data_8ZAO # _model_server_result.job_id KGWcSV2QlStf22qPjNYXyQ _model_server_result.datetime_utc '2024-10-16 10:33:46' _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 8zao # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":306}' # _entry.id 8ZAO # _exptl.entry_id 8ZAO _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 _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 I N N ? 3 O N N ? 3 U 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 233 1_555 I C15 RET . A RET 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale2 B NZ LYS 232 B LYS 233 1_555 O C15 RET . B RET 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale3 C NZ LYS 232 C LYS 233 1_555 U C15 RET . C RET 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? metalc ? metalc1 A OD1 ASN 66 A ASN 67 1_555 G K K . A K 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.959 ? metalc ? metalc2 A O ASN 66 A ASN 67 1_555 H K K . A K 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? metalc ? metalc3 A O SER 96 A SER 97 1_555 F K K . A K 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? metalc ? metalc4 A O ASN 98 A ASN 99 1_555 D K K . A K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.017 ? metalc ? metalc5 A O TRP 99 A TRP 100 1_555 E K K . A K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.996 ? metalc ? metalc6 A OG1 THR 119 A THR 120 1_555 G K K . A K 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.432 ? metalc ? metalc7 A OE1 GLN 217 A GLN 218 1_555 E K K . A K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.894 ? metalc ? metalc8 D K K . A K 301 1_555 V O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.148 ? metalc ? metalc9 E K K . A K 302 1_555 V O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc10 E K K . A K 302 1_555 V O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc11 E K K . A K 302 1_555 V O HOH . A HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.755 ? metalc ? metalc12 F K K . A K 303 1_555 V O HOH . A HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.03 ? metalc ? metalc13 H K K . A K 305 1_555 V O HOH . A HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc14 B OD1 ASN 66 B ASN 67 1_555 M K K . B K 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.891 ? metalc ? metalc15 B O ASN 66 B ASN 67 1_555 N K K . B K 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.799 ? metalc ? metalc16 B O SER 96 B SER 97 1_555 L K K . B K 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc17 B O ASN 98 B ASN 99 1_555 J K K . B K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.017 ? metalc ? metalc18 B O TRP 99 B TRP 100 1_555 K K K . B K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.004 ? metalc ? metalc19 B OG1 THR 119 B THR 120 1_555 M K K . B K 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.485 ? metalc ? metalc20 B OE1 GLN 217 B GLN 218 1_555 K K K . B K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? metalc ? metalc21 J K K . B K 301 1_555 W O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.148 ? metalc ? metalc22 K K K . B K 302 1_555 W O HOH . B HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc23 K K K . B K 302 1_555 W O HOH . B HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc24 K K K . B K 302 1_555 W O HOH . B HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.754 ? metalc ? metalc25 L K K . B K 303 1_555 W O HOH . B HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.024 ? metalc ? metalc26 M K K . B K 304 1_555 W O HOH . B HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc27 N K K . B K 305 1_555 W O HOH . B HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc28 C OD1 ASN 66 C ASN 67 1_555 S K K . C K 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc29 C O ASN 66 C ASN 67 1_555 T K K . C K 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? metalc ? metalc30 C O SER 96 C SER 97 1_555 R K K . C K 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc31 C O ASN 98 C ASN 99 1_555 P K K . C K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.012 ? metalc ? metalc32 C O TRP 99 C TRP 100 1_555 Q K K . C K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.003 ? metalc ? metalc33 C OG1 THR 119 C THR 120 1_555 S K K . C K 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.465 ? metalc ? metalc34 C OE1 GLN 217 C GLN 218 1_555 Q K K . C K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.893 ? metalc ? metalc35 P K K . C K 301 1_555 X O HOH . C HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.146 ? metalc ? metalc36 Q K K . C K 302 1_555 X O HOH . C HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc37 Q K K . C K 302 1_555 X O HOH . C HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc38 Q K K . C K 302 1_555 X O HOH . C HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? metalc ? metalc39 R K K . C K 303 1_555 X O HOH . C HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.026 ? metalc ? metalc40 S K K . C K 304 1_555 X O HOH . C HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc41 T K K . C K 305 1_555 X O HOH . C HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? # _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 8ZAO _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 1 301 282 K K . E 2 K A 1 302 285 K K . F 2 K A 1 303 286 K K . G 2 K A 1 304 287 K K . H 2 K A 1 305 288 K K . I 3 RET A 1 306 312 RET RET . J 2 K B 1 301 282 K K . K 2 K B 1 302 285 K K . L 2 K B 1 303 286 K K . M 2 K B 1 304 287 K K . N 2 K B 1 305 288 K K . O 3 RET B 1 306 312 RET RET . P 2 K C 1 301 282 K K . Q 2 K C 1 302 285 K K . R 2 K C 1 303 286 K K . S 2 K C 1 304 287 K K . T 2 K C 1 305 288 K K . U 3 RET C 1 306 312 RET RET . V 4 HOH A 1 401 308 HOH HOH . V 4 HOH A 2 402 306 HOH HOH . V 4 HOH A 3 403 309 HOH HOH . V 4 HOH A 4 404 310 HOH HOH . V 4 HOH A 5 405 305 HOH HOH . V 4 HOH A 6 406 301 HOH HOH . V 4 HOH A 7 407 307 HOH HOH . V 4 HOH A 8 408 302 HOH HOH . V 4 HOH A 9 409 311 HOH HOH . V 4 HOH A 10 410 304 HOH HOH . W 4 HOH B 1 401 308 HOH HOH . W 4 HOH B 2 402 306 HOH HOH . W 4 HOH B 3 403 309 HOH HOH . W 4 HOH B 4 404 310 HOH HOH . W 4 HOH B 5 405 301 HOH HOH . W 4 HOH B 6 406 305 HOH HOH . W 4 HOH B 7 407 307 HOH HOH . W 4 HOH B 8 408 302 HOH HOH . W 4 HOH B 9 409 311 HOH HOH . W 4 HOH B 10 410 304 HOH HOH . X 4 HOH C 1 401 308 HOH HOH . X 4 HOH C 2 402 306 HOH HOH . X 4 HOH C 3 403 309 HOH HOH . X 4 HOH C 4 404 310 HOH HOH . X 4 HOH C 5 405 305 HOH HOH . X 4 HOH C 6 406 301 HOH HOH . X 4 HOH C 7 407 307 HOH HOH . X 4 HOH C 8 408 302 HOH HOH . X 4 HOH C 9 409 311 HOH HOH . X 4 HOH C 10 410 304 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 . . . O 3 130.971 111.894 99.465 1 77.63 ? C1 RET 306 B 1 HETATM 2 C C2 RET . . . O 3 130.919 113.153 98.583 1 75 ? C2 RET 306 B 1 HETATM 3 C C3 RET . . . O 3 131.916 114.232 98.936 1 75.95 ? C3 RET 306 B 1 HETATM 4 C C4 RET . . . O 3 131.734 114.61 100.385 1 79.08 ? C4 RET 306 B 1 HETATM 5 C C5 RET . . . O 3 131.803 113.426 101.295 1 79.13 ? C5 RET 306 B 1 HETATM 6 C C6 RET . . . O 3 131.349 112.208 100.919 1 75.89 ? C6 RET 306 B 1 HETATM 7 C C7 RET . . . O 3 131.422 111.155 101.93 1 75.16 ? C7 RET 306 B 1 HETATM 8 C C8 RET . . . O 3 130.426 110.494 102.553 1 79.7 ? C8 RET 306 B 1 HETATM 9 C C9 RET . . . O 3 130.574 109.459 103.554 1 80.14 ? C9 RET 306 B 1 HETATM 10 C C10 RET . . . O 3 129.736 108.395 103.459 1 80.14 ? C10 RET 306 B 1 HETATM 11 C C11 RET . . . O 3 129.653 107.248 104.312 1 81.04 ? C11 RET 306 B 1 HETATM 12 C C12 RET . . . O 3 128.97 106.14 103.949 1 82.92 ? C12 RET 306 B 1 HETATM 13 C C13 RET . . . O 3 128.816 104.946 104.747 1 81.85 ? C13 RET 306 B 1 HETATM 14 C C14 RET . . . O 3 128.103 103.914 104.226 1 83.03 ? C14 RET 306 B 1 HETATM 15 C C15 RET . . . O 3 127.84 102.65 104.88 1 82.93 ? C15 RET 306 B 1 HETATM 16 C C16 RET . . . O 3 129.549 111.326 99.374 1 78.23 ? C16 RET 306 B 1 HETATM 17 C C17 RET . . . O 3 131.965 110.905 98.839 1 74.78 ? C17 RET 306 B 1 HETATM 18 C C18 RET . . . O 3 132.921 113.585 102.288 1 77.35 ? C18 RET 306 B 1 HETATM 19 C C19 RET . . . O 3 131.61 109.619 104.622 1 76.77 ? C19 RET 306 B 1 HETATM 20 C C20 RET . . . O 3 129.435 104.933 106.109 1 78.81 ? C20 RET 306 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #