data_8JXP # _model_server_result.job_id 95HpEY3rduQ9jIi336jWkQ _model_server_result.datetime_utc '2024-10-25 20:36:14' _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 8jxp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":407}' # _entry.id 8JXP # _exptl.entry_id 8JXP _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 284.436 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RETINAL _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 J N N ? 3 Q N N ? 3 X N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order covale ? covale1 A NZ LYS 232 A LYS 232 1_555 J C15 RET . A RET 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.481 ? covale ? covale2 B NZ LYS 232 B LYS 232 1_555 Q C15 RET . B RET 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.481 ? covale ? covale3 C NZ LYS 232 C LYS 232 1_555 X C15 RET . C RET 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.481 ? metalc ? metalc1 A O THR 42 A THR 42 1_555 F K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.323 ? metalc ? metalc2 A O GLY 45 A GLY 45 1_555 F K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? metalc ? metalc3 A O GLU 61 A GLU 61 1_555 E K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.943 ? metalc ? metalc4 A O SER 65 A SER 65 1_555 I K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.219 ? metalc ? metalc5 A O LEU 97 A LEU 97 1_555 H K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.351 ? metalc ? metalc6 A OD2 ASP 104 A ASP 104 1_555 G K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc7 A OD1 ASP 115 A ASP 115 1_555 E K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.723 ? metalc ? metalc8 A OD2 ASP 228 A ASP 228 1_555 G K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.23 ? metalc ? metalc9 A O LYS 232 A LYS 232 1_555 I K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc10 H K K . A K 405 1_555 Y O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.448 ? metalc ? metalc11 H K K . A K 405 1_555 Y O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc12 B O THR 42 B THR 42 1_555 M K K . B K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.323 ? metalc ? metalc13 B O GLY 45 B GLY 45 1_555 M K K . B K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? metalc ? metalc14 B O GLU 61 B GLU 61 1_555 L K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? metalc ? metalc15 B O SER 65 B SER 65 1_555 P K K . B K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.219 ? metalc ? metalc16 B O LEU 97 B LEU 97 1_555 O K K . B K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.352 ? metalc ? metalc17 B OD2 ASP 104 B ASP 104 1_555 N K K . B K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc18 B OD1 ASP 115 B ASP 115 1_555 L K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.723 ? metalc ? metalc19 B OD2 ASP 228 B ASP 228 1_555 N K K . B K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.231 ? metalc ? metalc20 B O LYS 232 B LYS 232 1_555 P K K . B K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? metalc ? metalc21 O K K . B K 405 1_555 Z O HOH . B HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.448 ? metalc ? metalc22 O K K . B K 405 1_555 Z O HOH . B HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc23 C O THR 42 C THR 42 1_555 T K K . C K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.323 ? metalc ? metalc24 C O GLY 45 C GLY 45 1_555 T K K . C K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? metalc ? metalc25 C O GLU 61 C GLU 61 1_555 S K K . C K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? metalc ? metalc26 C O SER 65 C SER 65 1_555 W K K . C K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.218 ? metalc ? metalc27 C O LEU 97 C LEU 97 1_555 V K K . C K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.351 ? metalc ? metalc28 C OD2 ASP 104 C ASP 104 1_555 U K K . C K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc29 C OD1 ASP 115 C ASP 115 1_555 S K K . C K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.723 ? metalc ? metalc30 C OD2 ASP 228 C ASP 228 1_555 U K K . C K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.231 ? metalc ? metalc31 C O LYS 232 C LYS 232 1_555 W K K . C K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc32 V K K . C K 405 1_555 AA O HOH . C HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.448 ? metalc ? metalc33 V K K . C K 405 1_555 AA O HOH . C HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? # _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 8JXP _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 D 2 K A 1 401 286 K K . E 2 K A 1 402 287 K K . F 2 K A 1 403 288 K K . G 2 K A 1 404 289 K K . H 2 K A 1 405 290 K K . I 2 K A 1 406 291 K K . J 3 RET A 1 407 301 RET RET . K 2 K B 1 401 286 K K . L 2 K B 1 402 287 K K . M 2 K B 1 403 288 K K . N 2 K B 1 404 289 K K . O 2 K B 1 405 290 K K . P 2 K B 1 406 291 K K . Q 3 RET B 1 407 301 RET RET . R 2 K C 1 401 286 K K . S 2 K C 1 402 287 K K . T 2 K C 1 403 288 K K . U 2 K C 1 404 289 K K . V 2 K C 1 405 290 K K . W 2 K C 1 406 291 K K . X 3 RET C 1 407 301 RET RET . Y 4 HOH A 1 501 285 HOH HOH . Y 4 HOH A 2 502 283 HOH HOH . Y 4 HOH A 3 503 284 HOH HOH . Z 4 HOH B 1 501 285 HOH HOH . Z 4 HOH B 2 502 283 HOH HOH . Z 4 HOH B 3 503 284 HOH HOH . AA 4 HOH C 1 501 285 HOH HOH . AA 4 HOH C 2 502 283 HOH HOH . AA 4 HOH C 3 503 284 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 . . . Q 3 130.013 103.078 122.899 1 6.07 ? C1 RET 407 B 1 HETATM 2 C C2 RET . . . Q 3 129.767 102.222 124.131 1 6.07 ? C2 RET 407 B 1 HETATM 3 C C3 RET . . . Q 3 128.798 102.904 125.086 1 6.07 ? C3 RET 407 B 1 HETATM 4 C C4 RET . . . Q 3 129.35 104.232 125.594 1 6.07 ? C4 RET 407 B 1 HETATM 5 C C5 RET . . . Q 3 130.403 104.763 124.649 1 6.07 ? C5 RET 407 B 1 HETATM 6 C C6 RET . . . Q 3 130.355 104.477 123.347 1 6.07 ? C6 RET 407 B 1 HETATM 7 C C7 RET . . . Q 3 130.661 105.513 122.339 1 6.07 ? C7 RET 407 B 1 HETATM 8 C C8 RET . . . Q 3 129.845 106.538 122.105 1 6.07 ? C8 RET 407 B 1 HETATM 9 C C9 RET . . . Q 3 130.219 107.53 121.082 1 6.07 ? C9 RET 407 B 1 HETATM 10 C C10 RET . . . Q 3 129.755 108.784 121.161 1 6.07 ? C10 RET 407 B 1 HETATM 11 C C11 RET . . . Q 3 130.126 109.767 120.148 1 6.07 ? C11 RET 407 B 1 HETATM 12 C C12 RET . . . Q 3 129.801 111.043 120.328 1 6.07 ? C12 RET 407 B 1 HETATM 13 C C13 RET . . . Q 3 130.163 112.059 119.322 1 6.07 ? C13 RET 407 B 1 HETATM 14 C C14 RET . . . Q 3 129.487 113.212 119.268 1 6.07 ? C14 RET 407 B 1 HETATM 15 C C15 RET . . . Q 3 129.837 114.228 118.281 1 6.07 ? C15 RET 407 B 1 HETATM 16 C C16 RET . . . Q 3 131.18 102.525 122.096 1 6.07 ? C16 RET 407 B 1 HETATM 17 C C17 RET . . . Q 3 128.763 103.108 122.025 1 6.07 ? C17 RET 407 B 1 HETATM 18 C C18 RET . . . Q 3 131.511 105.611 125.198 1 6.07 ? C18 RET 407 B 1 HETATM 19 C C19 RET . . . Q 3 131.119 107.135 119.951 1 6.07 ? C19 RET 407 B 1 HETATM 20 C C20 RET . . . Q 3 131.289 111.802 118.369 1 6.07 ? C20 RET 407 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 348 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #