data_7QPI
#
_model_server_result.job_id            XaZPUZLwA8qzo072XXdDNQ 
_model_server_result.datetime_utc      '2025-08-04 02:57:04' 
_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          7qpi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    7QPI 
#
_exptl.entry_id    7QPI 
_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         90 
_cell.entry_id            7QPI 
_cell.length_a            37.32 
_cell.length_b            66.17 
_cell.length_c            105.69 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7QPI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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 
#
_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                     7QPI 
_atom_sites.fract_transf_matrix[1][1]    0.026795 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015113 
_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]    0.009462 
_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 1 301 525 VDX VDX . 
D 4 MG A 1 302 1 MG MG . 
E 4 MG A 1 303 2 MG MG . 
F 5 HOH A 1 401 56 HOH HOH . 
F 5 HOH A 2 402 40 HOH HOH . 
F 5 HOH A 3 403 37 HOH HOH . 
F 5 HOH A 4 404 6 HOH HOH . 
F 5 HOH A 5 405 30 HOH HOH . 
F 5 HOH A 6 406 53 HOH HOH . 
F 5 HOH A 7 407 32 HOH HOH . 
F 5 HOH A 8 408 1 HOH HOH . 
F 5 HOH A 9 409 25 HOH HOH . 
F 5 HOH A 10 410 18 HOH HOH . 
F 5 HOH A 11 411 57 HOH HOH . 
F 5 HOH A 12 412 4 HOH HOH . 
F 5 HOH A 13 413 19 HOH HOH . 
F 5 HOH A 14 414 10 HOH HOH . 
F 5 HOH A 15 415 3 HOH HOH . 
F 5 HOH A 16 416 29 HOH HOH . 
F 5 HOH A 17 417 51 HOH HOH . 
F 5 HOH A 18 418 2 HOH HOH . 
F 5 HOH A 19 419 11 HOH HOH . 
F 5 HOH A 20 420 27 HOH HOH . 
F 5 HOH A 21 421 33 HOH HOH . 
F 5 HOH A 22 422 12 HOH HOH . 
F 5 HOH A 23 423 60 HOH HOH . 
F 5 HOH A 24 424 21 HOH HOH . 
F 5 HOH A 25 425 20 HOH HOH . 
F 5 HOH A 26 426 5 HOH HOH . 
F 5 HOH A 27 427 54 HOH HOH . 
F 5 HOH A 28 428 17 HOH HOH . 
F 5 HOH A 29 429 58 HOH HOH . 
F 5 HOH A 30 430 43 HOH HOH . 
F 5 HOH A 31 431 49 HOH HOH . 
F 5 HOH A 32 432 7 HOH HOH . 
F 5 HOH A 33 433 63 HOH HOH . 
F 5 HOH A 34 434 22 HOH HOH . 
F 5 HOH A 35 435 15 HOH HOH . 
F 5 HOH A 36 436 38 HOH HOH . 
F 5 HOH A 37 437 24 HOH HOH . 
F 5 HOH A 38 438 46 HOH HOH . 
F 5 HOH A 39 439 9 HOH HOH . 
F 5 HOH A 40 440 34 HOH HOH . 
F 5 HOH A 41 441 8 HOH HOH . 
F 5 HOH A 42 442 13 HOH HOH . 
F 5 HOH A 43 443 52 HOH HOH . 
F 5 HOH A 44 444 59 HOH HOH . 
F 5 HOH A 45 445 55 HOH HOH . 
F 5 HOH A 46 446 48 HOH HOH . 
F 5 HOH A 47 447 26 HOH HOH . 
F 5 HOH A 48 448 47 HOH HOH . 
F 5 HOH A 49 449 35 HOH HOH . 
F 5 HOH A 50 450 16 HOH HOH . 
F 5 HOH A 51 451 36 HOH HOH . 
F 5 HOH A 52 452 42 HOH HOH . 
F 5 HOH A 53 453 23 HOH HOH . 
F 5 HOH A 54 454 61 HOH HOH . 
F 5 HOH A 55 455 62 HOH HOH . 
F 5 HOH A 56 456 31 HOH HOH . 
F 5 HOH A 57 457 41 HOH HOH . 
G 5 HOH U 1 401 28 HOH HOH . 
G 5 HOH U 2 402 45 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 45.53 30.175 72.13 1 39.73 ? O2 VDX 301 A 1 
HETATM 2 O O3 VDX . . . C 3 33.283 31.146 81.177 1 30.6 ? O3 VDX 301 A 1 
HETATM 3 C C1 VDX . . . C 3 43.088 31.582 72.341 1 18.05 ? C1 VDX 301 A 1 
HETATM 4 C C2 VDX . . . C 3 44.426 32.264 72.568 1 19.4 ? C2 VDX 301 A 1 
HETATM 5 C C3 VDX . . . C 3 45.437 31.258 73.071 1 30.78 ? C3 VDX 301 A 1 
HETATM 6 C C4 VDX . . . C 3 45.025 30.739 74.438 1 20.12 ? C4 VDX 301 A 1 
HETATM 7 C C5 VDX . . . C 3 43.566 30.343 74.489 1 22.18 ? C5 VDX 301 A 1 
HETATM 8 C C6 VDX . . . C 3 43.143 29.36 75.332 1 18.11 ? C6 VDX 301 A 1 
HETATM 9 C C7 VDX . . . C 3 41.81 28.876 75.473 1 21.3 ? C7 VDX 301 A 1 
HETATM 10 C C8 VDX . . . C 3 41.462 27.97 76.399 1 20.03 ? C8 VDX 301 A 1 
HETATM 11 C C9 VDX . . . C 3 42.37 27.373 77.437 1 12.59 ? C9 VDX 301 A 1 
HETATM 12 C C10 VDX . . . C 3 42.615 31.167 73.714 1 26.03 ? C10 VDX 301 A 1 
HETATM 13 C C11 VDX . . . C 3 41.944 27.888 78.804 1 17.68 ? C11 VDX 301 A 1 
HETATM 14 C C12 VDX . . . C 3 40.458 27.628 79.029 1 19.17 ? C12 VDX 301 A 1 
HETATM 15 C C13 VDX . . . C 3 39.58 28.154 77.88 1 25.61 ? C13 VDX 301 A 1 
HETATM 16 C C14 VDX . . . C 3 40.027 27.521 76.534 1 24.26 ? C14 VDX 301 A 1 
HETATM 17 C C15 VDX . . . C 3 38.877 27.881 75.563 1 21.23 ? C15 VDX 301 A 1 
HETATM 18 C C16 VDX . . . C 3 37.661 28.254 76.467 1 24.56 ? C16 VDX 301 A 1 
HETATM 19 C C17 VDX . . . C 3 38.114 27.713 77.828 1 20.04 ? C17 VDX 301 A 1 
HETATM 20 C C18 VDX . . . C 3 39.69 29.687 77.787 1 13.57 ? C18 VDX 301 A 1 
HETATM 21 C C19 VDX . . . C 3 41.429 31.57 74.155 1 22.73 ? C19 VDX 301 A 1 
HETATM 22 C C20 VDX . . . C 3 37.182 28.091 78.985 1 24.85 ? C20 VDX 301 A 1 
HETATM 23 C C21 VDX . . . C 3 36.363 26.906 79.489 1 29.02 ? C21 VDX 301 A 1 
HETATM 24 C C22 VDX . . . C 3 36.27 29.284 78.658 1 26.82 ? C22 VDX 301 A 1 
HETATM 25 C C23 VDX . . . C 3 35.765 29.936 79.939 1 23.78 ? C23 VDX 301 A 1 
HETATM 26 C C24 VDX . . . C 3 35.189 31.331 79.754 1 33.22 ? C24 VDX 301 A 1 
HETATM 27 C C25 VDX . . . C 3 34.538 31.837 81.033 1 26.71 ? C25 VDX 301 A 1 
HETATM 28 C C26 VDX . . . C 3 35.416 31.55 82.261 1 17 ? C26 VDX 301 A 1 
HETATM 29 C C27 VDX . . . C 3 34.222 33.313 80.925 1 24.7 ? C27 VDX 301 A 1 
HETATM 30 O O1 VDX . . . C 3 42.141 32.482 71.799 1 25.64 ? O1 VDX 301 A 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           426 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           30 
#