data_5LJD # _model_server_result.job_id 4FZY7c_6f-qmz_km14JzGg _model_server_result.datetime_utc '2024-11-04 20:22:21' _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 5ljd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5LJD # _exptl.entry_id 5LJD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 286.452 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RETINOL _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 5LJD _cell.length_a 34.483 _cell.length_b 47.187 _cell.length_c 81.033 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LJD _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,D _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OE1 GLU 19 A GLU 18 1_555 C NA NA . A NA 202 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc2 A OE2 GLU 19 A GLU 18 1_555 C NA NA . A NA 202 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc3 A OD1 ASP 64 A ASP 63 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? metalc ? metalc4 A OD2 ASP 64 A ASP 63 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc5 C NA NA . A NA 202 1_555 D O HOH . A HOH 320 4_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc6 C NA NA . A NA 202 1_555 D O HOH . A HOH 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc7 C NA NA . A NA 202 1_555 D O HOH . A HOH 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? # _chem_comp.formula 'C20 H30 O' _chem_comp.formula_weight 286.452 _chem_comp.id RTL _chem_comp.mon_nstd_flag . _chem_comp.name RETINOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C1 C2 RTL sing 277 n n C1 C6 RTL sing 278 n n C1 C16 RTL sing 279 n n C1 C17 RTL sing 280 n n C2 C3 RTL sing 281 n n C2 H21 RTL sing 282 n n C2 H22 RTL sing 283 n n C3 C4 RTL sing 284 n n C3 H31 RTL sing 285 n n C3 H32 RTL sing 286 n n C4 C5 RTL sing 287 n n C4 H41 RTL sing 288 n n C4 H42 RTL sing 289 n n C5 C6 RTL doub 290 n n C5 C18 RTL sing 291 n n C6 C7 RTL sing 292 n n C7 C8 RTL doub 293 e n C7 H7 RTL sing 294 n n C8 C9 RTL sing 295 n n C8 H8 RTL sing 296 n n C9 C10 RTL doub 297 e n C9 C19 RTL sing 298 n n C10 C11 RTL sing 299 n n C10 H10 RTL sing 300 n n C11 C12 RTL doub 301 e n C11 H11 RTL sing 302 n n C12 C13 RTL sing 303 n n C12 H12 RTL sing 304 n n C13 C14 RTL doub 305 e n C13 C20 RTL sing 306 n n C14 C15 RTL sing 307 n n C14 H14 RTL sing 308 n n C15 O1 RTL sing 309 n n C15 H151 RTL sing 310 n n C15 H152 RTL sing 311 n n O1 HO1 RTL sing 312 n n C16 H161 RTL sing 313 n n C16 H162 RTL sing 314 n n C16 H163 RTL sing 315 n n C17 H171 RTL sing 316 n n C17 H172 RTL sing 317 n n C17 H173 RTL sing 318 n n C18 H181 RTL sing 319 n n C18 H182 RTL sing 320 n n C18 H183 RTL sing 321 n n C19 H191 RTL sing 322 n n C19 H192 RTL sing 323 n n C19 H193 RTL sing 324 n n C20 H201 RTL sing 325 n n C20 H202 RTL sing 326 n n C20 H203 RTL sing 327 n n # _atom_sites.entry_id 5LJD _atom_sites.fract_transf_matrix[1][1] 0.029 _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] 0.021192 _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] 0.012341 _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 RTL A 1 201 1 RTL RTL . C 3 NA A 1 202 1 NA NA . D 4 HOH A 1 301 167 HOH HOH . D 4 HOH A 2 302 173 HOH HOH . D 4 HOH A 3 303 94 HOH HOH . D 4 HOH A 4 304 124 HOH HOH . D 4 HOH A 5 305 103 HOH HOH . D 4 HOH A 6 306 117 HOH HOH . D 4 HOH A 7 307 156 HOH HOH . D 4 HOH A 8 308 132 HOH HOH . D 4 HOH A 9 309 90 HOH HOH . D 4 HOH A 10 310 137 HOH HOH . D 4 HOH A 11 311 28 HOH HOH . D 4 HOH A 12 312 44 HOH HOH . D 4 HOH A 13 313 99 HOH HOH . D 4 HOH A 14 314 64 HOH HOH . D 4 HOH A 15 315 125 HOH HOH . D 4 HOH A 16 316 14 HOH HOH . D 4 HOH A 17 317 60 HOH HOH . D 4 HOH A 18 318 114 HOH HOH . D 4 HOH A 19 319 35 HOH HOH . D 4 HOH A 20 320 105 HOH HOH . D 4 HOH A 21 321 34 HOH HOH . D 4 HOH A 22 322 27 HOH HOH . D 4 HOH A 23 323 6 HOH HOH . D 4 HOH A 24 324 127 HOH HOH . D 4 HOH A 25 325 65 HOH HOH . D 4 HOH A 26 326 58 HOH HOH . D 4 HOH A 27 327 81 HOH HOH . D 4 HOH A 28 328 181 HOH HOH . D 4 HOH A 29 329 2 HOH HOH . D 4 HOH A 30 330 15 HOH HOH . D 4 HOH A 31 331 110 HOH HOH . D 4 HOH A 32 332 21 HOH HOH . D 4 HOH A 33 333 23 HOH HOH . D 4 HOH A 34 334 71 HOH HOH . D 4 HOH A 35 335 106 HOH HOH . D 4 HOH A 36 336 46 HOH HOH . D 4 HOH A 37 337 171 HOH HOH . D 4 HOH A 38 338 10 HOH HOH . D 4 HOH A 39 339 74 HOH HOH . D 4 HOH A 40 340 92 HOH HOH . D 4 HOH A 41 341 45 HOH HOH . D 4 HOH A 42 342 37 HOH HOH . D 4 HOH A 43 343 4 HOH HOH . D 4 HOH A 44 344 53 HOH HOH . D 4 HOH A 45 345 80 HOH HOH . D 4 HOH A 46 346 3 HOH HOH . D 4 HOH A 47 347 56 HOH HOH . D 4 HOH A 48 348 176 HOH HOH . D 4 HOH A 49 349 126 HOH HOH . D 4 HOH A 50 350 17 HOH HOH . D 4 HOH A 51 351 30 HOH HOH . D 4 HOH A 52 352 109 HOH HOH . D 4 HOH A 53 353 33 HOH HOH . D 4 HOH A 54 354 49 HOH HOH . D 4 HOH A 55 355 116 HOH HOH . D 4 HOH A 56 356 9 HOH HOH . D 4 HOH A 57 357 61 HOH HOH . D 4 HOH A 58 358 119 HOH HOH . D 4 HOH A 59 359 113 HOH HOH . D 4 HOH A 60 360 79 HOH HOH . D 4 HOH A 61 361 146 HOH HOH . D 4 HOH A 62 362 100 HOH HOH . D 4 HOH A 63 363 40 HOH HOH . D 4 HOH A 64 364 26 HOH HOH . D 4 HOH A 65 365 69 HOH HOH . D 4 HOH A 66 366 68 HOH HOH . D 4 HOH A 67 367 11 HOH HOH . D 4 HOH A 68 368 75 HOH HOH . D 4 HOH A 69 369 83 HOH HOH . D 4 HOH A 70 370 96 HOH HOH . D 4 HOH A 71 371 141 HOH HOH . D 4 HOH A 72 372 5 HOH HOH . D 4 HOH A 73 373 42 HOH HOH . D 4 HOH A 74 374 48 HOH HOH . D 4 HOH A 75 375 170 HOH HOH . D 4 HOH A 76 376 185 HOH HOH . D 4 HOH A 77 377 76 HOH HOH . D 4 HOH A 78 378 195 HOH HOH . D 4 HOH A 79 379 158 HOH HOH . D 4 HOH A 80 380 193 HOH HOH . D 4 HOH A 81 381 87 HOH HOH . D 4 HOH A 82 382 111 HOH HOH . D 4 HOH A 83 383 150 HOH HOH . D 4 HOH A 84 384 190 HOH HOH . D 4 HOH A 85 385 24 HOH HOH . D 4 HOH A 86 386 97 HOH HOH . D 4 HOH A 87 387 77 HOH HOH . D 4 HOH A 88 388 18 HOH HOH . D 4 HOH A 89 389 41 HOH HOH . D 4 HOH A 90 390 39 HOH HOH . D 4 HOH A 91 391 139 HOH HOH . D 4 HOH A 92 392 38 HOH HOH . D 4 HOH A 93 393 12 HOH HOH . D 4 HOH A 94 394 86 HOH HOH . D 4 HOH A 95 395 140 HOH HOH . D 4 HOH A 96 396 123 HOH HOH . D 4 HOH A 97 397 78 HOH HOH . D 4 HOH A 98 398 1 HOH HOH . D 4 HOH A 99 399 128 HOH HOH . D 4 HOH A 100 400 13 HOH HOH . D 4 HOH A 101 401 52 HOH HOH . D 4 HOH A 102 402 43 HOH HOH . D 4 HOH A 103 403 142 HOH HOH . D 4 HOH A 104 404 50 HOH HOH . D 4 HOH A 105 405 31 HOH HOH . D 4 HOH A 106 406 73 HOH HOH . D 4 HOH A 107 407 82 HOH HOH . D 4 HOH A 108 408 164 HOH HOH . D 4 HOH A 109 409 112 HOH HOH . D 4 HOH A 110 410 175 HOH HOH . D 4 HOH A 111 411 101 HOH HOH . D 4 HOH A 112 412 8 HOH HOH . D 4 HOH A 113 413 157 HOH HOH . D 4 HOH A 114 414 143 HOH HOH . D 4 HOH A 115 415 154 HOH HOH . D 4 HOH A 116 416 172 HOH HOH . D 4 HOH A 117 417 32 HOH HOH . D 4 HOH A 118 418 16 HOH HOH . D 4 HOH A 119 419 19 HOH HOH . D 4 HOH A 120 420 7 HOH HOH . D 4 HOH A 121 421 194 HOH HOH . D 4 HOH A 122 422 93 HOH HOH . D 4 HOH A 123 423 187 HOH HOH . D 4 HOH A 124 424 108 HOH HOH . D 4 HOH A 125 425 161 HOH HOH . D 4 HOH A 126 426 36 HOH HOH . D 4 HOH A 127 427 186 HOH HOH . D 4 HOH A 128 428 152 HOH HOH . D 4 HOH A 129 429 147 HOH HOH . D 4 HOH A 130 430 72 HOH HOH . D 4 HOH A 131 431 174 HOH HOH . D 4 HOH A 132 432 22 HOH HOH . D 4 HOH A 133 433 104 HOH HOH . D 4 HOH A 134 434 160 HOH HOH . D 4 HOH A 135 435 98 HOH HOH . D 4 HOH A 136 436 62 HOH HOH . D 4 HOH A 137 437 20 HOH HOH . D 4 HOH A 138 438 145 HOH HOH . D 4 HOH A 139 439 88 HOH HOH . D 4 HOH A 140 440 159 HOH HOH . D 4 HOH A 141 441 59 HOH HOH . D 4 HOH A 142 442 120 HOH HOH . D 4 HOH A 143 443 102 HOH HOH . D 4 HOH A 144 444 95 HOH HOH . D 4 HOH A 145 445 153 HOH HOH . D 4 HOH A 146 446 192 HOH HOH . D 4 HOH A 147 447 66 HOH HOH . D 4 HOH A 148 448 182 HOH HOH . D 4 HOH A 149 449 47 HOH HOH . D 4 HOH A 150 450 155 HOH HOH . D 4 HOH A 151 451 184 HOH HOH . D 4 HOH A 152 452 122 HOH HOH . D 4 HOH A 153 453 67 HOH HOH . D 4 HOH A 154 454 118 HOH HOH . D 4 HOH A 155 455 115 HOH HOH . D 4 HOH A 156 456 136 HOH HOH . D 4 HOH A 157 457 70 HOH HOH . D 4 HOH A 158 458 133 HOH HOH . D 4 HOH A 159 459 149 HOH HOH . D 4 HOH A 160 460 121 HOH HOH . D 4 HOH A 161 461 91 HOH HOH . D 4 HOH A 162 462 25 HOH HOH . D 4 HOH A 163 463 131 HOH HOH . D 4 HOH A 164 464 107 HOH HOH . D 4 HOH A 165 465 179 HOH HOH . D 4 HOH A 166 466 138 HOH HOH . D 4 HOH A 167 467 134 HOH HOH . D 4 HOH A 168 468 63 HOH HOH . D 4 HOH A 169 469 162 HOH HOH . D 4 HOH A 170 470 51 HOH HOH . D 4 HOH A 171 471 29 HOH HOH . D 4 HOH A 172 472 166 HOH HOH . D 4 HOH A 173 473 57 HOH HOH . D 4 HOH A 174 474 165 HOH HOH . D 4 HOH A 175 475 135 HOH HOH . D 4 HOH A 176 476 130 HOH HOH . D 4 HOH A 177 477 89 HOH HOH . D 4 HOH A 178 478 54 HOH HOH . D 4 HOH A 179 479 85 HOH HOH . D 4 HOH A 180 480 84 HOH HOH . D 4 HOH A 181 481 188 HOH HOH . D 4 HOH A 182 482 148 HOH HOH . D 4 HOH A 183 483 55 HOH HOH . D 4 HOH A 184 484 178 HOH HOH . D 4 HOH A 185 485 169 HOH HOH . D 4 HOH A 186 486 177 HOH HOH . D 4 HOH A 187 487 144 HOH HOH . D 4 HOH A 188 488 180 HOH HOH . D 4 HOH A 189 489 189 HOH HOH . D 4 HOH A 190 490 151 HOH HOH . D 4 HOH A 191 491 129 HOH HOH . D 4 HOH A 192 492 163 HOH HOH . D 4 HOH A 193 493 168 HOH HOH . D 4 HOH A 194 494 183 HOH HOH . D 4 HOH A 195 495 191 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 C C1 RTL . . . B 2 2.778 5.884 -15.154 1 20.33 ? C1 RTL 201 A 1 HETATM 2 C C2 RTL . . . B 2 3.034 7.026 -16.162 1 23.19 ? C2 RTL 201 A 1 HETATM 3 C C3 RTL . . . B 2 3.299 6.483 -17.517 1 25.65 ? C3 RTL 201 A 1 HETATM 4 C C4 RTL . . . B 2 4.587 5.64 -17.288 1 29.19 ? C4 RTL 201 A 1 HETATM 5 C C5 RTL . . . B 2 4.504 4.622 -16.378 1 25.4 ? C5 RTL 201 A 1 HETATM 6 C C6 RTL . . . B 2 3.656 4.754 -15.296 1 21.14 ? C6 RTL 201 A 1 HETATM 7 C C7 RTL . . . B 2 3.698 3.624 -14.47 1 24.38 ? C7 RTL 201 A 1 HETATM 8 C C8 RTL . . . B 2 2.746 3.574 -13.322 1 20.92 ? C8 RTL 201 A 1 HETATM 9 C C9 RTL . . . B 2 2.79 2.362 -12.435 1 21.14 ? C9 RTL 201 A 1 HETATM 10 C C10 RTL . . . B 2 1.819 2.397 -11.325 1 25.72 ? C10 RTL 201 A 1 HETATM 11 C C11 RTL . . . B 2 1.764 1.246 -10.364 1 24.71 ? C11 RTL 201 A 1 HETATM 12 C C12 RTL . . . B 2 0.684 1.633 -9.39 1 27.47 ? C12 RTL 201 A 1 HETATM 13 C C13 RTL . . . B 2 0.397 0.671 -8.291 1 25.05 ? C13 RTL 201 A 1 HETATM 14 C C14 RTL . . . B 2 -0.697 1.067 -7.299 1 25.13 ? C14 RTL 201 A 1 HETATM 15 C C15 RTL . . . B 2 -0.992 0.085 -6.167 1 20.88 ? C15 RTL 201 A 1 HETATM 16 O O1 RTL . . . B 2 -1.377 0.829 -5.004 1 31.29 ? O1 RTL 201 A 1 HETATM 17 C C16 RTL . . . B 2 1.523 5.187 -15.721 1 26.42 ? C16 RTL 201 A 1 HETATM 18 C C17 RTL . . . B 2 2.748 6.508 -13.763 1 23.47 ? C17 RTL 201 A 1 HETATM 19 C C18 RTL . . . B 2 5.377 3.515 -16.465 1 24.25 ? C18 RTL 201 A 1 HETATM 20 C C19 RTL . . . B 2 3.734 1.177 -12.633 1 23.01 ? C19 RTL 201 A 1 HETATM 21 C C20 RTL . . . B 2 1.175 -0.651 -8.234 1 22.29 ? C20 RTL 201 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 21 #