data_4KNF # _model_server_result.job_id lZd8Nr_ciM-S2WwUIGQupQ _model_server_result.datetime_utc '2025-01-10 15:05:16' _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 4knf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 4KNF # _exptl.entry_id 4KNF _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 5 _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 4KNF _cell.length_a 161.4 _cell.length_b 168.9 _cell.length_c 65.7 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KNF _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 ? 2 F N N ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J 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 233 A LYS 232 1_555 F C15 RET . A RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale2 B NZ LYS 233 B LYS 232 1_555 G C15 RET . B RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale3 C NZ LYS 233 C LYS 232 1_555 H C15 RET . C RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale4 D NZ LYS 233 D LYS 232 1_555 I C15 RET . D RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? covale ? covale5 E NZ LYS 233 E LYS 232 1_555 J C15 RET . E RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? # _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 4KNF _atom_sites.fract_transf_matrix[1][1] 0.006196 _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] 0.005921 _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] 0.015221 _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 F 2 RET A 1 301 301 RET RET . G 2 RET B 1 301 301 RET RET . H 2 RET C 1 301 301 RET RET . I 2 RET D 1 301 301 RET RET . J 2 RET E 1 301 301 RET RET . K 3 HOH A 1 401 401 HOH HOH . K 3 HOH A 2 502 502 HOH HOH . L 3 HOH B 1 401 401 HOH HOH . L 3 HOH B 2 406 406 HOH HOH . L 3 HOH B 3 502 502 HOH HOH . M 3 HOH C 1 401 401 HOH HOH . M 3 HOH C 2 502 502 HOH HOH . N 3 HOH D 1 401 401 HOH HOH . N 3 HOH D 2 502 502 HOH HOH . O 3 HOH E 1 401 401 HOH HOH . O 3 HOH E 2 502 502 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 . . . F 2 -30.259 -2.743 -6.422 1 61.18 ? C1 RET 301 A 1 HETATM 2 C C2 RET . . . F 2 -29.07 -3.019 -7.337 1 63.35 ? C2 RET 301 A 1 HETATM 3 C C3 RET . . . F 2 -28.002 -3.895 -6.684 1 68.74 ? C3 RET 301 A 1 HETATM 4 C C4 RET . . . F 2 -28.578 -4.888 -5.68 1 63.53 ? C4 RET 301 A 1 HETATM 5 C C5 RET . . . F 2 -29.377 -4.174 -4.612 1 66.34 ? C5 RET 301 A 1 HETATM 6 C C6 RET . . . F 2 -30.178 -3.12 -4.934 1 65.46 ? C6 RET 301 A 1 HETATM 7 C C7 RET . . . F 2 -30.97 -2.454 -3.85 1 62.03 ? C7 RET 301 A 1 HETATM 8 C C8 RET . . . F 2 -31.822 -1.423 -3.957 1 60.72 ? C8 RET 301 A 1 HETATM 9 C C9 RET . . . F 2 -32.531 -0.86 -2.766 1 66.78 ? C9 RET 301 A 1 HETATM 10 C C10 RET . . . F 2 -33.36 0.183 -2.932 1 66.37 ? C10 RET 301 A 1 HETATM 11 C C11 RET . . . F 2 -34.091 0.795 -1.821 1 62.79 ? C11 RET 301 A 1 HETATM 12 C C12 RET . . . F 2 -34.892 1.816 -2.119 1 64.32 ? C12 RET 301 A 1 HETATM 13 C C13 RET . . . F 2 -35.723 2.575 -1.157 1 69.82 ? C13 RET 301 A 1 HETATM 14 C C14 RET . . . F 2 -36.428 3.559 -1.734 1 68.49 ? C14 RET 301 A 1 HETATM 15 C C15 RET . . . F 2 -37.352 4.514 -1.126 1 68.07 ? C15 RET 301 A 1 HETATM 16 C C16 RET . . . F 2 -31.504 -2.056 -6.981 1 54.98 ? C16 RET 301 A 1 HETATM 17 C C17 RET . . . F 2 -29.637 -1.359 -6.152 1 58.19 ? C17 RET 301 A 1 HETATM 18 C C18 RET . . . F 2 -29.208 -4.718 -3.216 1 58.69 ? C18 RET 301 A 1 HETATM 19 C C19 RET . . . F 2 -32.361 -1.407 -1.37 1 58.52 ? C19 RET 301 A 1 HETATM 20 C C20 RET . . . F 2 -35.769 2.275 0.328 1 61.53 ? C20 RET 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 461 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 20 #