data_4YBP # _model_server_result.job_id CtEtL1VrU2oI126746mseg _model_server_result.datetime_utc '2024-11-28 08:33:29' _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 4ybp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4YBP # _exptl.entry_id 4YBP _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 4YBP _cell.length_a 58.552 _cell.length_b 58.552 _cell.length_c 99.392 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YBP _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' 4_465 y-1,x+1,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 -87.828 50.707519 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 # _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 1.268 _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 4YBP _atom_sites.fract_transf_matrix[1][1] 0.017079 _atom_sites.fract_transf_matrix[1][2] 0.00986 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019721 _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] 0.010061 _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 23 HOH HOH . C 3 HOH A 2 302 40 HOH HOH . C 3 HOH A 3 303 47 HOH HOH . C 3 HOH A 4 304 57 HOH HOH . C 3 HOH A 5 305 46 HOH HOH . C 3 HOH A 6 306 111 HOH HOH . C 3 HOH A 7 307 164 HOH HOH . C 3 HOH A 8 308 50 HOH HOH . C 3 HOH A 9 309 31 HOH HOH . C 3 HOH A 10 310 107 HOH HOH . C 3 HOH A 11 311 103 HOH HOH . C 3 HOH A 12 312 28 HOH HOH . C 3 HOH A 13 313 138 HOH HOH . C 3 HOH A 14 314 76 HOH HOH . C 3 HOH A 15 315 139 HOH HOH . C 3 HOH A 16 316 8 HOH HOH . C 3 HOH A 17 317 11 HOH HOH . C 3 HOH A 18 318 123 HOH HOH . C 3 HOH A 19 319 36 HOH HOH . C 3 HOH A 20 320 67 HOH HOH . C 3 HOH A 21 321 180 HOH HOH . C 3 HOH A 22 322 6 HOH HOH . C 3 HOH A 23 323 125 HOH HOH . C 3 HOH A 24 324 16 HOH HOH . C 3 HOH A 25 325 9 HOH HOH . C 3 HOH A 26 326 65 HOH HOH . C 3 HOH A 27 327 171 HOH HOH . C 3 HOH A 28 328 169 HOH HOH . C 3 HOH A 29 329 81 HOH HOH . C 3 HOH A 30 330 51 HOH HOH . C 3 HOH A 31 331 174 HOH HOH . C 3 HOH A 32 332 90 HOH HOH . C 3 HOH A 33 333 1 HOH HOH . C 3 HOH A 34 334 13 HOH HOH . C 3 HOH A 35 335 74 HOH HOH . C 3 HOH A 36 336 2 HOH HOH . C 3 HOH A 37 337 165 HOH HOH . C 3 HOH A 38 338 15 HOH HOH . C 3 HOH A 39 339 99 HOH HOH . C 3 HOH A 40 340 149 HOH HOH . C 3 HOH A 41 341 45 HOH HOH . C 3 HOH A 42 342 163 HOH HOH . C 3 HOH A 43 343 161 HOH HOH . C 3 HOH A 44 344 170 HOH HOH . C 3 HOH A 45 345 71 HOH HOH . C 3 HOH A 46 346 177 HOH HOH . C 3 HOH A 47 347 93 HOH HOH . C 3 HOH A 48 348 179 HOH HOH . C 3 HOH A 49 349 144 HOH HOH . C 3 HOH A 50 350 91 HOH HOH . C 3 HOH A 51 351 29 HOH HOH . C 3 HOH A 52 352 146 HOH HOH . C 3 HOH A 53 353 85 HOH HOH . C 3 HOH A 54 354 113 HOH HOH . C 3 HOH A 55 355 148 HOH HOH . C 3 HOH A 56 356 127 HOH HOH . C 3 HOH A 57 357 3 HOH HOH . C 3 HOH A 58 358 4 HOH HOH . C 3 HOH A 59 359 5 HOH HOH . C 3 HOH A 60 360 7 HOH HOH . C 3 HOH A 61 361 10 HOH HOH . C 3 HOH A 62 362 12 HOH HOH . C 3 HOH A 63 363 14 HOH HOH . C 3 HOH A 64 364 17 HOH HOH . C 3 HOH A 65 365 18 HOH HOH . C 3 HOH A 66 366 19 HOH HOH . C 3 HOH A 67 367 20 HOH HOH . C 3 HOH A 68 368 21 HOH HOH . C 3 HOH A 69 369 22 HOH HOH . C 3 HOH A 70 370 24 HOH HOH . C 3 HOH A 71 371 25 HOH HOH . C 3 HOH A 72 372 26 HOH HOH . C 3 HOH A 73 373 27 HOH HOH . C 3 HOH A 74 374 30 HOH HOH . C 3 HOH A 75 375 32 HOH HOH . C 3 HOH A 76 376 33 HOH HOH . C 3 HOH A 77 377 34 HOH HOH . C 3 HOH A 78 378 35 HOH HOH . C 3 HOH A 79 379 37 HOH HOH . C 3 HOH A 80 380 38 HOH HOH . C 3 HOH A 81 381 39 HOH HOH . C 3 HOH A 82 382 41 HOH HOH . C 3 HOH A 83 383 42 HOH HOH . C 3 HOH A 84 384 43 HOH HOH . C 3 HOH A 85 385 44 HOH HOH . C 3 HOH A 86 386 48 HOH HOH . C 3 HOH A 87 387 49 HOH HOH . C 3 HOH A 88 388 52 HOH HOH . C 3 HOH A 89 389 53 HOH HOH . C 3 HOH A 90 390 54 HOH HOH . C 3 HOH A 91 391 55 HOH HOH . C 3 HOH A 92 392 56 HOH HOH . C 3 HOH A 93 393 58 HOH HOH . C 3 HOH A 94 394 59 HOH HOH . C 3 HOH A 95 395 60 HOH HOH . C 3 HOH A 96 396 61 HOH HOH . C 3 HOH A 97 397 62 HOH HOH . C 3 HOH A 98 398 63 HOH HOH . C 3 HOH A 99 399 64 HOH HOH . C 3 HOH A 100 400 66 HOH HOH . C 3 HOH A 101 401 68 HOH HOH . C 3 HOH A 102 402 69 HOH HOH . C 3 HOH A 103 403 70 HOH HOH . C 3 HOH A 104 404 72 HOH HOH . C 3 HOH A 105 405 73 HOH HOH . C 3 HOH A 106 406 75 HOH HOH . C 3 HOH A 107 407 77 HOH HOH . C 3 HOH A 108 408 78 HOH HOH . C 3 HOH A 109 409 79 HOH HOH . C 3 HOH A 110 410 80 HOH HOH . C 3 HOH A 111 411 82 HOH HOH . C 3 HOH A 112 412 83 HOH HOH . C 3 HOH A 113 413 84 HOH HOH . C 3 HOH A 114 414 86 HOH HOH . C 3 HOH A 115 415 87 HOH HOH . C 3 HOH A 116 416 88 HOH HOH . C 3 HOH A 117 417 89 HOH HOH . C 3 HOH A 118 418 92 HOH HOH . C 3 HOH A 119 419 94 HOH HOH . C 3 HOH A 120 420 95 HOH HOH . C 3 HOH A 121 421 96 HOH HOH . C 3 HOH A 122 422 97 HOH HOH . C 3 HOH A 123 423 98 HOH HOH . C 3 HOH A 124 424 100 HOH HOH . C 3 HOH A 125 425 101 HOH HOH . C 3 HOH A 126 426 102 HOH HOH . C 3 HOH A 127 427 104 HOH HOH . C 3 HOH A 128 428 105 HOH HOH . C 3 HOH A 129 429 106 HOH HOH . C 3 HOH A 130 430 108 HOH HOH . C 3 HOH A 131 431 109 HOH HOH . C 3 HOH A 132 432 110 HOH HOH . C 3 HOH A 133 433 112 HOH HOH . C 3 HOH A 134 434 114 HOH HOH . C 3 HOH A 135 435 115 HOH HOH . C 3 HOH A 136 436 116 HOH HOH . C 3 HOH A 137 437 117 HOH HOH . C 3 HOH A 138 438 118 HOH HOH . C 3 HOH A 139 439 119 HOH HOH . C 3 HOH A 140 440 120 HOH HOH . C 3 HOH A 141 441 121 HOH HOH . C 3 HOH A 142 442 122 HOH HOH . C 3 HOH A 143 443 124 HOH HOH . C 3 HOH A 144 444 126 HOH HOH . C 3 HOH A 145 445 128 HOH HOH . C 3 HOH A 146 446 129 HOH HOH . C 3 HOH A 147 447 130 HOH HOH . C 3 HOH A 148 448 131 HOH HOH . C 3 HOH A 149 449 132 HOH HOH . C 3 HOH A 150 450 133 HOH HOH . C 3 HOH A 151 451 134 HOH HOH . C 3 HOH A 152 452 135 HOH HOH . C 3 HOH A 153 453 136 HOH HOH . C 3 HOH A 154 454 137 HOH HOH . C 3 HOH A 155 455 140 HOH HOH . C 3 HOH A 156 456 141 HOH HOH . C 3 HOH A 157 457 142 HOH HOH . C 3 HOH A 158 458 143 HOH HOH . C 3 HOH A 159 459 145 HOH HOH . C 3 HOH A 160 460 147 HOH HOH . C 3 HOH A 161 461 150 HOH HOH . C 3 HOH A 162 462 151 HOH HOH . C 3 HOH A 163 463 152 HOH HOH . C 3 HOH A 164 464 153 HOH HOH . C 3 HOH A 165 465 154 HOH HOH . C 3 HOH A 166 466 155 HOH HOH . C 3 HOH A 167 467 156 HOH HOH . C 3 HOH A 168 468 157 HOH HOH . C 3 HOH A 169 469 158 HOH HOH . C 3 HOH A 170 470 159 HOH HOH . C 3 HOH A 171 471 160 HOH HOH . C 3 HOH A 172 472 162 HOH HOH . C 3 HOH A 173 473 166 HOH HOH . C 3 HOH A 174 474 167 HOH HOH . C 3 HOH A 175 475 168 HOH HOH . C 3 HOH A 176 476 172 HOH HOH . C 3 HOH A 177 477 173 HOH HOH . C 3 HOH A 178 478 175 HOH HOH . C 3 HOH A 179 479 176 HOH HOH . C 3 HOH A 180 480 178 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 -39.592 19.344 6.865 1 51.92 ? C1 RET 201 A 1 HETATM 2 C C2 RET . . . B 2 -40.136 20.243 5.757 1 37.34 ? C2 RET 201 A 1 HETATM 3 C C3 RET . . . B 2 -41.623 20.072 5.536 1 51.64 ? C3 RET 201 A 1 HETATM 4 C C4 RET . . . B 2 -41.836 18.628 5.127 1 46.72 ? C4 RET 201 A 1 HETATM 5 C C5 RET . . . B 2 -41.431 17.765 6.298 1 42.14 ? C5 RET 201 A 1 HETATM 6 C C6 RET . . . B 2 -40.413 18.079 7.108 1 42.71 ? C6 RET 201 A 1 HETATM 7 C C7 RET . . . B 2 -40.136 17.125 8.233 1 40.44 ? C7 RET 201 A 1 HETATM 8 C C8 RET . . . B 2 -39.062 17.129 9.038 1 40.86 ? C8 RET 201 A 1 HETATM 9 C C9 RET . . . B 2 -38.835 16.167 10.143 1 37.17 ? C9 RET 201 A 1 HETATM 10 C C10 RET . . . B 2 -37.739 16.328 10.914 1 36.45 ? C10 RET 201 A 1 HETATM 11 C C11 RET . . . B 2 -37.36 15.461 12.037 1 30.04 ? C11 RET 201 A 1 HETATM 12 C C12 RET . . . B 2 -36.226 15.762 12.681 1 30.29 ? C12 RET 201 A 1 HETATM 13 C C13 RET . . . B 2 -35.682 14.995 13.827 1 25.1 ? C13 RET 201 A 1 HETATM 14 C C14 RET . . . B 2 -34.525 15.404 14.383 1 23.98 ? C14 RET 201 A 1 HETATM 15 C C15 RET . . . B 2 -33.885 14.724 15.507 1 21.82 ? C15 RET 201 A 1 HETATM 16 C C16 RET . . . B 2 -39.539 20.178 8.143 1 44.2 ? C16 RET 201 A 1 HETATM 17 C C17 RET . . . B 2 -38.219 18.914 6.377 1 45.19 ? C17 RET 201 A 1 HETATM 18 C C18 RET . . . B 2 -42.222 16.52 6.557 1 49.5 ? C18 RET 201 A 1 HETATM 19 C C19 RET . . . B 2 -39.806 15.047 10.39 1 48.11 ? C19 RET 201 A 1 HETATM 20 C C20 RET . . . B 2 -36.405 13.78 14.339 1 35.39 ? C20 RET 201 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #