data_1OPB # _model_server_result.job_id FZ2df-DTUYYU2Ux-OQKg2w _model_server_result.datetime_utc '2024-11-23 04:40:59' _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 1opb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":134}' # _entry.id 1OPB # _exptl.entry_id 1OPB _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 92.6 _cell.angle_beta 102.9 _cell.angle_gamma 92.5 _cell.entry_id 1OPB _cell.length_a 37 _cell.length_b 64.6 _cell.length_c 56 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1OPB _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 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 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I 1 1 B,F,J 2 1 C,G,K 3 1 D,H,L 4 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _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 260 n n C1 C6 RET sing 261 n n C1 C16 RET sing 262 n n C1 C17 RET sing 263 n n C2 C3 RET sing 264 n n C2 H21 RET sing 265 n n C2 H22 RET sing 266 n n C3 C4 RET sing 267 n n C3 H31 RET sing 268 n n C3 H32 RET sing 269 n n C4 C5 RET sing 270 n n C4 H41 RET sing 271 n n C4 H42 RET sing 272 n n C5 C6 RET doub 273 n n C5 C18 RET sing 274 n n C6 C7 RET sing 275 n n C7 C8 RET doub 276 e n C7 H7 RET sing 277 n n C8 C9 RET sing 278 n n C8 H8 RET sing 279 n n C9 C10 RET doub 280 e n C9 C19 RET sing 281 n n C10 C11 RET sing 282 n n C10 H10 RET sing 283 n n C11 C12 RET doub 284 e n C11 H11 RET sing 285 n n C12 C13 RET sing 286 n n C12 H12 RET sing 287 n n C13 C14 RET doub 288 e n C13 C20 RET sing 289 n n C14 C15 RET sing 290 n n C14 H14 RET sing 291 n n C15 O1 RET doub 292 n n C15 H15 RET sing 293 n n C16 H161 RET sing 294 n n C16 H162 RET sing 295 n n C16 H163 RET sing 296 n n C17 H171 RET sing 297 n n C17 H172 RET sing 298 n n C17 H173 RET sing 299 n n C18 H181 RET sing 300 n n C18 H182 RET sing 301 n n C18 H183 RET sing 302 n n C19 H191 RET sing 303 n n C19 H192 RET sing 304 n n C19 H193 RET sing 305 n n C20 H201 RET sing 306 n n C20 H202 RET sing 307 n n C20 H203 RET sing 308 n n # _atom_sites.entry_id 1OPB _atom_sites.fract_transf_matrix[1][1] 0.027027 _atom_sites.fract_transf_matrix[1][2] 0.00118 _atom_sites.fract_transf_matrix[1][3] 0.006267 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015495 _atom_sites.fract_transf_matrix[2][3] 0.000878 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.018349 _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 E 2 RET A 1 134 134 RET RET . F 2 RET B 1 134 134 RET RET . G 2 RET C 1 134 134 RET RET . H 2 RET D 1 134 134 RET RET . I 3 HOH A 1 135 100 HOH HOH . I 3 HOH A 2 136 101 HOH HOH . I 3 HOH A 3 137 102 HOH HOH . I 3 HOH A 4 138 104 HOH HOH . I 3 HOH A 5 139 105 HOH HOH . I 3 HOH A 6 140 106 HOH HOH . I 3 HOH A 7 141 107 HOH HOH . I 3 HOH A 8 142 108 HOH HOH . I 3 HOH A 9 143 109 HOH HOH . I 3 HOH A 10 144 110 HOH HOH . I 3 HOH A 11 145 111 HOH HOH . I 3 HOH A 12 146 112 HOH HOH . I 3 HOH A 13 147 113 HOH HOH . I 3 HOH A 14 148 114 HOH HOH . I 3 HOH A 15 149 117 HOH HOH . I 3 HOH A 16 150 133 HOH HOH . I 3 HOH A 17 151 122 HOH HOH . I 3 HOH A 18 152 123 HOH HOH . I 3 HOH A 19 153 124 HOH HOH . I 3 HOH A 20 154 125 HOH HOH . I 3 HOH A 21 155 126 HOH HOH . I 3 HOH A 22 156 130 HOH HOH . I 3 HOH A 23 157 132 HOH HOH . I 3 HOH A 24 158 131 HOH HOH . I 3 HOH A 25 159 135 HOH HOH . I 3 HOH A 26 160 138 HOH HOH . I 3 HOH A 27 161 139 HOH HOH . I 3 HOH A 28 162 141 HOH HOH . I 3 HOH A 29 163 143 HOH HOH . I 3 HOH A 30 164 144 HOH HOH . I 3 HOH A 31 165 162 HOH HOH . I 3 HOH A 32 166 165 HOH HOH . I 3 HOH A 33 167 176 HOH HOH . I 3 HOH A 34 168 195 HOH HOH . I 3 HOH A 35 169 219 HOH HOH . J 3 HOH B 1 135 119 HOH HOH . J 3 HOH B 2 136 200 HOH HOH . J 3 HOH B 3 137 201 HOH HOH . J 3 HOH B 4 138 202 HOH HOH . J 3 HOH B 5 139 206 HOH HOH . J 3 HOH B 6 140 207 HOH HOH . J 3 HOH B 7 141 209 HOH HOH . J 3 HOH B 8 142 210 HOH HOH . J 3 HOH B 9 143 214 HOH HOH . J 3 HOH B 10 144 217 HOH HOH . J 3 HOH B 11 145 218 HOH HOH . J 3 HOH B 12 146 223 HOH HOH . J 3 HOH B 13 147 224 HOH HOH . J 3 HOH B 14 148 225 HOH HOH . J 3 HOH B 15 149 230 HOH HOH . J 3 HOH B 16 150 231 HOH HOH . J 3 HOH B 17 151 232 HOH HOH . J 3 HOH B 18 152 233 HOH HOH . J 3 HOH B 19 153 235 HOH HOH . J 3 HOH B 20 154 237 HOH HOH . J 3 HOH B 21 155 241 HOH HOH . J 3 HOH B 22 156 242 HOH HOH . J 3 HOH B 23 157 243 HOH HOH . J 3 HOH B 24 158 247 HOH HOH . J 3 HOH B 25 159 255 HOH HOH . J 3 HOH B 26 160 257 HOH HOH . J 3 HOH B 27 161 259 HOH HOH . J 3 HOH B 28 162 260 HOH HOH . J 3 HOH B 29 163 261 HOH HOH . J 3 HOH B 30 164 267 HOH HOH . J 3 HOH B 31 165 268 HOH HOH . J 3 HOH B 32 166 275 HOH HOH . J 3 HOH B 33 167 276 HOH HOH . J 3 HOH B 34 168 282 HOH HOH . J 3 HOH B 35 169 288 HOH HOH . J 3 HOH B 36 170 292 HOH HOH . K 3 HOH C 1 300 300 HOH HOH . K 3 HOH C 2 302 302 HOH HOH . K 3 HOH C 3 303 303 HOH HOH . K 3 HOH C 4 306 306 HOH HOH . K 3 HOH C 5 307 307 HOH HOH . K 3 HOH C 6 309 309 HOH HOH . K 3 HOH C 7 310 310 HOH HOH . K 3 HOH C 8 314 314 HOH HOH . K 3 HOH C 9 316 316 HOH HOH . K 3 HOH C 10 317 317 HOH HOH . K 3 HOH C 11 318 318 HOH HOH . K 3 HOH C 12 319 319 HOH HOH . K 3 HOH C 13 320 320 HOH HOH . K 3 HOH C 14 323 323 HOH HOH . K 3 HOH C 15 324 324 HOH HOH . K 3 HOH C 16 325 325 HOH HOH . K 3 HOH C 17 328 328 HOH HOH . K 3 HOH C 18 330 330 HOH HOH . K 3 HOH C 19 331 331 HOH HOH . K 3 HOH C 20 332 332 HOH HOH . K 3 HOH C 21 333 333 HOH HOH . K 3 HOH C 22 335 335 HOH HOH . K 3 HOH C 23 337 337 HOH HOH . K 3 HOH C 24 341 341 HOH HOH . K 3 HOH C 25 343 343 HOH HOH . K 3 HOH C 26 344 344 HOH HOH . K 3 HOH C 27 349 349 HOH HOH . K 3 HOH C 28 351 351 HOH HOH . K 3 HOH C 29 352 352 HOH HOH . K 3 HOH C 30 356 356 HOH HOH . K 3 HOH C 31 357 357 HOH HOH . K 3 HOH C 32 358 358 HOH HOH . K 3 HOH C 33 359 359 HOH HOH . K 3 HOH C 34 368 368 HOH HOH . K 3 HOH C 35 369 369 HOH HOH . K 3 HOH C 36 370 370 HOH HOH . K 3 HOH C 37 371 371 HOH HOH . K 3 HOH C 38 375 375 HOH HOH . K 3 HOH C 39 376 376 HOH HOH . K 3 HOH C 40 418 418 HOH HOH . L 3 HOH D 1 400 400 HOH HOH . L 3 HOH D 2 402 402 HOH HOH . L 3 HOH D 3 403 403 HOH HOH . L 3 HOH D 4 404 404 HOH HOH . L 3 HOH D 5 406 406 HOH HOH . L 3 HOH D 6 408 408 HOH HOH . L 3 HOH D 7 409 409 HOH HOH . L 3 HOH D 8 410 410 HOH HOH . L 3 HOH D 9 411 411 HOH HOH . L 3 HOH D 10 414 414 HOH HOH . L 3 HOH D 11 417 417 HOH HOH . L 3 HOH D 12 419 419 HOH HOH . L 3 HOH D 13 422 422 HOH HOH . L 3 HOH D 14 423 423 HOH HOH . L 3 HOH D 15 424 424 HOH HOH . L 3 HOH D 16 427 427 HOH HOH . L 3 HOH D 17 428 428 HOH HOH . L 3 HOH D 18 430 430 HOH HOH . L 3 HOH D 19 431 431 HOH HOH . L 3 HOH D 20 432 432 HOH HOH . L 3 HOH D 21 433 433 HOH HOH . L 3 HOH D 22 434 434 HOH HOH . L 3 HOH D 23 435 435 HOH HOH . L 3 HOH D 24 436 436 HOH HOH . L 3 HOH D 25 437 437 HOH HOH . L 3 HOH D 26 439 439 HOH HOH . L 3 HOH D 27 440 440 HOH HOH . L 3 HOH D 28 441 441 HOH HOH . L 3 HOH D 29 443 443 HOH HOH . L 3 HOH D 30 445 445 HOH HOH . L 3 HOH D 31 446 446 HOH HOH . L 3 HOH D 32 447 447 HOH HOH . L 3 HOH D 33 448 448 HOH HOH . L 3 HOH D 34 463 463 HOH HOH . L 3 HOH D 35 464 464 HOH HOH . L 3 HOH D 36 465 465 HOH HOH . L 3 HOH D 37 466 466 HOH HOH . L 3 HOH D 38 467 467 HOH HOH . L 3 HOH D 39 468 468 HOH HOH . L 3 HOH D 40 472 472 HOH HOH . L 3 HOH D 41 473 473 HOH HOH . L 3 HOH D 42 474 474 HOH HOH . L 3 HOH D 43 476 476 HOH HOH . L 3 HOH D 44 489 489 HOH HOH . L 3 HOH D 45 493 493 HOH HOH . L 3 HOH D 46 496 496 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 . . . G 2 19.398 14.473 25.718 1 40.73 ? C1 RET 134 C 1 HETATM 2 C C2 RET . . . G 2 19.974 13.097 26.127 1 38.29 ? C2 RET 134 C 1 HETATM 3 C C3 RET . . . G 2 21.267 13.142 26.702 1 39.26 ? C3 RET 134 C 1 HETATM 4 C C4 RET . . . G 2 22.293 13.816 25.855 1 40.08 ? C4 RET 134 C 1 HETATM 5 C C5 RET . . . G 2 21.752 14.837 24.886 1 39.46 ? C5 RET 134 C 1 HETATM 6 C C6 RET . . . G 2 20.445 15.153 24.796 1 39.75 ? C6 RET 134 C 1 HETATM 7 C C7 RET . . . G 2 19.971 16.162 23.791 1 39.4 ? C7 RET 134 C 1 HETATM 8 C C8 RET . . . G 2 19.31 17.305 23.965 1 37.39 ? C8 RET 134 C 1 HETATM 9 C C9 RET . . . G 2 18.889 18.226 22.906 1 38.63 ? C9 RET 134 C 1 HETATM 10 C C10 RET . . . G 2 17.844 19.027 23.197 1 33.49 ? C10 RET 134 C 1 HETATM 11 C C11 RET . . . G 2 17.211 20.013 22.36 1 35.68 ? C11 RET 134 C 1 HETATM 12 C C12 RET . . . G 2 16.196 20.771 22.764 1 36.8 ? C12 RET 134 C 1 HETATM 13 C C13 RET . . . G 2 15.465 21.783 21.999 1 38.8 ? C13 RET 134 C 1 HETATM 14 C C14 RET . . . G 2 14.236 22.054 22.475 1 42.28 ? C14 RET 134 C 1 HETATM 15 C C15 RET . . . G 2 13.255 22.986 21.946 1 44.4 ? C15 RET 134 C 1 HETATM 16 O O1 RET . . . G 2 12.022 22.577 21.382 1 47.81 ? O1 RET 134 C 1 HETATM 17 C C16 RET . . . G 2 18.048 14.172 25.068 1 41.21 ? C16 RET 134 C 1 HETATM 18 C C17 RET . . . G 2 19.107 15.318 26.961 1 38.68 ? C17 RET 134 C 1 HETATM 19 C C18 RET . . . G 2 22.88 15.475 24.103 1 36.71 ? C18 RET 134 C 1 HETATM 20 C C19 RET . . . G 2 19.951 18.611 21.924 1 37.61 ? C19 RET 134 C 1 HETATM 21 C C20 RET . . . G 2 15.792 21.942 20.552 1 33.21 ? C20 RET 134 C 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 4 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 219 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 21 #