 72 72 HOH HOH . 
D 4 HOH A 70 73 73 HOH HOH . 
D 4 HOH A 71 74 74 HOH HOH . 
D 4 HOH A 72 75 75 HOH HOH . 
D 4 HOH A 73 76 76 HOH HOH . 
D 4 HOH A 74 77 77 HOH HOH . 
D 4 HOH A 75 78 78 HOH HOH . 
D 4 HOH A 76 79 79 HOH HOH . 
D 4 HOH A 77 80 80 HOH HOH . 
D 4 HOH A 78 81 81 HOH HOH . 
D 4 HOH A 79 82 82 HOH HOH . 
D 4 HOH A 80 83 83 HOH HOH . 
D 4 HOH A 81 84 84 HOH HOH . 
D 4 HOH A 82 85 85 HOH HOH . 
D 4 HOH A 83 86 86 HOH HOH . 
D 4 HOH A 84 87 87 HOH HOH . 
D 4 HOH A 85 88 88 HOH HOH . 
D 4 HOH A 86 89 89 HOH HOH . 
D 4 HOH A 87 90 90 HOH HOH . 
D 4 HOH A 88 91 91 HOH HOH . 
D 4 HOH A 89 92 92 HOH HOH . 
E 4 HOH C 1 36 36 HOH HOH . 
E 4 HOH C 2 55 55 HOH HOH . 
E 4 HOH C 3 56 56 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 58.862 8.247 1.194 1 21.01 ? O2 VDX 500 A 1 
HETATM 2 O O3 VDX . . . C 3 65.838 -2.563 -7.417 1 25.96 ? O3 VDX 500 A 1 
HETATM 3 C C1 VDX . . . C 3 60.388 5.713 1.651 1 23.61 ? C1 VDX 500 A 1 
HETATM 4 C C2 VDX . . . C 3 60.762 7.078 2.316 1 21.39 ? C2 VDX 500 A 1 
HETATM 5 C C3 VDX . . . C 3 60.291 8.305 1.4 1 24.66 ? C3 VDX 500 A 1 
HETATM 6 C C4 VDX . . . C 3 61.032 8.237 0 1 25.54 ? C4 VDX 500 A 1 
HETATM 7 C C5 VDX . . . C 3 60.843 6.897 -0.7 1 25.26 ? C5 VDX 500 A 1 
HETATM 8 C C6 VDX . . . C 3 60.636 6.726 -2.067 1 24.95 ? C6 VDX 500 A 1 
HETATM 9 C C7 VDX . . . C 3 60.419 5.49 -2.883 1 25.4 ? C7 VDX 500 A 1 
HETATM 10 C C8 VDX . . . C 3 60.481 5.412 -4.178 1 24.95 ? C8 VDX 500 A 1 
HETATM 11 C C9 VDX . . . C 3 60.912 6.657 -5.102 1 25.63 ? C9 VDX 500 A 1 
HETATM 12 C C10 VDX . . . C 3 60.987 5.675 0.224 1 23.45 ? C10 VDX 500 A 1 
HETATM 13 C C11 VDX . . . C 3 62.295 6.306 -5.869 1 25.29 ? C11 VDX 500 A 1 
HETATM 14 C C12 VDX . . . C 3 62.184 4.818 -6.518 1 22.61 ? C12 VDX 500 A 1 
HETATM 15 C C13 VDX . . . C 3 61.654 3.603 -5.555 1 24.44 ? C13 VDX 500 A 1 
HETATM 16 C C14 VDX . . . C 3 60.249 4.127 -4.95 1 24.59 ? C14 VDX 500 A 1 
HETATM 17 C C15 VDX . . . C 3 59.68 2.75 -4.199 1 20.66 ? C15 VDX 500 A 1 
HETATM 18 C C16 VDX . . . C 3 60.288 1.587 -5.077 1 23.07 ? C16 VDX 500 A 1 
HETATM 19 C C17 VDX . . . C 3 61.135 2.301 -6.211 1 25.23 ? C17 VDX 500 A 1 
HETATM 20 C C18 VDX . . . C 3 62.885 3.43 -4.424 1 23.15 ? C18 VDX 500 A 1 
HETATM 21 C C19 VDX . . . C 3 61.721 4.589 -0.193 1 25.48 ? C19 VDX 500 A 1 
HETATM 22 C C20 VDX . . . C 3 62.304 1.501 -6.966 1 24.47 ? C20 VDX 500 A 1 
HETATM 23 C C21 VDX . . . C 3 61.497 0.615 -8.054 1 21.26 ? C21 VDX 500 A 1 
HETATM 24 C C22 VDX . . . C 3 63.109 0.439 -6.131 1 26.06 ? C22 VDX 500 A 1 
HETATM 25 C C23 VDX . . . C 3 64.472 0.096 -6.734 1 26.22 ? C23 VDX 500 A 1 
HETATM 26 C C24 VDX . . . C 3 65.349 -0.743 -5.949 1 26.23 ? C24 VDX 500 A 1 
HETATM 27 C C25 VDX . . . C 3 66.425 -1.55 -6.635 1 27.83 ? C25 VDX 500 A 1 
HETATM 28 C C26 VDX . . . C 3 67.27 -0.623 -7.481 1 27.05 ? C26 VDX 500 A 1 
HETATM 29 C C27 VDX . . . C 3 67.4 -2.249 -5.611 1 25.81 ? C27 VDX 500 A 1 
HETATM 30 O O1 VDX . . . C 3 60.945 4.605 2.423 1 24.67 ? O1 VDX 500 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           30 
#