data_4YBU # _model_server_result.job_id PTOkk_D2S2Dz-KM45XWxGg _model_server_result.datetime_utc '2024-12-29 19:20:07' _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 4ybu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4YBU # _exptl.entry_id 4YBU _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 4YBU _cell.length_a 58.326 _cell.length_b 58.326 _cell.length_c 99.936 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YBU _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 -33.312 # _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 1.258 _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 4YBU _atom_sites.fract_transf_matrix[1][1] 0.017145 _atom_sites.fract_transf_matrix[1][2] 0.009899 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019797 _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] 0.010006 _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 27 HOH HOH . C 3 HOH A 2 302 56 HOH HOH . C 3 HOH A 3 303 3 HOH HOH . C 3 HOH A 4 304 140 HOH HOH . C 3 HOH A 5 305 128 HOH HOH . C 3 HOH A 6 306 53 HOH HOH . C 3 HOH A 7 307 66 HOH HOH . C 3 HOH A 8 308 127 HOH HOH . C 3 HOH A 9 309 124 HOH HOH . C 3 HOH A 10 310 21 HOH HOH . C 3 HOH A 11 311 16 HOH HOH . C 3 HOH A 12 312 87 HOH HOH . C 3 HOH A 13 313 70 HOH HOH . C 3 HOH A 14 314 4 HOH HOH . C 3 HOH A 15 315 130 HOH HOH . C 3 HOH A 16 316 37 HOH HOH . C 3 HOH A 17 317 57 HOH HOH . C 3 HOH A 18 318 120 HOH HOH . C 3 HOH A 19 319 43 HOH HOH . C 3 HOH A 20 320 12 HOH HOH . C 3 HOH A 21 321 41 HOH HOH . C 3 HOH A 22 322 59 HOH HOH . C 3 HOH A 23 323 11 HOH HOH . C 3 HOH A 24 324 122 HOH HOH . C 3 HOH A 25 325 47 HOH HOH . C 3 HOH A 26 326 138 HOH HOH . C 3 HOH A 27 327 61 HOH HOH . C 3 HOH A 28 328 17 HOH HOH . C 3 HOH A 29 329 123 HOH HOH . C 3 HOH A 30 330 141 HOH HOH . C 3 HOH A 31 331 68 HOH HOH . C 3 HOH A 32 332 14 HOH HOH . C 3 HOH A 33 333 121 HOH HOH . C 3 HOH A 34 334 105 HOH HOH . C 3 HOH A 35 335 55 HOH HOH . C 3 HOH A 36 336 60 HOH HOH . C 3 HOH A 37 337 15 HOH HOH . C 3 HOH A 38 338 83 HOH HOH . C 3 HOH A 39 339 34 HOH HOH . C 3 HOH A 40 340 45 HOH HOH . C 3 HOH A 41 341 75 HOH HOH . C 3 HOH A 42 342 116 HOH HOH . C 3 HOH A 43 343 19 HOH HOH . C 3 HOH A 44 344 40 HOH HOH . C 3 HOH A 45 345 107 HOH HOH . C 3 HOH A 46 346 108 HOH HOH . C 3 HOH A 47 347 1 HOH HOH . C 3 HOH A 48 348 2 HOH HOH . C 3 HOH A 49 349 5 HOH HOH . C 3 HOH A 50 350 6 HOH HOH . C 3 HOH A 51 351 7 HOH HOH . C 3 HOH A 52 352 8 HOH HOH . C 3 HOH A 53 353 9 HOH HOH . C 3 HOH A 54 354 10 HOH HOH . C 3 HOH A 55 355 13 HOH HOH . C 3 HOH A 56 356 18 HOH HOH . C 3 HOH A 57 357 22 HOH HOH . C 3 HOH A 58 358 23 HOH HOH . C 3 HOH A 59 359 24 HOH HOH . C 3 HOH A 60 360 25 HOH HOH . C 3 HOH A 61 361 26 HOH HOH . C 3 HOH A 62 362 28 HOH HOH . C 3 HOH A 63 363 29 HOH HOH . C 3 HOH A 64 364 30 HOH HOH . C 3 HOH A 65 365 31 HOH HOH . C 3 HOH A 66 366 32 HOH HOH . C 3 HOH A 67 367 33 HOH HOH . C 3 HOH A 68 368 35 HOH HOH . C 3 HOH A 69 369 36 HOH HOH . C 3 HOH A 70 370 38 HOH HOH . C 3 HOH A 71 371 39 HOH HOH . C 3 HOH A 72 372 42 HOH HOH . C 3 HOH A 73 373 44 HOH HOH . C 3 HOH A 74 374 46 HOH HOH . C 3 HOH A 75 375 48 HOH HOH . C 3 HOH A 76 376 49 HOH HOH . C 3 HOH A 77 377 50 HOH HOH . C 3 HOH A 78 378 51 HOH HOH . C 3 HOH A 79 379 52 HOH HOH . C 3 HOH A 80 380 54 HOH HOH . C 3 HOH A 81 381 58 HOH HOH . C 3 HOH A 82 382 62 HOH HOH . C 3 HOH A 83 383 63 HOH HOH . C 3 HOH A 84 384 64 HOH HOH . C 3 HOH A 85 385 65 HOH HOH . C 3 HOH A 86 386 67 HOH HOH . C 3 HOH A 87 387 69 HOH HOH . C 3 HOH A 88 388 71 HOH HOH . C 3 HOH A 89 389 72 HOH HOH . C 3 HOH A 90 390 73 HOH HOH . C 3 HOH A 91 391 74 HOH HOH . C 3 HOH A 92 392 76 HOH HOH . C 3 HOH A 93 393 77 HOH HOH . C 3 HOH A 94 394 78 HOH HOH . C 3 HOH A 95 395 79 HOH HOH . C 3 HOH A 96 396 80 HOH HOH . C 3 HOH A 97 397 81 HOH HOH . C 3 HOH A 98 398 82 HOH HOH . C 3 HOH A 99 399 84 HOH HOH . C 3 HOH A 100 400 85 HOH HOH . C 3 HOH A 101 401 86 HOH HOH . C 3 HOH A 102 402 88 HOH HOH . C 3 HOH A 103 403 90 HOH HOH . C 3 HOH A 104 404 91 HOH HOH . C 3 HOH A 105 405 92 HOH HOH . C 3 HOH A 106 406 94 HOH HOH . C 3 HOH A 107 407 95 HOH HOH . C 3 HOH A 108 408 97 HOH HOH . C 3 HOH A 109 409 98 HOH HOH . C 3 HOH A 110 410 99 HOH HOH . C 3 HOH A 111 411 100 HOH HOH . C 3 HOH A 112 412 101 HOH HOH . C 3 HOH A 113 413 103 HOH HOH . C 3 HOH A 114 414 104 HOH HOH . C 3 HOH A 115 415 106 HOH HOH . C 3 HOH A 116 416 109 HOH HOH . C 3 HOH A 117 417 110 HOH HOH . C 3 HOH A 118 418 111 HOH HOH . C 3 HOH A 119 419 113 HOH HOH . C 3 HOH A 120 420 115 HOH HOH . C 3 HOH A 121 421 119 HOH HOH . C 3 HOH A 122 422 125 HOH HOH . C 3 HOH A 123 423 126 HOH HOH . C 3 HOH A 124 424 129 HOH HOH . C 3 HOH A 125 425 131 HOH HOH . C 3 HOH A 126 426 132 HOH HOH . C 3 HOH A 127 427 133 HOH HOH . C 3 HOH A 128 428 134 HOH HOH . C 3 HOH A 129 429 135 HOH HOH . C 3 HOH A 130 430 136 HOH HOH . C 3 HOH A 131 431 137 HOH HOH . C 3 HOH A 132 432 139 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 26.007 -6.051 -10.281 1 51.58 ? C1 RET 201 A 1 HETATM 2 C C2 RET . . . B 2 26.414 -5.604 -11.671 1 47.7 ? C2 RET 201 A 1 HETATM 3 C C3 RET . . . B 2 25.489 -4.52 -12.178 1 49.97 ? C3 RET 201 A 1 HETATM 4 C C4 RET . . . B 2 24.108 -5.101 -12.382 1 49.34 ? C4 RET 201 A 1 HETATM 5 C C5 RET . . . B 2 23.66 -5.79 -11.116 1 53.05 ? C5 RET 201 A 1 HETATM 6 C C6 RET . . . B 2 24.494 -6.232 -10.168 1 49.89 ? C6 RET 201 A 1 HETATM 7 C C7 RET . . . B 2 23.82 -6.875 -9.007 1 45 ? C7 RET 201 A 1 HETATM 8 C C8 RET . . . B 2 24.432 -7.436 -7.97 1 49.96 ? C8 RET 201 A 1 HETATM 9 C C9 RET . . . B 2 23.675 -8.048 -6.87 1 47.51 ? C9 RET 201 A 1 HETATM 10 C C10 RET . . . B 2 24.284 -9.015 -6.172 1 44.08 ? C10 RET 201 A 1 HETATM 11 C C11 RET . . . B 2 23.649 -9.706 -5.062 1 45.73 ? C11 RET 201 A 1 HETATM 12 C C12 RET . . . B 2 24.275 -10.772 -4.575 1 42.64 ? C12 RET 201 A 1 HETATM 13 C C13 RET . . . B 2 23.677 -11.505 -3.45 1 40.04 ? C13 RET 201 A 1 HETATM 14 C C14 RET . . . B 2 24.438 -12.314 -2.7 1 33.55 ? C14 RET 201 A 1 HETATM 15 C C15 RET . . . B 2 23.8 -13.009 -1.59 1 38.23 ? C15 RET 201 A 1 HETATM 16 C C16 RET . . . B 2 26.409 -4.996 -9.261 1 50.85 ? C16 RET 201 A 1 HETATM 17 C C17 RET . . . B 2 26.797 -7.336 -10.073 1 44.34 ? C17 RET 201 A 1 HETATM 18 C C18 RET . . . B 2 22.19 -5.993 -10.931 1 50.9 ? C18 RET 201 A 1 HETATM 19 C C19 RET . . . B 2 22.284 -7.577 -6.557 1 43.34 ? C19 RET 201 A 1 HETATM 20 C C20 RET . . . B 2 22.212 -11.342 -3.155 1 46.22 ? C20 RET 201 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 20 #