data_5LJE # _model_server_result.job_id bH51ulqDb4nIBCYwnQ7Wqw _model_server_result.datetime_utc '2024-11-28 09:32:05' _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 5lje # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5LJE # _exptl.entry_id 5LJE _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 5LJE _cell.length_a 34.554 _cell.length_b 47.414 _cell.length_c 80.595 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LJE _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_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.741 ? metalc ? metalc2 A OE2 GLU 19 A GLU 18 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc3 A OD1 ASP 64 A ASP 63 1_555 C NA NA . A NA 202 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.99 ? metalc ? metalc4 A OD2 ASP 64 A ASP 63 1_555 C NA NA . A NA 202 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? metalc ? metalc5 C NA NA . A NA 202 1_555 D O HOH . A HOH 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc6 C NA NA . A NA 202 1_555 D O HOH . A HOH 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc7 C NA NA . A NA 202 1_555 D O HOH . A HOH 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? # _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 5LJE _atom_sites.fract_transf_matrix[1][1] 0.02894 _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] 0.021091 _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] 0.012408 _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 ZN . D 4 HOH A 1 301 70 HOH HOH . D 4 HOH A 2 302 110 HOH HOH . D 4 HOH A 3 303 59 HOH HOH . D 4 HOH A 4 304 108 HOH HOH . D 4 HOH A 5 305 20 HOH HOH . D 4 HOH A 6 306 82 HOH HOH . D 4 HOH A 7 307 97 HOH HOH . D 4 HOH A 8 308 76 HOH HOH . D 4 HOH A 9 309 55 HOH HOH . D 4 HOH A 10 310 115 HOH HOH . D 4 HOH A 11 311 73 HOH HOH . D 4 HOH A 12 312 67 HOH HOH . D 4 HOH A 13 313 64 HOH HOH . D 4 HOH A 14 314 61 HOH HOH . D 4 HOH A 15 315 56 HOH HOH . D 4 HOH A 16 316 30 HOH HOH . D 4 HOH A 17 317 15 HOH HOH . D 4 HOH A 18 318 33 HOH HOH . D 4 HOH A 19 319 93 HOH HOH . D 4 HOH A 20 320 107 HOH HOH . D 4 HOH A 21 321 8 HOH HOH . D 4 HOH A 22 322 39 HOH HOH . D 4 HOH A 23 323 109 HOH HOH . D 4 HOH A 24 324 91 HOH HOH . D 4 HOH A 25 325 89 HOH HOH . D 4 HOH A 26 326 17 HOH HOH . D 4 HOH A 27 327 111 HOH HOH . D 4 HOH A 28 328 94 HOH HOH . D 4 HOH A 29 329 74 HOH HOH . D 4 HOH A 30 330 10 HOH HOH . D 4 HOH A 31 331 98 HOH HOH . D 4 HOH A 32 332 5 HOH HOH . D 4 HOH A 33 333 62 HOH HOH . D 4 HOH A 34 334 3 HOH HOH . D 4 HOH A 35 335 16 HOH HOH . D 4 HOH A 36 336 24 HOH HOH . D 4 HOH A 37 337 26 HOH HOH . D 4 HOH A 38 338 11 HOH HOH . D 4 HOH A 39 339 43 HOH HOH . D 4 HOH A 40 340 57 HOH HOH . D 4 HOH A 41 341 87 HOH HOH . D 4 HOH A 42 342 51 HOH HOH . D 4 HOH A 43 343 101 HOH HOH . D 4 HOH A 44 344 14 HOH HOH . D 4 HOH A 45 345 41 HOH HOH . D 4 HOH A 46 346 84 HOH HOH . D 4 HOH A 47 347 28 HOH HOH . D 4 HOH A 48 348 32 HOH HOH . D 4 HOH A 49 349 105 HOH HOH . D 4 HOH A 50 350 81 HOH HOH . D 4 HOH A 51 351 50 HOH HOH . D 4 HOH A 52 352 6 HOH HOH . D 4 HOH A 53 353 54 HOH HOH . D 4 HOH A 54 354 12 HOH HOH . D 4 HOH A 55 355 53 HOH HOH . D 4 HOH A 56 356 37 HOH HOH . D 4 HOH A 57 357 85 HOH HOH . D 4 HOH A 58 358 49 HOH HOH . D 4 HOH A 59 359 21 HOH HOH . D 4 HOH A 60 360 99 HOH HOH . D 4 HOH A 61 361 25 HOH HOH . D 4 HOH A 62 362 100 HOH HOH . D 4 HOH A 63 363 23 HOH HOH . D 4 HOH A 64 364 95 HOH HOH . D 4 HOH A 65 365 9 HOH HOH . D 4 HOH A 66 366 4 HOH HOH . D 4 HOH A 67 367 106 HOH HOH . D 4 HOH A 68 368 69 HOH HOH . D 4 HOH A 69 369 46 HOH HOH . D 4 HOH A 70 370 22 HOH HOH . D 4 HOH A 71 371 31 HOH HOH . D 4 HOH A 72 372 52 HOH HOH . D 4 HOH A 73 373 19 HOH HOH . D 4 HOH A 74 374 35 HOH HOH . D 4 HOH A 75 375 42 HOH HOH . D 4 HOH A 76 376 13 HOH HOH . D 4 HOH A 77 377 60 HOH HOH . D 4 HOH A 78 378 114 HOH HOH . D 4 HOH A 79 379 72 HOH HOH . D 4 HOH A 80 380 18 HOH HOH . D 4 HOH A 81 381 83 HOH HOH . D 4 HOH A 82 382 29 HOH HOH . D 4 HOH A 83 383 1 HOH HOH . D 4 HOH A 84 384 47 HOH HOH . D 4 HOH A 85 385 48 HOH HOH . D 4 HOH A 86 386 80 HOH HOH . D 4 HOH A 87 387 65 HOH HOH . D 4 HOH A 88 388 7 HOH HOH . D 4 HOH A 89 389 63 HOH HOH . D 4 HOH A 90 390 68 HOH HOH . D 4 HOH A 91 391 45 HOH HOH . D 4 HOH A 92 392 112 HOH HOH . D 4 HOH A 93 393 75 HOH HOH . D 4 HOH A 94 394 113 HOH HOH . D 4 HOH A 95 395 27 HOH HOH . D 4 HOH A 96 396 58 HOH HOH . D 4 HOH A 97 397 66 HOH HOH . D 4 HOH A 98 398 88 HOH HOH . D 4 HOH A 99 399 2 HOH HOH . D 4 HOH A 100 400 71 HOH HOH . D 4 HOH A 101 401 38 HOH HOH . D 4 HOH A 102 402 40 HOH HOH . D 4 HOH A 103 403 36 HOH HOH . D 4 HOH A 104 404 34 HOH HOH . D 4 HOH A 105 405 77 HOH HOH . D 4 HOH A 106 406 90 HOH HOH . D 4 HOH A 107 407 92 HOH HOH . D 4 HOH A 108 408 78 HOH HOH . D 4 HOH A 109 409 102 HOH HOH . D 4 HOH A 110 410 104 HOH HOH . D 4 HOH A 111 411 103 HOH HOH . D 4 HOH A 112 412 86 HOH HOH . D 4 HOH A 113 413 44 HOH HOH . D 4 HOH A 114 414 79 HOH HOH . D 4 HOH A 115 415 96 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 2.696 5.895 -15.022 1 40.39 ? C1 RTL 201 A 1 HETATM 2 C C2 RTL . . . B 2 3.04 7.01 -16.042 1 38.92 ? C2 RTL 201 A 1 HETATM 3 C C3 RTL . . . B 2 3.392 6.464 -17.384 1 37.05 ? C3 RTL 201 A 1 HETATM 4 C C4 RTL . . . B 2 4.619 5.627 -17.073 1 40.6 ? C4 RTL 201 A 1 HETATM 5 C C5 RTL . . . B 2 4.489 4.613 -16.181 1 30.67 ? C5 RTL 201 A 1 HETATM 6 C C6 RTL . . . B 2 3.588 4.749 -15.128 1 29.88 ? C6 RTL 201 A 1 HETATM 7 C C7 RTL . . . B 2 3.546 3.653 -14.285 1 32.44 ? C7 RTL 201 A 1 HETATM 8 C C8 RTL . . . B 2 2.58 3.536 -13.167 1 32.96 ? C8 RTL 201 A 1 HETATM 9 C C9 RTL . . . B 2 2.605 2.325 -12.308 1 39.24 ? C9 RTL 201 A 1 HETATM 10 C C10 RTL . . . B 2 1.591 2.326 -11.216 1 36.58 ? C10 RTL 201 A 1 HETATM 11 C C11 RTL . . . B 2 1.534 1.168 -10.302 1 35.13 ? C11 RTL 201 A 1 HETATM 12 C C12 RTL . . . B 2 0.515 1.189 -9.207 1 38.14 ? C12 RTL 201 A 1 HETATM 13 C C13 RTL . . . B 2 0.455 0.016 -8.274 1 40.88 ? C13 RTL 201 A 1 HETATM 14 C C14 RTL . . . B 2 -0.555 0.008 -7.158 1 48.31 ? C14 RTL 201 A 1 HETATM 15 C C15 RTL . . . B 2 -1.461 1.187 -7.034 1 50.43 ? C15 RTL 201 A 1 HETATM 16 O O1 RTL . . . B 2 -2.282 1.235 -8.214 1 53.53 ? O1 RTL 201 A 1 HETATM 17 C C16 RTL . . . B 2 1.46 5.179 -15.622 1 44.49 ? C16 RTL 201 A 1 HETATM 18 C C17 RTL . . . B 2 2.573 6.66 -13.67 1 35.5 ? C17 RTL 201 A 1 HETATM 19 C C18 RTL . . . B 2 5.41 3.549 -16.357 1 33.36 ? C18 RTL 201 A 1 HETATM 20 C C19 RTL . . . B 2 3.582 1.157 -12.534 1 37.24 ? C19 RTL 201 A 1 HETATM 21 C C20 RTL . . . B 2 1.375 -1.157 -8.473 1 40.24 ? C20 RTL 201 A 1 HETATM 22 H H21 RTL . . . B 2 3.884 7.585 -15.666 1 46.7 ? H21 RTL 201 A 1 HETATM 23 H H22 RTL . . . B 2 2.18 7.669 -16.148 1 46.7 ? H22 RTL 201 A 1 HETATM 24 H H31 RTL . . . B 2 3.632 7.273 -18.079 1 44.46 ? H31 RTL 201 A 1 HETATM 25 H H32 RTL . . . B 2 2.581 5.846 -17.775 1 44.46 ? H32 RTL 201 A 1 HETATM 26 H H41 RTL . . . B 2 5.39 6.296 -16.697 1 48.71 ? H41 RTL 201 A 1 HETATM 27 H H42 RTL . . . B 2 4.972 5.195 -18.008 1 48.71 ? H42 RTL 201 A 1 HETATM 28 H H7 RTL . . . B 2 4.213 2.815 -14.486 1 38.92 ? H7 RTL 201 A 1 HETATM 29 H H8 RTL . . . B 2 1.86 4.331 -12.976 1 39.56 ? H8 RTL 201 A 1 HETATM 30 H H10 RTL . . . B 2 0.917 3.172 -11.084 1 43.9 ? H10 RTL 201 A 1 HETATM 31 H H11 RTL . . . B 2 2.202 0.316 -10.432 1 42.16 ? H11 RTL 201 A 1 HETATM 32 H H12 RTL . . . B 2 -0.15 2.043 -9.078 1 45.77 ? H12 RTL 201 A 1 HETATM 33 H H14 RTL . . . B 2 -0.621 -0.83 -6.464 1 57.97 ? H14 RTL 201 A 1 HETATM 34 H H151 RTL . . . B 2 -0.869 2.1 -6.955 1 60.51 ? H151 RTL 201 A 1 HETATM 35 H H152 RTL . . . B 2 -2.088 1.078 -6.148 1 60.51 ? H152 RTL 201 A 1 HETATM 36 H HO1 RTL . . . B 2 -2.816 0.392 -8.283 1 64.23 ? HO1 RTL 201 A 1 HETATM 37 H H161 RTL . . . B 2 1.204 4.318 -15.005 1 53.38 ? H161 RTL 201 A 1 HETATM 38 H H162 RTL . . . B 2 1.69 4.845 -16.634 1 53.38 ? H162 RTL 201 A 1 HETATM 39 H H163 RTL . . . B 2 0.618 5.87 -15.65 1 53.38 ? H163 RTL 201 A 1 HETATM 40 H H171 RTL . . . B 2 2.265 5.966 -12.888 1 42.6 ? H171 RTL 201 A 1 HETATM 41 H H172 RTL . . . B 2 1.83 7.451 -13.765 1 42.6 ? H172 RTL 201 A 1 HETATM 42 H H173 RTL . . . B 2 3.537 7.095 -13.409 1 42.6 ? H173 RTL 201 A 1 HETATM 43 H H181 RTL . . . B 2 5.672 3.467 -17.412 1 40.04 ? H181 RTL 201 A 1 HETATM 44 H H182 RTL . . . B 2 4.956 2.616 -16.023 1 40.04 ? H182 RTL 201 A 1 HETATM 45 H H183 RTL . . . B 2 6.309 3.745 -15.774 1 40.04 ? H183 RTL 201 A 1 HETATM 46 H H191 RTL . . . B 2 4.503 1.535 -12.977 1 44.69 ? H191 RTL 201 A 1 HETATM 47 H H192 RTL . . . B 2 3.128 0.429 -13.206 1 44.69 ? H192 RTL 201 A 1 HETATM 48 H H193 RTL . . . B 2 3.807 0.681 -11.58 1 44.69 ? H193 RTL 201 A 1 HETATM 49 H H201 RTL . . . B 2 2.305 -0.817 -8.927 1 48.29 ? H201 RTL 201 A 1 HETATM 50 H H202 RTL . . . B 2 0.896 -1.887 -9.127 1 48.29 ? H202 RTL 201 A 1 HETATM 51 H H203 RTL . . . B 2 1.587 -1.619 -7.509 1 48.29 ? H203 RTL 201 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 51 #