data_3M7R # _model_server_result.job_id yMKBhU0koaSfqIUiAWnE1Q _model_server_result.datetime_utc '2024-10-11 11:21:31' _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 3m7r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":425}' # _entry.id 3M7R # _exptl.entry_id 3M7R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 416.636 _entity.id 2 _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 3M7R _cell.length_a 44.402 _cell.length_b 51.67 _cell.length_c 131.888 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3M7R _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _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 3M7R _atom_sites.fract_transf_matrix[1][1] 0.022522 _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] 0.019354 _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] 0.007582 _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 B 2 VDX A 1 425 425 VDX VDX . C 3 HOH A 1 1 1 HOH TIP . C 3 HOH A 2 2 2 HOH TIP . C 3 HOH A 3 3 3 HOH TIP . C 3 HOH A 4 4 4 HOH TIP . C 3 HOH A 5 5 5 HOH TIP . C 3 HOH A 6 6 6 HOH TIP . C 3 HOH A 7 7 7 HOH TIP . C 3 HOH A 8 8 8 HOH TIP . C 3 HOH A 9 9 9 HOH TIP . C 3 HOH A 10 10 10 HOH TIP . C 3 HOH A 11 11 11 HOH TIP . C 3 HOH A 12 12 12 HOH TIP . C 3 HOH A 13 13 13 HOH TIP . C 3 HOH A 14 14 14 HOH TIP . C 3 HOH A 15 15 15 HOH TIP . C 3 HOH A 16 16 16 HOH TIP . C 3 HOH A 17 17 17 HOH TIP . C 3 HOH A 18 18 18 HOH TIP . C 3 HOH A 19 19 19 HOH TIP . C 3 HOH A 20 20 20 HOH TIP . C 3 HOH A 21 21 21 HOH TIP . C 3 HOH A 22 22 22 HOH TIP . C 3 HOH A 23 23 23 HOH TIP . C 3 HOH A 24 24 24 HOH TIP . C 3 HOH A 25 25 25 HOH TIP . C 3 HOH A 26 26 26 HOH TIP . C 3 HOH A 27 27 27 HOH TIP . C 3 HOH A 28 28 28 HOH TIP . C 3 HOH A 29 29 29 HOH TIP . C 3 HOH A 30 30 30 HOH TIP . C 3 HOH A 31 31 31 HOH TIP . C 3 HOH A 32 32 32 HOH TIP . C 3 HOH A 33 33 33 HOH TIP . C 3 HOH A 34 34 34 HOH TIP . C 3 HOH A 35 35 35 HOH TIP . C 3 HOH A 36 36 36 HOH TIP . C 3 HOH A 37 37 37 HOH TIP . C 3 HOH A 38 38 38 HOH TIP . C 3 HOH A 39 39 39 HOH TIP . C 3 HOH A 40 40 40 HOH TIP . C 3 HOH A 41 41 41 HOH TIP . C 3 HOH A 42 42 42 HOH TIP . C 3 HOH A 43 43 43 HOH TIP . C 3 HOH A 44 44 44 HOH TIP . C 3 HOH A 45 45 45 HOH TIP . C 3 HOH A 46 46 46 HOH TIP . C 3 HOH A 47 47 47 HOH TIP . C 3 HOH A 48 48 48 HOH TIP . C 3 HOH A 49 49 49 HOH TIP . C 3 HOH A 50 50 50 HOH TIP . C 3 HOH A 51 51 51 HOH TIP . C 3 HOH A 52 52 52 HOH TIP . C 3 HOH A 53 53 53 HOH TIP . C 3 HOH A 54 54 54 HOH TIP . C 3 HOH A 55 55 55 HOH TIP . C 3 HOH A 56 56 56 HOH TIP . C 3 HOH A 57 57 57 HOH TIP . C 3 HOH A 58 58 58 HOH TIP . C 3 HOH A 59 59 59 HOH TIP . C 3 HOH A 60 60 60 HOH TIP . C 3 HOH A 61 61 61 HOH TIP . C 3 HOH A 62 62 62 HOH TIP . C 3 HOH A 63 63 63 HOH TIP . C 3 HOH A 64 64 64 HOH TIP . C 3 HOH A 65 65 65 HOH TIP . C 3 HOH A 66 66 66 HOH TIP . C 3 HOH A 67 67 67 HOH TIP . C 3 HOH A 68 68 68 HOH TIP . C 3 HOH A 69 69 69 HOH TIP . C 3 HOH A 70 70 70 HOH TIP . C 3 HOH A 71 71 71 HOH TIP . C 3 HOH A 72 72 72 HOH TIP . C 3 HOH A 73 73 73 HOH TIP . C 3 HOH A 74 74 74 HOH TIP . C 3 HOH A 75 75 75 HOH TIP . C 3 HOH A 76 76 76 HOH TIP . C 3 HOH A 77 77 77 HOH TIP . C 3 HOH A 78 78 78 HOH TIP . C 3 HOH A 79 79 79 HOH TIP . C 3 HOH A 80 80 80 HOH TIP . C 3 HOH A 81 81 81 HOH TIP . C 3 HOH A 82 82 82 HOH TIP . C 3 HOH A 83 83 83 HOH TIP . C 3 HOH A 84 84 84 HOH TIP . C 3 HOH A 85 85 85 HOH TIP . C 3 HOH A 86 86 86 HOH TIP . C 3 HOH A 87 87 87 HOH TIP . C 3 HOH A 88 88 88 HOH TIP . C 3 HOH A 89 89 89 HOH TIP . C 3 HOH A 90 90 90 HOH TIP . C 3 HOH A 91 91 91 HOH TIP . C 3 HOH A 92 92 92 HOH TIP . C 3 HOH A 93 93 93 HOH TIP . C 3 HOH A 94 94 94 HOH TIP . C 3 HOH A 95 95 95 HOH TIP . C 3 HOH A 96 96 96 HOH TIP . C 3 HOH A 97 97 97 HOH TIP . C 3 HOH A 98 98 98 HOH TIP . C 3 HOH A 99 99 99 HOH TIP . C 3 HOH A 100 100 100 HOH TIP . C 3 HOH A 101 101 101 HOH TIP . C 3 HOH A 102 102 102 HOH TIP . C 3 HOH A 103 103 103 HOH TIP . C 3 HOH A 104 104 104 HOH TIP . C 3 HOH A 105 105 105 HOH TIP . C 3 HOH A 106 106 106 HOH TIP . C 3 HOH A 107 107 107 HOH TIP . C 3 HOH A 108 108 108 HOH TIP . C 3 HOH A 109 109 109 HOH TIP . C 3 HOH A 110 110 110 HOH TIP . C 3 HOH A 111 111 111 HOH TIP . C 3 HOH A 112 112 112 HOH TIP . C 3 HOH A 113 113 113 HOH TIP . C 3 HOH A 114 114 114 HOH TIP . C 3 HOH A 115 115 115 HOH TIP . C 3 HOH A 116 116 116 HOH TIP . C 3 HOH A 117 117 117 HOH TIP . C 3 HOH A 118 118 118 HOH TIP . C 3 HOH A 119 119 119 HOH TIP . C 3 HOH A 120 424 120 HOH TIP . C 3 HOH A 121 426 121 HOH TIP . C 3 HOH A 122 427 122 HOH TIP . C 3 HOH A 123 428 123 HOH TIP . C 3 HOH A 124 429 124 HOH TIP . C 3 HOH A 125 430 125 HOH TIP . C 3 HOH A 126 431 126 HOH TIP . C 3 HOH A 127 432 127 HOH TIP . C 3 HOH A 128 433 128 HOH TIP . C 3 HOH A 129 434 129 HOH TIP . C 3 HOH A 130 435 130 HOH TIP . C 3 HOH A 131 436 131 HOH TIP . C 3 HOH A 132 437 132 HOH TIP . C 3 HOH A 133 438 133 HOH TIP . C 3 HOH A 134 439 134 HOH TIP . C 3 HOH A 135 440 135 HOH TIP . C 3 HOH A 136 441 136 HOH TIP . C 3 HOH A 137 442 137 HOH TIP . C 3 HOH A 138 443 138 HOH TIP . C 3 HOH A 139 444 139 HOH TIP . C 3 HOH A 140 445 140 HOH TIP . C 3 HOH A 141 446 141 HOH TIP . C 3 HOH A 142 447 142 HOH TIP . C 3 HOH A 143 448 143 HOH TIP . C 3 HOH A 144 449 144 HOH TIP . C 3 HOH A 145 450 145 HOH TIP . C 3 HOH A 146 451 146 HOH TIP . C 3 HOH A 147 452 147 HOH TIP . C 3 HOH A 148 453 148 HOH TIP . C 3 HOH A 149 454 149 HOH TIP . C 3 HOH A 150 455 150 HOH TIP . C 3 HOH A 151 456 151 HOH TIP . C 3 HOH A 152 457 152 HOH TIP . C 3 HOH A 153 458 153 HOH TIP . C 3 HOH A 154 459 154 HOH TIP . C 3 HOH A 155 460 155 HOH TIP . C 3 HOH A 156 461 156 HOH TIP . C 3 HOH A 157 462 157 HOH TIP . C 3 HOH A 158 463 158 HOH TIP . C 3 HOH A 159 464 159 HOH TIP . C 3 HOH A 160 465 160 HOH TIP . C 3 HOH A 161 466 161 HOH TIP . C 3 HOH A 162 467 162 HOH TIP . C 3 HOH A 163 468 163 HOH TIP . C 3 HOH A 164 469 164 HOH TIP . # 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 . . . B 2 16.692 17.936 34.492 1 9.22 ? O2 VDX 425 A 1 HETATM 2 O O3 VDX . . . B 2 4.138 26.747 34.891 1 11.22 ? O3 VDX 425 A 1 HETATM 3 C C1 VDX . . . B 2 13.873 17.799 35.514 1 12.07 ? C1 VDX 425 A 1 HETATM 4 C C2 VDX . . . B 2 14.573 16.704 34.664 1 10.98 ? C2 VDX 425 A 1 HETATM 5 C C3 VDX . . . B 2 15.659 17.331 33.684 1 11.11 ? C3 VDX 425 A 1 HETATM 6 C C4 VDX . . . B 2 14.993 18.418 32.748 1 9.42 ? C4 VDX 425 A 1 HETATM 7 C C5 VDX . . . B 2 14.27 19.493 33.555 1 8.51 ? C5 VDX 425 A 1 HETATM 8 C C6 VDX . . . B 2 14.452 20.885 33.459 1 7.61 ? C6 VDX 425 A 1 HETATM 9 C C7 VDX . . . B 2 13.841 22.064 34.169 1 6.24 ? C7 VDX 425 A 1 HETATM 10 C C8 VDX . . . B 2 13.592 23.245 33.66 1 7.57 ? C8 VDX 425 A 1 HETATM 11 C C9 VDX . . . B 2 13.926 23.65 32.137 1 7.66 ? C9 VDX 425 A 1 HETATM 12 C C10 VDX . . . B 2 13.269 18.85 34.546 1 11.17 ? C10 VDX 425 A 1 HETATM 13 C C11 VDX . . . B 2 12.61 24.124 31.286 1 6.69 ? C11 VDX 425 A 1 HETATM 14 C C12 VDX . . . B 2 11.682 25.106 32.162 1 8.86 ? C12 VDX 425 A 1 HETATM 15 C C13 VDX . . . B 2 11.376 24.64 33.717 1 7.81 ? C13 VDX 425 A 1 HETATM 16 C C14 VDX . . . B 2 12.81 24.325 34.379 1 8.62 ? C14 VDX 425 A 1 HETATM 17 C C15 VDX . . . B 2 12.38 24.125 35.983 1 9.75 ? C15 VDX 425 A 1 HETATM 18 C C16 VDX . . . B 2 11.144 25.087 36.124 1 9.94 ? C16 VDX 425 A 1 HETATM 19 C C17 VDX . . . B 2 10.968 25.735 34.715 1 8.75 ? C17 VDX 425 A 1 HETATM 20 C C18 VDX . . . B 2 10.389 23.291 33.549 1 8.38 ? C18 VDX 425 A 1 HETATM 21 C C19 VDX . . . B 2 11.932 19.169 34.547 1 13.87 ? C19 VDX 425 A 1 HETATM 22 C C20 VDX . . . B 2 9.511 26.319 34.359 1 12.04 ? C20 VDX 425 A 1 HETATM 23 C C21 VDX . . . B 2 9.515 27.767 35.034 1 14 ? C21 VDX 425 A 1 HETATM 24 C C22 VDX . . . B 2 8.248 25.655 35.003 1 11.22 ? C22 VDX 425 A 1 HETATM 25 C C23 VDX . . . B 2 6.962 25.884 34.2 1 12.49 ? C23 VDX 425 A 1 HETATM 26 C C24 VDX . . . B 2 5.808 25.078 34.542 1 12.4 ? C24 VDX 425 A 1 HETATM 27 C C25 VDX . . . B 2 4.413 25.54 34.229 1 14.15 ? C25 VDX 425 A 1 HETATM 28 C C26 VDX . . . B 2 4.276 25.681 32.727 1 15.45 ? C26 VDX 425 A 1 HETATM 29 C C27 VDX . . . B 2 3.345 24.495 34.71 1 13.65 ? C27 VDX 425 A 1 HETATM 30 O O1 VDX . . . B 2 12.872 17.194 36.407 1 12.61 ? O1 VDX 425 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 30 #