data_8YEK # _model_server_result.job_id 3qpa6Y-O_AgycqYQJ_5spQ _model_server_result.datetime_utc '2024-12-22 03:06:18' _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 8yek # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8YEK # _exptl.entry_id 8YEK _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 8YEK _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YEK _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_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E 1 1 A,B,C,D,E 1 2 A,B,C,D,E 1 3 # 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 'point symmetry operation' ? ? -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 314.20816 84.19182 0 3 'point symmetry operation' ? ? -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 84.19182 314.20816 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 418 n n C1 C6 RET sing 419 n n C1 C16 RET sing 420 n n C1 C17 RET sing 421 n n C2 C3 RET sing 422 n n C2 H21 RET sing 423 n n C2 H22 RET sing 424 n n C3 C4 RET sing 425 n n C3 H31 RET sing 426 n n C3 H32 RET sing 427 n n C4 C5 RET sing 428 n n C4 H41 RET sing 429 n n C4 H42 RET sing 430 n n C5 C6 RET doub 431 n n C5 C18 RET sing 432 n n C6 C7 RET sing 433 n n C7 C8 RET doub 434 e n C7 H7 RET sing 435 n n C8 C9 RET sing 436 n n C8 H8 RET sing 437 n n C9 C10 RET doub 438 e n C9 C19 RET sing 439 n n C10 C11 RET sing 440 n n C10 H10 RET sing 441 n n C11 C12 RET doub 442 e n C11 H11 RET sing 443 n n C12 C13 RET sing 444 n n C12 H12 RET sing 445 n n C13 C14 RET doub 446 e n C13 C20 RET sing 447 n n C14 C15 RET sing 448 n n C14 H14 RET sing 449 n n C15 O1 RET doub 450 n n C15 H15 RET sing 451 n n C16 H161 RET sing 452 n n C16 H162 RET sing 453 n n C16 H163 RET sing 454 n n C17 H171 RET sing 455 n n C17 H172 RET sing 456 n n C17 H173 RET sing 457 n n C18 H181 RET sing 458 n n C18 H182 RET sing 459 n n C18 H183 RET sing 460 n n C19 H191 RET sing 461 n n C19 H192 RET sing 462 n n C19 H193 RET sing 463 n n C20 H201 RET sing 464 n n C20 H202 RET sing 465 n n C20 H203 RET sing 466 n n # _atom_sites.entry_id 8YEK _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 PC1 A 1 502 302 PC1 PC1 . D 3 PC1 A 1 503 303 PC1 PC1 . E 4 HOH A 1 601 3 HOH HOH . E 4 HOH A 2 602 4 HOH HOH . E 4 HOH A 3 603 6 HOH HOH . E 4 HOH A 4 604 2 HOH HOH . E 4 HOH A 5 605 5 HOH HOH . E 4 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 2 137.805 113.528 126.87 1 69.11 ? C1 RET 501 A 1 HETATM 2 C C2 RET . . . B 2 138.832 113.409 125.735 1 69.02 ? C2 RET 501 A 1 HETATM 3 C C3 RET . . . B 2 140.179 113.878 126.097 1 69.29 ? C3 RET 501 A 1 HETATM 4 C C4 RET . . . B 2 140.659 113.059 127.278 1 69.76 ? C4 RET 501 A 1 HETATM 5 C C5 RET . . . B 2 139.706 113.113 128.436 1 69.4 ? C5 RET 501 A 1 HETATM 6 C C6 RET . . . B 2 138.378 113.33 128.275 1 68.78 ? C6 RET 501 A 1 HETATM 7 C C7 RET . . . B 2 137.51 113.389 129.454 1 68.34 ? C7 RET 501 A 1 HETATM 8 C C8 RET . . . B 2 136.158 113.602 129.516 1 68.5 ? C8 RET 501 A 1 HETATM 9 C C9 RET . . . B 2 135.335 113.65 130.647 1 68.66 ? C9 RET 501 A 1 HETATM 10 C C10 RET . . . B 2 133.947 113.877 130.487 1 68.78 ? C10 RET 501 A 1 HETATM 11 C C11 RET . . . B 2 132.94 113.968 131.427 1 69.27 ? C11 RET 501 A 1 HETATM 12 C C12 RET . . . B 2 131.598 114.194 131.187 1 69.52 ? C12 RET 501 A 1 HETATM 13 C C13 RET . . . B 2 130.532 114.299 132.11 1 69.61 ? C13 RET 501 A 1 HETATM 14 C C14 RET . . . B 2 129.225 114.534 131.675 1 69.55 ? C14 RET 501 A 1 HETATM 15 C C15 RET . . . B 2 128.107 114.67 132.487 1 69.19 ? C15 RET 501 A 1 HETATM 16 C C16 RET . . . B 2 137.156 114.92 126.772 1 69.67 ? C16 RET 501 A 1 HETATM 17 C C17 RET . . . B 2 136.737 112.46 126.569 1 69.81 ? C17 RET 501 A 1 HETATM 18 C C18 RET . . . B 2 140.408 112.911 129.753 1 69.78 ? C18 RET 501 A 1 HETATM 19 C C19 RET . . . B 2 135.874 113.465 132.03 1 68.39 ? C19 RET 501 A 1 HETATM 20 C C20 RET . . . B 2 130.871 114.145 133.551 1 69.45 ? C20 RET 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #