data_5G2A # _model_server_result.job_id tYQcOnokyacR6BVODNYZmw _model_server_result.datetime_utc '2024-11-21 13:59:54' _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 5g2a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1268}' # _entry.id 5G2A # _exptl.entry_id 5G2A _exptl.method 'X-RAY DIFFRACTION' # _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 110.13 _cell.angle_gamma 90 _cell.entry_id 5G2A _cell.length_a 102.774 _cell.length_b 48.85 _cell.length_c 69.363 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5G2A _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _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 238 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 235 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id D _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 1268 _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 1.08 _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 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 5G2A _atom_sites.fract_transf_matrix[1][1] 0.00973 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003566 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020471 _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] 0.015355 _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 BR A 1 1266 1266 BR BR . C 2 BR A 1 1267 1267 BR BR . D 3 RET A 1 1268 1268 RET RET . E 4 HOH A 1 2001 2001 HOH HOH . E 4 HOH A 2 2002 2002 HOH HOH . E 4 HOH A 3 2003 2003 HOH HOH . E 4 HOH A 4 2004 2004 HOH HOH . E 4 HOH A 5 2005 2005 HOH HOH . E 4 HOH A 6 2006 2006 HOH HOH . E 4 HOH A 7 2007 2007 HOH HOH . E 4 HOH A 8 2008 2008 HOH HOH . E 4 HOH A 9 2009 2009 HOH HOH . E 4 HOH A 10 2010 2010 HOH HOH . E 4 HOH A 11 2011 2011 HOH HOH . E 4 HOH A 12 2012 2012 HOH HOH . E 4 HOH A 13 2013 2013 HOH HOH . E 4 HOH A 14 2014 2014 HOH HOH . E 4 HOH A 15 2015 2015 HOH HOH . E 4 HOH A 16 2016 2016 HOH HOH . E 4 HOH A 17 2017 2017 HOH HOH . E 4 HOH A 18 2018 2018 HOH HOH . E 4 HOH A 19 2019 2019 HOH HOH . E 4 HOH A 20 2020 2020 HOH HOH . E 4 HOH A 21 2021 2021 HOH HOH . E 4 HOH A 22 2022 2022 HOH HOH . E 4 HOH A 23 2023 2023 HOH HOH . E 4 HOH A 24 2024 2024 HOH HOH . E 4 HOH A 25 2025 2025 HOH HOH . E 4 HOH A 26 2026 2026 HOH HOH . E 4 HOH A 27 2027 2027 HOH HOH . E 4 HOH A 28 2028 2028 HOH HOH . E 4 HOH A 29 2029 2029 HOH HOH . E 4 HOH A 30 2030 2030 HOH HOH . E 4 HOH A 31 2031 2031 HOH HOH . E 4 HOH A 32 2032 2032 HOH HOH . E 4 HOH A 33 2033 2033 HOH HOH . E 4 HOH A 34 2034 2034 HOH HOH . E 4 HOH A 35 2035 2035 HOH HOH . E 4 HOH A 36 2036 2036 HOH HOH . E 4 HOH A 37 2037 2037 HOH HOH . E 4 HOH A 38 2038 2038 HOH HOH . E 4 HOH A 39 2039 2039 HOH HOH . E 4 HOH A 40 2040 2040 HOH HOH . E 4 HOH A 41 2041 2041 HOH HOH . E 4 HOH A 42 2042 2042 HOH HOH . E 4 HOH A 43 2043 2043 HOH HOH . E 4 HOH A 44 2044 2044 HOH HOH . E 4 HOH A 45 2045 2045 HOH HOH . E 4 HOH A 46 2046 2046 HOH HOH . E 4 HOH A 47 2047 2047 HOH HOH . E 4 HOH A 48 2048 2048 HOH HOH . E 4 HOH A 49 2049 2049 HOH HOH . E 4 HOH A 50 2050 2050 HOH HOH . E 4 HOH A 51 2051 2051 HOH HOH . E 4 HOH A 52 2052 2052 HOH HOH . E 4 HOH A 53 2053 2053 HOH HOH . E 4 HOH A 54 2054 2054 HOH HOH . E 4 HOH A 55 2055 2055 HOH HOH . E 4 HOH A 56 2056 2056 HOH HOH . E 4 HOH A 57 2057 2057 HOH HOH . E 4 HOH A 58 2058 2058 HOH HOH . E 4 HOH A 59 2059 2059 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 . . . D 3 -20.319 7.985 5.206 1 20.49 ? C1 RET 1268 A 1 HETATM 2 C C2 RET . . . D 3 -21.112 8.878 6.152 1 20.25 ? C2 RET 1268 A 1 HETATM 3 C C3 RET . . . D 3 -22.596 8.863 5.921 1 19.57 ? C3 RET 1268 A 1 HETATM 4 C C4 RET . . . D 3 -22.877 9.35 4.516 1 19.55 ? C4 RET 1268 A 1 HETATM 5 C C5 RET . . . D 3 -22.035 8.688 3.485 1 20.93 ? C5 RET 1268 A 1 HETATM 6 C C6 RET . . . D 3 -20.924 7.98 3.79 1 22.17 ? C6 RET 1268 A 1 HETATM 7 C C7 RET . . . D 3 -20.297 7.154 2.714 1 21.53 ? C7 RET 1268 A 1 HETATM 8 C C8 RET . . . D 3 -19.177 6.425 2.808 1 18.34 ? C8 RET 1268 A 1 HETATM 9 C C9 RET . . . D 3 -18.739 5.637 1.659 1 21.19 ? C9 RET 1268 A 1 HETATM 10 C C10 RET . . . D 3 -17.689 4.789 1.879 1 23.29 ? C10 RET 1268 A 1 HETATM 11 C C11 RET . . . D 3 -17.105 3.879 0.939 1 19.4 ? C11 RET 1268 A 1 HETATM 12 C C12 RET . . . D 3 -16.117 3.108 1.365 1 20.2 ? C12 RET 1268 A 1 HETATM 13 C C13 RET . . . D 3 -15.438 2.158 0.452 1 23.1 ? C13 RET 1268 A 1 HETATM 14 C C14 RET . . . D 3 -14.457 1.432 0.993 1 24.87 ? C14 RET 1268 A 1 HETATM 15 C C15 RET . . . D 3 -13.76 0.469 0.243 1 33.14 ? C15 RET 1268 A 1 HETATM 16 C C16 RET . . . D 3 -20.379 6.52 5.735 1 19.88 ? C16 RET 1268 A 1 HETATM 17 C C17 RET . . . D 3 -18.878 8.54 5.165 1 19.5 ? C17 RET 1268 A 1 HETATM 18 C C18 RET . . . D 3 -22.53 8.854 2.083 1 20.96 ? C18 RET 1268 A 1 HETATM 19 C C19 RET . . . D 3 -19.446 5.678 0.342 1 20.23 ? C19 RET 1268 A 1 HETATM 20 C C20 RET . . . D 3 -15.862 2.065 -1.027 1 24.67 ? C20 RET 1268 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #