data_5AHY # _model_server_result.job_id i4hIFWR6tjYGkfWUL1tdGw _model_server_result.datetime_utc '2024-11-30 19:34:17' _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 5ahy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":900}' # _entry.id 5AHY # _exptl.entry_id 5AHY _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 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 120 _cell.entry_id 5AHY _cell.length_a 103.651 _cell.length_b 103.651 _cell.length_c 138.588 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5AHY _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 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 223 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 242 _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 900 _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 1.355 _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 325 n n C1 C6 RET sing 326 n n C1 C16 RET sing 327 n n C1 C17 RET sing 328 n n C2 C3 RET sing 329 n n C2 H21 RET sing 330 n n C2 H22 RET sing 331 n n C3 C4 RET sing 332 n n C3 H31 RET sing 333 n n C3 H32 RET sing 334 n n C4 C5 RET sing 335 n n C4 H41 RET sing 336 n n C4 H42 RET sing 337 n n C5 C6 RET doub 338 n n C5 C18 RET sing 339 n n C6 C7 RET sing 340 n n C7 C8 RET doub 341 e n C7 H7 RET sing 342 n n C8 C9 RET sing 343 n n C8 H8 RET sing 344 n n C9 C10 RET doub 345 e n C9 C19 RET sing 346 n n C10 C11 RET sing 347 n n C10 H10 RET sing 348 n n C11 C12 RET doub 349 e n C11 H11 RET sing 350 n n C12 C13 RET sing 351 n n C12 H12 RET sing 352 n n C13 C14 RET doub 353 e n C13 C20 RET sing 354 n n C14 C15 RET sing 355 n n C14 H14 RET sing 356 n n C15 O1 RET doub 357 n n C15 H15 RET sing 358 n n C16 H161 RET sing 359 n n C16 H162 RET sing 360 n n C16 H163 RET sing 361 n n C17 H171 RET sing 362 n n C17 H172 RET sing 363 n n C17 H173 RET sing 364 n n C18 H181 RET sing 365 n n C18 H182 RET sing 366 n n C18 H183 RET sing 367 n n C19 H191 RET sing 368 n n C19 H192 RET sing 369 n n C19 H193 RET sing 370 n n C20 H201 RET sing 371 n n C20 H202 RET sing 372 n n C20 H203 RET sing 373 n n # _atom_sites.entry_id 5AHY _atom_sites.fract_transf_matrix[1][1] 0.009648 _atom_sites.fract_transf_matrix[1][2] 0.00557 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01114 _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] 0.007216 _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 1 900 900 RET RET . C 3 CL A 1 1263 1263 CL CL . D 3 CL A 1 1264 1264 CL CL . E 4 BOG A 1 1265 1265 BOG BOG . F 5 HOH A 1 2001 2001 HOH HOH . F 5 HOH A 2 2002 2002 HOH HOH . F 5 HOH A 3 2003 2003 HOH HOH . F 5 HOH A 4 2004 2004 HOH HOH . F 5 HOH A 5 2005 2005 HOH HOH . F 5 HOH A 6 2006 2006 HOH HOH . F 5 HOH A 7 2007 2007 HOH HOH . F 5 HOH A 8 2008 2008 HOH HOH . F 5 HOH A 9 2009 2009 HOH HOH . F 5 HOH A 10 2010 2010 HOH HOH . F 5 HOH A 11 2011 2011 HOH HOH . F 5 HOH A 12 2012 2012 HOH HOH . F 5 HOH A 13 2013 2013 HOH HOH . F 5 HOH A 14 2014 2014 HOH HOH . F 5 HOH A 15 2015 2015 HOH HOH . F 5 HOH A 16 2016 2016 HOH HOH . F 5 HOH A 17 2017 2017 HOH HOH . F 5 HOH A 18 2018 2018 HOH HOH . F 5 HOH A 19 2019 2019 HOH HOH . F 5 HOH A 20 2020 2020 HOH HOH . F 5 HOH A 21 2021 2021 HOH HOH . F 5 HOH A 22 2022 2022 HOH HOH . F 5 HOH A 23 2023 2023 HOH HOH . F 5 HOH A 24 2024 2024 HOH HOH . F 5 HOH A 25 2025 2025 HOH HOH . F 5 HOH A 26 2026 2026 HOH HOH . F 5 HOH A 27 2027 2027 HOH HOH . F 5 HOH A 28 2028 2028 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 -17.147 -4.789 21.751 1 25.68 ? C1 RET 900 A 1 HETATM 2 C C2 RET . . . B 2 -17.329 -5.882 20.707 1 19.62 ? C2 RET 900 A 1 HETATM 3 C C3 RET . . . B 2 -16.824 -7.223 21.2 1 21.25 ? C3 RET 900 A 1 HETATM 4 C C4 RET . . . B 2 -17.619 -7.665 22.42 1 19.67 ? C4 RET 900 A 1 HETATM 5 C C5 RET . . . B 2 -17.649 -6.569 23.462 1 20.12 ? C5 RET 900 A 1 HETATM 6 C C6 RET . . . B 2 -17.451 -5.268 23.175 1 21.58 ? C6 RET 900 A 1 HETATM 7 C C7 RET . . . B 2 -17.581 -4.324 24.341 1 23.61 ? C7 RET 900 A 1 HETATM 8 C C8 RET . . . B 2 -17.297 -3.017 24.302 1 17.71 ? C8 RET 900 A 1 HETATM 9 C C9 RET . . . B 2 -17.434 -2.091 25.438 1 23 ? C9 RET 900 A 1 HETATM 10 C C10 RET . . . B 2 -17.109 -0.802 25.208 1 20.91 ? C10 RET 900 A 1 HETATM 11 C C11 RET . . . B 2 -17.186 0.273 26.202 1 20.98 ? C11 RET 900 A 1 HETATM 12 C C12 RET . . . B 2 -16.921 1.494 25.732 1 17.8 ? C12 RET 900 A 1 HETATM 13 C C13 RET . . . B 2 -16.931 2.688 26.587 1 24.55 ? C13 RET 900 A 1 HETATM 14 C C14 RET . . . B 2 -16.367 3.793 26.082 1 22.93 ? C14 RET 900 A 1 HETATM 15 C C15 RET . . . B 2 -16.282 5.02 26.844 1 22.2 ? C15 RET 900 A 1 HETATM 16 C C16 RET . . . B 2 -15.7 -4.295 21.694 1 17.69 ? C16 RET 900 A 1 HETATM 17 C C17 RET . . . B 2 -18.119 -3.693 21.3 1 19.87 ? C17 RET 900 A 1 HETATM 18 C C18 RET . . . B 2 -17.933 -6.96 24.893 1 19.51 ? C18 RET 900 A 1 HETATM 19 C C19 RET . . . B 2 -17.944 -2.579 26.765 1 19.71 ? C19 RET 900 A 1 HETATM 20 C C20 RET . . . B 2 -17.529 2.65 27.971 1 19.46 ? C20 RET 900 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 20 #