data_4YFQ # _model_server_result.job_id rjiibxA0n8ukhtQhcyHedA _model_server_result.datetime_utc '2024-10-24 16:32:31' _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 4yfq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4YFQ # _exptl.entry_id 4YFQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RETINAL _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 120 _cell.entry_id 4YFQ _cell.length_a 58.869 _cell.length_b 58.869 _cell.length_c 99.71 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YFQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 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 ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 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 1 1 A,B,C 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' 5_554 x-y,-y,-z-1/3 1 0 0 0 -1 0 0 0 -1 0 0 -33.236667 # _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 111 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 111 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C15 _struct_conn.ptnr2_label_comp_id RET _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id RET _struct_conn.ptnr2_auth_seq_id 201 _struct_conn.ptnr2_symmetry 1_555 _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 1.271 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C20 H28 O' _chem_comp.formula_weight 284.436 _chem_comp.id RET _chem_comp.mon_nstd_flag . _chem_comp.name RETINAL _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 RET sing 256 n n C1 C6 RET sing 257 n n C1 C16 RET sing 258 n n C1 C17 RET sing 259 n n C2 C3 RET sing 260 n n C2 H21 RET sing 261 n n C2 H22 RET sing 262 n n C3 C4 RET sing 263 n n C3 H31 RET sing 264 n n C3 H32 RET sing 265 n n C4 C5 RET sing 266 n n C4 H41 RET sing 267 n n C4 H42 RET sing 268 n n C5 C6 RET doub 269 n n C5 C18 RET sing 270 n n C6 C7 RET sing 271 n n C7 C8 RET doub 272 e n C7 H7 RET sing 273 n n C8 C9 RET sing 274 n n C8 H8 RET sing 275 n n C9 C10 RET doub 276 e n C9 C19 RET sing 277 n n C10 C11 RET sing 278 n n C10 H10 RET sing 279 n n C11 C12 RET doub 280 e n C11 H11 RET sing 281 n n C12 C13 RET sing 282 n n C12 H12 RET sing 283 n n C13 C14 RET doub 284 e n C13 C20 RET sing 285 n n C14 C15 RET sing 286 n n C14 H14 RET sing 287 n n C15 O1 RET doub 288 n n C15 H15 RET sing 289 n n C16 H161 RET sing 290 n n C16 H162 RET sing 291 n n C16 H163 RET sing 292 n n C17 H171 RET sing 293 n n C17 H172 RET sing 294 n n C17 H173 RET sing 295 n n C18 H181 RET sing 296 n n C18 H182 RET sing 297 n n C18 H183 RET sing 298 n n C19 H191 RET sing 299 n n C19 H192 RET sing 300 n n C19 H193 RET sing 301 n n C20 H201 RET sing 302 n n C20 H202 RET sing 303 n n C20 H203 RET sing 304 n n # _atom_sites.entry_id 4YFQ _atom_sites.fract_transf_matrix[1][1] 0.016987 _atom_sites.fract_transf_matrix[1][2] 0.009807 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019615 _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] 0.010029 _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 RET A 1 201 1 RET RET . C 3 HOH A 1 301 38 HOH HOH . C 3 HOH A 2 302 81 HOH HOH . C 3 HOH A 3 303 186 HOH HOH . C 3 HOH A 4 304 185 HOH HOH . C 3 HOH A 5 305 48 HOH HOH . C 3 HOH A 6 306 113 HOH HOH . C 3 HOH A 7 307 190 HOH HOH . C 3 HOH A 8 308 183 HOH HOH . C 3 HOH A 9 309 164 HOH HOH . C 3 HOH A 10 310 123 HOH HOH . C 3 HOH A 11 311 133 HOH HOH . C 3 HOH A 12 312 23 HOH HOH . C 3 HOH A 13 313 203 HOH HOH . C 3 HOH A 14 314 149 HOH HOH . C 3 HOH A 15 315 86 HOH HOH . C 3 HOH A 16 316 107 HOH HOH . C 3 HOH A 17 317 205 HOH HOH . C 3 HOH A 18 318 26 HOH HOH . C 3 HOH A 19 319 71 HOH HOH . C 3 HOH A 20 320 152 HOH HOH . C 3 HOH A 21 321 24 HOH HOH . C 3 HOH A 22 322 27 HOH HOH . C 3 HOH A 23 323 17 HOH HOH . C 3 HOH A 24 324 87 HOH HOH . C 3 HOH A 25 325 80 HOH HOH . C 3 HOH A 26 326 30 HOH HOH . C 3 HOH A 27 327 179 HOH HOH . C 3 HOH A 28 328 112 HOH HOH . C 3 HOH A 29 329 188 HOH HOH . C 3 HOH A 30 330 6 HOH HOH . C 3 HOH A 31 331 25 HOH HOH . C 3 HOH A 32 332 106 HOH HOH . C 3 HOH A 33 333 114 HOH HOH . C 3 HOH A 34 334 53 HOH HOH . C 3 HOH A 35 335 197 HOH HOH . C 3 HOH A 36 336 184 HOH HOH . C 3 HOH A 37 337 8 HOH HOH . C 3 HOH A 38 338 15 HOH HOH . C 3 HOH A 39 339 120 HOH HOH . C 3 HOH A 40 340 42 HOH HOH . C 3 HOH A 41 341 96 HOH HOH . C 3 HOH A 42 342 36 HOH HOH . C 3 HOH A 43 343 144 HOH HOH . C 3 HOH A 44 344 18 HOH HOH . C 3 HOH A 45 345 62 HOH HOH . C 3 HOH A 46 346 55 HOH HOH . C 3 HOH A 47 347 51 HOH HOH . C 3 HOH A 48 348 64 HOH HOH . C 3 HOH A 49 349 211 HOH HOH . C 3 HOH A 50 350 161 HOH HOH . C 3 HOH A 51 351 116 HOH HOH . C 3 HOH A 52 352 109 HOH HOH . C 3 HOH A 53 353 208 HOH HOH . C 3 HOH A 54 354 165 HOH HOH . C 3 HOH A 55 355 10 HOH HOH . C 3 HOH A 56 356 156 HOH HOH . C 3 HOH A 57 357 200 HOH HOH . C 3 HOH A 58 358 172 HOH HOH . C 3 HOH A 59 359 47 HOH HOH . C 3 HOH A 60 360 77 HOH HOH . C 3 HOH A 61 361 41 HOH HOH . C 3 HOH A 62 362 157 HOH HOH . C 3 HOH A 63 363 168 HOH HOH . C 3 HOH A 64 364 154 HOH HOH . C 3 HOH A 65 365 136 HOH HOH . C 3 HOH A 66 366 173 HOH HOH . C 3 HOH A 67 367 177 HOH HOH . C 3 HOH A 68 368 79 HOH HOH . C 3 HOH A 69 369 145 HOH HOH . C 3 HOH A 70 370 66 HOH HOH . C 3 HOH A 71 371 60 HOH HOH . C 3 HOH A 72 372 162 HOH HOH . C 3 HOH A 73 373 34 HOH HOH . C 3 HOH A 74 374 137 HOH HOH . C 3 HOH A 75 375 1 HOH HOH . C 3 HOH A 76 376 2 HOH HOH . C 3 HOH A 77 377 3 HOH HOH . C 3 HOH A 78 378 4 HOH HOH . C 3 HOH A 79 379 5 HOH HOH . C 3 HOH A 80 380 7 HOH HOH . C 3 HOH A 81 381 9 HOH HOH . C 3 HOH A 82 382 11 HOH HOH . C 3 HOH A 83 383 12 HOH HOH . C 3 HOH A 84 384 13 HOH HOH . C 3 HOH A 85 385 14 HOH HOH . C 3 HOH A 86 386 16 HOH HOH . C 3 HOH A 87 387 19 HOH HOH . C 3 HOH A 88 388 20 HOH HOH . C 3 HOH A 89 389 21 HOH HOH . C 3 HOH A 90 390 22 HOH HOH . C 3 HOH A 91 391 28 HOH HOH . C 3 HOH A 92 392 29 HOH HOH . C 3 HOH A 93 393 31 HOH HOH . C 3 HOH A 94 394 32 HOH HOH . C 3 HOH A 95 395 33 HOH HOH . C 3 HOH A 96 396 35 HOH HOH . C 3 HOH A 97 397 37 HOH HOH . C 3 HOH A 98 398 39 HOH HOH . C 3 HOH A 99 399 40 HOH HOH . C 3 HOH A 100 400 43 HOH HOH . C 3 HOH A 101 401 44 HOH HOH . C 3 HOH A 102 402 45 HOH HOH . C 3 HOH A 103 403 46 HOH HOH . C 3 HOH A 104 404 49 HOH HOH . C 3 HOH A 105 405 50 HOH HOH . C 3 HOH A 106 406 52 HOH HOH . C 3 HOH A 107 407 54 HOH HOH . C 3 HOH A 108 408 56 HOH HOH . C 3 HOH A 109 409 57 HOH HOH . C 3 HOH A 110 410 58 HOH HOH . C 3 HOH A 111 411 59 HOH HOH . C 3 HOH A 112 412 61 HOH HOH . C 3 HOH A 113 413 63 HOH HOH . C 3 HOH A 114 414 65 HOH HOH . C 3 HOH A 115 415 67 HOH HOH . C 3 HOH A 116 416 68 HOH HOH . C 3 HOH A 117 417 69 HOH HOH . C 3 HOH A 118 418 70 HOH HOH . C 3 HOH A 119 419 72 HOH HOH . C 3 HOH A 120 420 73 HOH HOH . C 3 HOH A 121 421 74 HOH HOH . C 3 HOH A 122 422 75 HOH HOH . C 3 HOH A 123 423 76 HOH HOH . C 3 HOH A 124 424 78 HOH HOH . C 3 HOH A 125 425 82 HOH HOH . C 3 HOH A 126 426 83 HOH HOH . C 3 HOH A 127 427 84 HOH HOH . C 3 HOH A 128 428 85 HOH HOH . C 3 HOH A 129 429 88 HOH HOH . C 3 HOH A 130 430 89 HOH HOH . C 3 HOH A 131 431 90 HOH HOH . C 3 HOH A 132 432 91 HOH HOH . C 3 HOH A 133 433 92 HOH HOH . C 3 HOH A 134 434 93 HOH HOH . C 3 HOH A 135 435 94 HOH HOH . C 3 HOH A 136 436 95 HOH HOH . C 3 HOH A 137 437 97 HOH HOH . C 3 HOH A 138 438 98 HOH HOH . C 3 HOH A 139 439 99 HOH HOH . C 3 HOH A 140 440 100 HOH HOH . C 3 HOH A 141 441 101 HOH HOH . C 3 HOH A 142 442 102 HOH HOH . C 3 HOH A 143 443 103 HOH HOH . C 3 HOH A 144 444 104 HOH HOH . C 3 HOH A 145 445 105 HOH HOH . C 3 HOH A 146 446 108 HOH HOH . C 3 HOH A 147 447 110 HOH HOH . C 3 HOH A 148 448 111 HOH HOH . C 3 HOH A 149 449 115 HOH HOH . C 3 HOH A 150 450 117 HOH HOH . C 3 HOH A 151 451 118 HOH HOH . C 3 HOH A 152 452 119 HOH HOH . C 3 HOH A 153 453 121 HOH HOH . C 3 HOH A 154 454 122 HOH HOH . C 3 HOH A 155 455 124 HOH HOH . C 3 HOH A 156 456 125 HOH HOH . C 3 HOH A 157 457 126 HOH HOH . C 3 HOH A 158 458 127 HOH HOH . C 3 HOH A 159 459 128 HOH HOH . C 3 HOH A 160 460 129 HOH HOH . C 3 HOH A 161 461 130 HOH HOH . C 3 HOH A 162 462 131 HOH HOH . C 3 HOH A 163 463 132 HOH HOH . C 3 HOH A 164 464 134 HOH HOH . C 3 HOH A 165 465 135 HOH HOH . C 3 HOH A 166 466 138 HOH HOH . C 3 HOH A 167 467 139 HOH HOH . C 3 HOH A 168 468 140 HOH HOH . C 3 HOH A 169 469 141 HOH HOH . C 3 HOH A 170 470 142 HOH HOH . C 3 HOH A 171 471 143 HOH HOH . C 3 HOH A 172 472 146 HOH HOH . C 3 HOH A 173 473 147 HOH HOH . C 3 HOH A 174 474 148 HOH HOH . C 3 HOH A 175 475 150 HOH HOH . C 3 HOH A 176 476 151 HOH HOH . C 3 HOH A 177 477 153 HOH HOH . C 3 HOH A 178 478 155 HOH HOH . C 3 HOH A 179 479 158 HOH HOH . C 3 HOH A 180 480 159 HOH HOH . C 3 HOH A 181 481 160 HOH HOH . C 3 HOH A 182 482 163 HOH HOH . C 3 HOH A 183 483 166 HOH HOH . C 3 HOH A 184 484 167 HOH HOH . C 3 HOH A 185 485 169 HOH HOH . C 3 HOH A 186 486 170 HOH HOH . C 3 HOH A 187 487 171 HOH HOH . C 3 HOH A 188 488 174 HOH HOH . C 3 HOH A 189 489 175 HOH HOH . C 3 HOH A 190 490 176 HOH HOH . C 3 HOH A 191 491 178 HOH HOH . C 3 HOH A 192 492 180 HOH HOH . C 3 HOH A 193 493 181 HOH HOH . C 3 HOH A 194 494 182 HOH HOH . C 3 HOH A 195 495 187 HOH HOH . C 3 HOH A 196 496 189 HOH HOH . C 3 HOH A 197 497 191 HOH HOH . C 3 HOH A 198 498 192 HOH HOH . C 3 HOH A 199 499 193 HOH HOH . C 3 HOH A 200 500 194 HOH HOH . C 3 HOH A 201 501 195 HOH HOH . C 3 HOH A 202 502 196 HOH HOH . C 3 HOH A 203 503 198 HOH HOH . C 3 HOH A 204 504 199 HOH HOH . C 3 HOH A 205 505 201 HOH HOH . C 3 HOH A 206 506 202 HOH HOH . C 3 HOH A 207 507 206 HOH HOH . C 3 HOH A 208 508 207 HOH HOH . C 3 HOH A 209 509 209 HOH HOH . C 3 HOH A 210 510 210 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 RET . . . B 2 -26.52 7.112 -10.343 1 27.3 ? C1 RET 201 A 1 HETATM 2 C C2 RET . . . B 2 -26.899 6.449 -11.659 1 35.33 ? C2 RET 201 A 1 HETATM 3 C C3 RET . . . B 2 -26.4 5.019 -11.715 1 34.24 ? C3 RET 201 A 1 HETATM 4 C C4 RET . . . B 2 -24.88 5.066 -11.766 1 28.38 ? C4 RET 201 A 1 HETATM 5 C C5 RET . . . B 2 -24.338 5.923 -10.64 1 30.79 ? C5 RET 201 A 1 HETATM 6 C C6 RET . . . B 2 -25.066 6.839 -9.979 1 27.5 ? C6 RET 201 A 1 HETATM 7 C C7 RET . . . B 2 -24.362 7.607 -8.9 1 27.36 ? C7 RET 201 A 1 HETATM 8 C C8 RET . . . B 2 -24.953 8.152 -7.824 1 33.23 ? C8 RET 201 A 1 HETATM 9 C C9 RET . . . B 2 -24.217 8.902 -6.779 1 31.87 ? C9 RET 201 A 1 HETATM 10 C C10 RET . . . B 2 -24.915 9.721 -5.967 1 26.62 ? C10 RET 201 A 1 HETATM 11 C C11 RET . . . B 2 -24.346 10.535 -4.885 1 26.89 ? C11 RET 201 A 1 HETATM 12 C C12 RET . . . B 2 -25.188 11.326 -4.218 1 23.96 ? C12 RET 201 A 1 HETATM 13 C C13 RET . . . B 2 -24.788 12.215 -3.105 1 23.59 ? C13 RET 201 A 1 HETATM 14 C C14 RET . . . B 2 -25.727 12.935 -2.464 1 27.05 ? C14 RET 201 A 1 HETATM 15 C C15 RET . . . B 2 -25.394 13.839 -1.363 1 22.51 ? C15 RET 201 A 1 HETATM 16 C C16 RET . . . B 2 -27.451 6.599 -9.247 1 32.22 ? C16 RET 201 A 1 HETATM 17 C C17 RET . . . B 2 -26.685 8.614 -10.571 1 31.83 ? C17 RET 201 A 1 HETATM 18 C C18 RET . . . B 2 -22.9 5.72 -10.251 1 30.54 ? C18 RET 201 A 1 HETATM 19 C C19 RET . . . B 2 -22.731 8.723 -6.635 1 32.39 ? C19 RET 201 A 1 HETATM 20 C C20 RET . . . B 2 -23.347 12.322 -2.7 1 28.04 ? C20 RET 201 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 232 _model_server_stats.encode_time_ms 21 _model_server_stats.element_count 20 #