data_8YEJ # _model_server_result.job_id JbKaqqHPo3l7RYoVu3GsOA _model_server_result.datetime_utc '2024-12-21 16:21:13' _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 8yej # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8YEJ # _exptl.entry_id 8YEJ _exptl.method 'ELECTRON MICROSCOPY' # _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 90 _cell.entry_id 8YEJ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YEJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _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 248 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 223 _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 501 _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 1.337 _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 277 n n C1 C6 RET sing 278 n n C1 C16 RET sing 279 n n C1 C17 RET sing 280 n n C2 C3 RET sing 281 n n C2 H21 RET sing 282 n n C2 H22 RET sing 283 n n C3 C4 RET sing 284 n n C3 H31 RET sing 285 n n C3 H32 RET sing 286 n n C4 C5 RET sing 287 n n C4 H41 RET sing 288 n n C4 H42 RET sing 289 n n C5 C6 RET doub 290 n n C5 C18 RET sing 291 n n C6 C7 RET sing 292 n n C7 C8 RET doub 293 e n C7 H7 RET sing 294 n n C8 C9 RET sing 295 n n C8 H8 RET sing 296 n n C9 C10 RET doub 297 e n C9 C19 RET sing 298 n n C10 C11 RET sing 299 n n C10 H10 RET sing 300 n n C11 C12 RET doub 301 e n C11 H11 RET sing 302 n n C12 C13 RET sing 303 n n C12 H12 RET sing 304 n n C13 C14 RET doub 305 e n C13 C20 RET sing 306 n n C14 C15 RET sing 307 n n C14 H14 RET sing 308 n n C15 O1 RET doub 309 n n C15 H15 RET sing 310 n n C16 H161 RET sing 311 n n C16 H162 RET sing 312 n n C16 H163 RET sing 313 n n C17 H171 RET sing 314 n n C17 H172 RET sing 315 n n C17 H173 RET sing 316 n n C18 H181 RET sing 317 n n C18 H182 RET sing 318 n n C18 H183 RET sing 319 n n C19 H191 RET sing 320 n n C19 H192 RET sing 321 n n C19 H193 RET sing 322 n n C20 H201 RET sing 323 n n C20 H202 RET sing 324 n n C20 H203 RET sing 325 n n # _atom_sites.entry_id 8YEJ _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _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] 1 _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 1 501 301 RET RET . C 3 HOH A 1 601 3 HOH HOH . C 3 HOH A 2 602 4 HOH HOH . C 3 HOH A 3 603 6 HOH HOH . C 3 HOH A 4 604 2 HOH HOH . C 3 HOH A 5 605 5 HOH HOH . C 3 HOH A 6 606 1 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 2 137.807 113.539 126.874 1 95.54 ? C1 RET 501 A 1 HETATM 2 C C2 RET . . . B 2 138.83 113.419 125.735 1 93.57 ? C2 RET 501 A 1 HETATM 3 C C3 RET . . . B 2 140.177 113.902 126.095 1 93.61 ? C3 RET 501 A 1 HETATM 4 C C4 RET . . . B 2 140.665 113.089 127.278 1 97.42 ? C4 RET 501 A 1 HETATM 5 C C5 RET . . . B 2 139.711 113.132 128.436 1 95.41 ? C5 RET 501 A 1 HETATM 6 C C6 RET . . . B 2 138.383 113.349 128.279 1 90.71 ? C6 RET 501 A 1 HETATM 7 C C7 RET . . . B 2 137.519 113.404 129.46 1 84.6 ? C7 RET 501 A 1 HETATM 8 C C8 RET . . . B 2 136.167 113.613 129.523 1 86.29 ? C8 RET 501 A 1 HETATM 9 C C9 RET . . . B 2 135.343 113.66 130.651 1 87.75 ? C9 RET 501 A 1 HETATM 10 C C10 RET . . . B 2 133.954 113.887 130.492 1 86.25 ? C10 RET 501 A 1 HETATM 11 C C11 RET . . . B 2 132.946 113.972 131.431 1 88.43 ? C11 RET 501 A 1 HETATM 12 C C12 RET . . . B 2 131.605 114.201 131.188 1 90.72 ? C12 RET 501 A 1 HETATM 13 C C13 RET . . . B 2 130.536 114.297 132.106 1 91.46 ? C13 RET 501 A 1 HETATM 14 C C14 RET . . . B 2 129.227 114.528 131.671 1 91.79 ? C14 RET 501 A 1 HETATM 15 C C15 RET . . . B 2 128.111 114.667 132.484 1 88.74 ? C15 RET 501 A 1 HETATM 16 C C16 RET . . . B 2 137.154 114.928 126.775 1 100.5 ? C16 RET 501 A 1 HETATM 17 C C17 RET . . . B 2 136.741 112.472 126.572 1 101.01 ? C17 RET 501 A 1 HETATM 18 C C18 RET . . . B 2 140.411 112.926 129.752 1 96.85 ? C18 RET 501 A 1 HETATM 19 C C19 RET . . . B 2 135.883 113.465 132.032 1 87.96 ? C19 RET 501 A 1 HETATM 20 C C20 RET . . . B 2 130.876 114.129 133.54 1 91.96 ? C20 RET 501 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #