data_3COD # _model_server_result.job_id 08KrmeHu-g_02_7XM-fY7g _model_server_result.datetime_utc '2025-09-14 18:31:16' _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 3cod # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 3COD # _exptl.entry_id 3COD _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 113.37 _cell.angle_gamma 90 _cell.entry_id 3COD _cell.length_a 43.974 _cell.length_b 109.658 _cell.length_c 55.517 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3COD _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 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 C N N ? 2 D 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 216 A LYS 216 1_555 C C15 RET . A RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 B NZ LYS 216 B LYS 216 1_555 D C15 RET . B RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _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 243 n n C1 C6 RET sing 244 n n C1 C16 RET sing 245 n n C1 C17 RET sing 246 n n C2 C3 RET sing 247 n n C2 H21 RET sing 248 n n C2 H22 RET sing 249 n n C3 C4 RET sing 250 n n C3 H31 RET sing 251 n n C3 H32 RET sing 252 n n C4 C5 RET sing 253 n n C4 H41 RET sing 254 n n C4 H42 RET sing 255 n n C5 C6 RET doub 256 n n C5 C18 RET sing 257 n n C6 C7 RET sing 258 n n C7 C8 RET doub 259 e n C7 H7 RET sing 260 n n C8 C9 RET sing 261 n n C8 H8 RET sing 262 n n C9 C10 RET doub 263 e n C9 C19 RET sing 264 n n C10 C11 RET sing 265 n n C10 H10 RET sing 266 n n C11 C12 RET doub 267 e n C11 H11 RET sing 268 n n C12 C13 RET sing 269 n n C12 H12 RET sing 270 n n C13 C14 RET doub 271 e n C13 C20 RET sing 272 n n C14 C15 RET sing 273 n n C14 H14 RET sing 274 n n C15 O1 RET doub 275 n n C15 H15 RET sing 276 n n C16 H161 RET sing 277 n n C16 H162 RET sing 278 n n C16 H163 RET sing 279 n n C17 H171 RET sing 280 n n C17 H172 RET sing 281 n n C17 H173 RET sing 282 n n C18 H181 RET sing 283 n n C18 H182 RET sing 284 n n C18 H183 RET sing 285 n n C19 H191 RET sing 286 n n C19 H192 RET sing 287 n n C19 H193 RET sing 288 n n C20 H201 RET sing 289 n n C20 H202 RET sing 290 n n C20 H203 RET sing 291 n n # _atom_sites.entry_id 3COD _atom_sites.fract_transf_matrix[1][1] 0.022741 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.009827 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009119 _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] 0.019622 _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 C 2 RET A 1 301 301 RET RET . D 2 RET B 1 301 301 RET RET . E 3 HOH A 1 302 4 HOH TIP . E 3 HOH A 2 303 5 HOH TIP . E 3 HOH A 3 304 8 HOH TIP . E 3 HOH A 4 305 12 HOH TIP . E 3 HOH A 5 306 13 HOH TIP . E 3 HOH A 6 307 15 HOH TIP . E 3 HOH A 7 308 17 HOH TIP . E 3 HOH A 8 309 18 HOH TIP . E 3 HOH A 9 310 19 HOH TIP . E 3 HOH A 10 311 21 HOH TIP . E 3 HOH A 11 312 23 HOH TIP . E 3 HOH A 12 313 25 HOH TIP . E 3 HOH A 13 314 26 HOH TIP . E 3 HOH A 14 315 28 HOH TIP . E 3 HOH A 15 316 29 HOH TIP . E 3 HOH A 16 317 30 HOH TIP . E 3 HOH A 17 318 31 HOH TIP . E 3 HOH A 18 319 34 HOH TIP . E 3 HOH A 19 320 35 HOH TIP . E 3 HOH A 20 321 36 HOH TIP . F 3 HOH B 1 302 1 HOH TIP . F 3 HOH B 2 303 2 HOH TIP . F 3 HOH B 3 304 3 HOH TIP . F 3 HOH B 4 305 6 HOH TIP . F 3 HOH B 5 306 7 HOH TIP . F 3 HOH B 6 307 9 HOH TIP . F 3 HOH B 7 308 10 HOH TIP . F 3 HOH B 8 309 11 HOH TIP . F 3 HOH B 9 310 14 HOH TIP . F 3 HOH B 10 311 16 HOH TIP . F 3 HOH B 11 312 20 HOH TIP . F 3 HOH B 12 313 22 HOH TIP . F 3 HOH B 13 314 24 HOH TIP . F 3 HOH B 14 315 27 HOH TIP . F 3 HOH B 15 316 32 HOH TIP . F 3 HOH B 16 317 33 HOH TIP . F 3 HOH B 17 318 37 HOH TIP . F 3 HOH B 18 319 38 HOH TIP . # 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 . . . C 2 40.28 54.867 2.228 1 22 ? C1 RET 301 A 1 HETATM 2 C C2 RET . . . C 2 41.1 56.097 1.748 1 22.06 ? C2 RET 301 A 1 HETATM 3 C C3 RET . . . C 2 41.662 56.088 0.366 1 22.23 ? C3 RET 301 A 1 HETATM 4 C C4 RET . . . C 2 42.188 54.747 -0.142 1 22.45 ? C4 RET 301 A 1 HETATM 5 C C5 RET . . . C 2 41.408 53.475 0.292 1 22.38 ? C5 RET 301 A 1 HETATM 6 C C6 RET . . . C 2 40.52 53.511 1.386 1 22.3 ? C6 RET 301 A 1 HETATM 7 C C7 RET . . . C 2 39.854 52.184 1.658 1 22.84 ? C7 RET 301 A 1 HETATM 8 C C8 RET . . . C 2 38.944 51.772 2.591 1 23.47 ? C8 RET 301 A 1 HETATM 9 C C9 RET . . . C 2 38.352 50.45 2.781 1 24 ? C9 RET 301 A 1 HETATM 10 C C10 RET . . . C 2 37.466 50.466 3.833 1 24.84 ? C10 RET 301 A 1 HETATM 11 C C11 RET . . . C 2 36.693 49.295 4.28 1 25.6 ? C11 RET 301 A 1 HETATM 12 C C12 RET . . . C 2 35.878 49.617 5.337 1 26.1 ? C12 RET 301 A 1 HETATM 13 C C13 RET . . . C 2 34.974 48.683 6.009 1 26.51 ? C13 RET 301 A 1 HETATM 14 C C14 RET . . . C 2 34.283 49.316 7.023 1 26.63 ? C14 RET 301 A 1 HETATM 15 C C15 RET . . . C 2 33.301 48.659 7.869 1 26.77 ? C15 RET 301 A 1 HETATM 16 C C16 RET . . . C 2 40.648 54.677 3.748 1 21.97 ? C16 RET 301 A 1 HETATM 17 C C17 RET . . . C 2 38.802 55.429 2.103 1 21.72 ? C17 RET 301 A 1 HETATM 18 C C18 RET . . . C 2 41.795 52.355 -0.633 1 22.33 ? C18 RET 301 A 1 HETATM 19 C C19 RET . . . C 2 38.686 49.258 1.909 1 24.12 ? C19 RET 301 A 1 HETATM 20 C C20 RET . . . C 2 34.84 47.241 5.606 1 26.49 ? C20 RET 301 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #