data_4YDB # _model_server_result.job_id Zx8mv1g7WAtBEAo7xPBzBg _model_server_result.datetime_utc '2024-11-24 15:52:30' _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 4ydb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4YDB # _exptl.entry_id 4YDB _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 4YDB _cell.length_a 58.655 _cell.length_b 58.655 _cell.length_c 100.352 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YDB _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 -87.9825 50.79672 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 1.26 _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 4YDB _atom_sites.fract_transf_matrix[1][1] 0.017049 _atom_sites.fract_transf_matrix[1][2] 0.009843 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019686 _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] 0.009965 _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 76 HOH HOH . C 3 HOH A 2 302 98 HOH HOH . C 3 HOH A 3 303 94 HOH HOH . C 3 HOH A 4 304 30 HOH HOH . C 3 HOH A 5 305 27 HOH HOH . C 3 HOH A 6 306 88 HOH HOH . C 3 HOH A 7 307 65 HOH HOH . C 3 HOH A 8 308 63 HOH HOH . C 3 HOH A 9 309 18 HOH HOH . C 3 HOH A 10 310 34 HOH HOH . C 3 HOH A 11 311 21 HOH HOH . C 3 HOH A 12 312 90 HOH HOH . C 3 HOH A 13 313 4 HOH HOH . C 3 HOH A 14 314 42 HOH HOH . C 3 HOH A 15 315 43 HOH HOH . C 3 HOH A 16 316 35 HOH HOH . C 3 HOH A 17 317 62 HOH HOH . C 3 HOH A 18 318 8 HOH HOH . C 3 HOH A 19 319 71 HOH HOH . C 3 HOH A 20 320 87 HOH HOH . C 3 HOH A 21 321 14 HOH HOH . C 3 HOH A 22 322 3 HOH HOH . C 3 HOH A 23 323 1 HOH HOH . C 3 HOH A 24 324 2 HOH HOH . C 3 HOH A 25 325 81 HOH HOH . C 3 HOH A 26 326 24 HOH HOH . C 3 HOH A 27 327 68 HOH HOH . C 3 HOH A 28 328 36 HOH HOH . C 3 HOH A 29 329 38 HOH HOH . C 3 HOH A 30 330 78 HOH HOH . C 3 HOH A 31 331 70 HOH HOH . C 3 HOH A 32 332 102 HOH HOH . C 3 HOH A 33 333 53 HOH HOH . C 3 HOH A 34 334 75 HOH HOH . C 3 HOH A 35 335 32 HOH HOH . C 3 HOH A 36 336 89 HOH HOH . C 3 HOH A 37 337 83 HOH HOH . C 3 HOH A 38 338 5 HOH HOH . C 3 HOH A 39 339 6 HOH HOH . C 3 HOH A 40 340 7 HOH HOH . C 3 HOH A 41 341 9 HOH HOH . C 3 HOH A 42 342 10 HOH HOH . C 3 HOH A 43 343 11 HOH HOH . C 3 HOH A 44 344 12 HOH HOH . C 3 HOH A 45 345 13 HOH HOH . C 3 HOH A 46 346 15 HOH HOH . C 3 HOH A 47 347 16 HOH HOH . C 3 HOH A 48 348 17 HOH HOH . C 3 HOH A 49 349 19 HOH HOH . C 3 HOH A 50 350 20 HOH HOH . C 3 HOH A 51 351 22 HOH HOH . C 3 HOH A 52 352 23 HOH HOH . C 3 HOH A 53 353 25 HOH HOH . C 3 HOH A 54 354 26 HOH HOH . C 3 HOH A 55 355 28 HOH HOH . C 3 HOH A 56 356 29 HOH HOH . C 3 HOH A 57 357 31 HOH HOH . C 3 HOH A 58 358 33 HOH HOH . C 3 HOH A 59 359 37 HOH HOH . C 3 HOH A 60 360 39 HOH HOH . C 3 HOH A 61 361 40 HOH HOH . C 3 HOH A 62 362 41 HOH HOH . C 3 HOH A 63 363 44 HOH HOH . C 3 HOH A 64 364 45 HOH HOH . C 3 HOH A 65 365 46 HOH HOH . C 3 HOH A 66 366 47 HOH HOH . C 3 HOH A 67 367 48 HOH HOH . C 3 HOH A 68 368 49 HOH HOH . C 3 HOH A 69 369 50 HOH HOH . C 3 HOH A 70 370 51 HOH HOH . C 3 HOH A 71 371 52 HOH HOH . C 3 HOH A 72 372 54 HOH HOH . C 3 HOH A 73 373 55 HOH HOH . C 3 HOH A 74 374 56 HOH HOH . C 3 HOH A 75 375 57 HOH HOH . C 3 HOH A 76 376 58 HOH HOH . C 3 HOH A 77 377 59 HOH HOH . C 3 HOH A 78 378 60 HOH HOH . C 3 HOH A 79 379 61 HOH HOH . C 3 HOH A 80 380 64 HOH HOH . C 3 HOH A 81 381 66 HOH HOH . C 3 HOH A 82 382 67 HOH HOH . C 3 HOH A 83 383 69 HOH HOH . C 3 HOH A 84 384 72 HOH HOH . C 3 HOH A 85 385 73 HOH HOH . C 3 HOH A 86 386 74 HOH HOH . C 3 HOH A 87 387 77 HOH HOH . C 3 HOH A 88 388 79 HOH HOH . C 3 HOH A 89 389 80 HOH HOH . C 3 HOH A 90 390 82 HOH HOH . C 3 HOH A 91 391 84 HOH HOH . C 3 HOH A 92 392 85 HOH HOH . C 3 HOH A 93 393 86 HOH HOH . C 3 HOH A 94 394 91 HOH HOH . C 3 HOH A 95 395 92 HOH HOH . C 3 HOH A 96 396 93 HOH HOH . C 3 HOH A 97 397 95 HOH HOH . C 3 HOH A 98 398 96 HOH HOH . C 3 HOH A 99 399 97 HOH HOH . C 3 HOH A 100 400 99 HOH HOH . C 3 HOH A 101 401 100 HOH HOH . C 3 HOH A 102 402 101 HOH HOH . C 3 HOH A 103 403 103 HOH HOH . C 3 HOH A 104 404 104 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 -39.777 19.228 6.318 1 54.27 ? C1 RET 201 A 1 HETATM 2 C C2 RET . . . B 2 -40.092 20.016 5.057 1 49.68 ? C2 RET 201 A 1 HETATM 3 C C3 RET . . . B 2 -41.584 20.187 4.863 1 53.9 ? C3 RET 201 A 1 HETATM 4 C C4 RET . . . B 2 -42.174 18.817 4.597 1 53.66 ? C4 RET 201 A 1 HETATM 5 C C5 RET . . . B 2 -41.923 17.984 5.824 1 53 ? C5 RET 201 A 1 HETATM 6 C C6 RET . . . B 2 -40.849 18.165 6.609 1 54.2 ? C6 RET 201 A 1 HETATM 7 C C7 RET . . . B 2 -40.779 17.245 7.776 1 56.9 ? C7 RET 201 A 1 HETATM 8 C C8 RET . . . B 2 -39.761 17.212 8.627 1 51.35 ? C8 RET 201 A 1 HETATM 9 C C9 RET . . . B 2 -39.69 16.303 9.773 1 56.75 ? C9 RET 201 A 1 HETATM 10 C C10 RET . . . B 2 -38.589 16.405 10.525 1 53.13 ? C10 RET 201 A 1 HETATM 11 C C11 RET . . . B 2 -38.352 15.566 11.683 1 52.9 ? C11 RET 201 A 1 HETATM 12 C C12 RET . . . B 2 -37.149 15.647 12.23 1 47.4 ? C12 RET 201 A 1 HETATM 13 C C13 RET . . . B 2 -36.841 14.818 13.396 1 45.37 ? C13 RET 201 A 1 HETATM 14 C C14 RET . . . B 2 -35.65 14.958 13.998 1 40.28 ? C14 RET 201 A 1 HETATM 15 C C15 RET . . . B 2 -35.325 14.134 15.153 1 47.64 ? C15 RET 201 A 1 HETATM 16 C C16 RET . . . B 2 -39.678 20.227 7.472 1 48.63 ? C16 RET 201 A 1 HETATM 17 C C17 RET . . . B 2 -38.411 18.591 6.052 1 52.17 ? C17 RET 201 A 1 HETATM 18 C C18 RET . . . B 2 -42.934 16.925 6.164 1 50.79 ? C18 RET 201 A 1 HETATM 19 C C19 RET . . . B 2 -40.785 15.313 10.063 1 56.33 ? C19 RET 201 A 1 HETATM 20 C C20 RET . . . B 2 -37.868 13.832 13.875 1 53.68 ? C20 RET 201 A 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #