data_5G2D # _model_server_result.job_id S79nB0-Z4-SbpfluI7zZaw _model_server_result.datetime_utc '2024-11-23 01:48:28' _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 5g2d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1274}' # _entry.id 5G2D # _exptl.entry_id 5G2D _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 131.89 _cell.angle_gamma 90 _cell.entry_id 5G2D _cell.length_a 103.252 _cell.length_b 49.447 _cell.length_c 78.402 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5G2D _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,F,G,H,I,J,K,L,M,N _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 J _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 J _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 1274 _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 1.055 _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 346 n n C1 C6 RET sing 347 n n C1 C16 RET sing 348 n n C1 C17 RET sing 349 n n C2 C3 RET sing 350 n n C2 H21 RET sing 351 n n C2 H22 RET sing 352 n n C3 C4 RET sing 353 n n C3 H31 RET sing 354 n n C3 H32 RET sing 355 n n C4 C5 RET sing 356 n n C4 H41 RET sing 357 n n C4 H42 RET sing 358 n n C5 C6 RET doub 359 n n C5 C18 RET sing 360 n n C6 C7 RET sing 361 n n C7 C8 RET doub 362 e n C7 H7 RET sing 363 n n C8 C9 RET sing 364 n n C8 H8 RET sing 365 n n C9 C10 RET doub 366 e n C9 C19 RET sing 367 n n C10 C11 RET sing 368 n n C10 H10 RET sing 369 n n C11 C12 RET doub 370 e n C11 H11 RET sing 371 n n C12 C13 RET sing 372 n n C12 H12 RET sing 373 n n C13 C14 RET doub 374 e n C13 C20 RET sing 375 n n C14 C15 RET sing 376 n n C14 H14 RET sing 377 n n C15 O1 RET doub 378 n n C15 H15 RET sing 379 n n C16 H161 RET sing 380 n n C16 H162 RET sing 381 n n C16 H163 RET sing 382 n n C17 H171 RET sing 383 n n C17 H172 RET sing 384 n n C17 H173 RET sing 385 n n C18 H181 RET sing 386 n n C18 H182 RET sing 387 n n C18 H183 RET sing 388 n n C19 H191 RET sing 389 n n C19 H192 RET sing 390 n n C19 H193 RET sing 391 n n C20 H201 RET sing 392 n n C20 H202 RET sing 393 n n C20 H203 RET sing 394 n n # _atom_sites.entry_id 5G2D _atom_sites.fract_transf_matrix[1][1] 0.009685 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.008687 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020224 _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] 0.017134 _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 OLA A 1 1266 1266 OLA OLA . C 2 OLA A 1 1267 1267 OLA OLA . D 2 OLA A 1 1268 1268 OLA OLA . E 2 OLA A 1 1269 1269 OLA OLA . F 2 OLA A 1 1270 1270 OLA OLA . G 2 OLA A 1 1271 1271 OLA OLA . H 2 OLA A 1 1272 1272 OLA OLA . I 2 OLA A 1 1273 1273 OLA OLA . J 3 RET A 1 1274 1274 RET RET . K 4 PEG A 1 1275 1275 PEG PEG . L 5 CL A 1 1276 1276 CL CL . M 5 CL A 1 1277 1277 CL CL . N 6 HOH A 1 2001 2001 HOH HOH . N 6 HOH A 2 2002 2002 HOH HOH . N 6 HOH A 3 2003 2003 HOH HOH . N 6 HOH A 4 2004 2004 HOH HOH . N 6 HOH A 5 2005 2005 HOH HOH . N 6 HOH A 6 2006 2006 HOH HOH . N 6 HOH A 7 2007 2007 HOH HOH . N 6 HOH A 8 2008 2008 HOH HOH . N 6 HOH A 9 2009 2009 HOH HOH . N 6 HOH A 10 2010 2010 HOH HOH . N 6 HOH A 11 2011 2011 HOH HOH . N 6 HOH A 12 2012 2012 HOH HOH . N 6 HOH A 13 2013 2013 HOH HOH . N 6 HOH A 14 2014 2014 HOH HOH . N 6 HOH A 15 2015 2015 HOH HOH . N 6 HOH A 16 2016 2016 HOH HOH . N 6 HOH A 17 2017 2017 HOH HOH . N 6 HOH A 18 2018 2018 HOH HOH . N 6 HOH A 19 2019 2019 HOH HOH . N 6 HOH A 20 2020 2020 HOH HOH . N 6 HOH A 21 2021 2021 HOH HOH . N 6 HOH A 22 2022 2022 HOH HOH . N 6 HOH A 23 2023 2023 HOH HOH . N 6 HOH A 24 2024 2024 HOH HOH . N 6 HOH A 25 2025 2025 HOH HOH . N 6 HOH A 26 2026 2026 HOH HOH . N 6 HOH A 27 2027 2027 HOH HOH . N 6 HOH A 28 2028 2028 HOH HOH . N 6 HOH A 29 2029 2029 HOH HOH . N 6 HOH A 30 2030 2030 HOH HOH . N 6 HOH A 31 2031 2031 HOH HOH . N 6 HOH A 32 2032 2032 HOH HOH . N 6 HOH A 33 2033 2033 HOH HOH . N 6 HOH A 34 2034 2034 HOH HOH . N 6 HOH A 35 2035 2035 HOH HOH . N 6 HOH A 36 2036 2036 HOH HOH . N 6 HOH A 37 2037 2037 HOH HOH . N 6 HOH A 38 2038 2038 HOH HOH . N 6 HOH A 39 2039 2039 HOH HOH . N 6 HOH A 40 2040 2040 HOH HOH . N 6 HOH A 41 2041 2041 HOH HOH . N 6 HOH A 42 2042 2042 HOH HOH . N 6 HOH A 43 2043 2043 HOH HOH . N 6 HOH A 44 2044 2044 HOH HOH . N 6 HOH A 45 2045 2045 HOH HOH . N 6 HOH A 46 2046 2046 HOH HOH . N 6 HOH A 47 2047 2047 HOH HOH . N 6 HOH A 48 2048 2048 HOH HOH . N 6 HOH A 49 2049 2049 HOH HOH . N 6 HOH A 50 2050 2050 HOH HOH . N 6 HOH A 51 2051 2051 HOH HOH . N 6 HOH A 52 2052 2052 HOH HOH . N 6 HOH A 53 2053 2053 HOH HOH . N 6 HOH A 54 2054 2054 HOH HOH . N 6 HOH A 55 2055 2055 HOH HOH . N 6 HOH A 56 2056 2056 HOH HOH . N 6 HOH A 57 2057 2057 HOH HOH . N 6 HOH A 58 2058 2058 HOH HOH . N 6 HOH A 59 2059 2059 HOH HOH . N 6 HOH A 60 2060 2060 HOH HOH . N 6 HOH A 61 2061 2061 HOH HOH . N 6 HOH A 62 2062 2062 HOH HOH . N 6 HOH A 63 2063 2063 HOH HOH . N 6 HOH A 64 2064 2064 HOH HOH . N 6 HOH A 65 2065 2065 HOH HOH . N 6 HOH A 66 2066 2066 HOH HOH . N 6 HOH A 67 2067 2067 HOH HOH . N 6 HOH A 68 2068 2068 HOH HOH . N 6 HOH A 69 2069 2069 HOH HOH . N 6 HOH A 70 2070 2070 HOH HOH . N 6 HOH A 71 2071 2071 HOH HOH . N 6 HOH A 72 2072 2072 HOH HOH . N 6 HOH A 73 2073 2073 HOH HOH . N 6 HOH A 74 2074 2074 HOH HOH . N 6 HOH A 75 2075 2075 HOH HOH . N 6 HOH A 76 2076 2076 HOH HOH . N 6 HOH A 77 2077 2077 HOH HOH . N 6 HOH A 78 2078 2078 HOH HOH . N 6 HOH A 79 2079 2079 HOH HOH . N 6 HOH A 80 2080 2080 HOH HOH . N 6 HOH A 81 2081 2081 HOH HOH . N 6 HOH A 82 2082 2082 HOH HOH . N 6 HOH A 83 2083 2083 HOH HOH . N 6 HOH A 84 2084 2084 HOH HOH . N 6 HOH A 85 2085 2085 HOH HOH . N 6 HOH A 86 2086 2086 HOH HOH . N 6 HOH A 87 2087 2087 HOH HOH . N 6 HOH A 88 2088 2088 HOH HOH . N 6 HOH A 89 2089 2089 HOH HOH . N 6 HOH A 90 2090 2090 HOH HOH . N 6 HOH A 91 2091 2091 HOH HOH . N 6 HOH A 92 2092 2092 HOH HOH . N 6 HOH A 93 2093 2093 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 . . . J 3 20.547 7.705 -5.047 1 16.85 ? C1 RET 1274 A 1 HETATM 2 C C2 RET . . . J 3 21.234 8.632 -6.044 1 15.52 ? C2 RET 1274 A 1 HETATM 3 C C3 RET . . . J 3 22.737 8.611 -5.897 1 14.91 ? C3 RET 1274 A 1 HETATM 4 C C4 RET . . . J 3 23.115 9.044 -4.544 1 16.19 ? C4 RET 1274 A 1 HETATM 5 C C5 RET . . . J 3 22.34 8.353 -3.43 1 16.51 ? C5 RET 1274 A 1 HETATM 6 C C6 RET . . . J 3 21.212 7.649 -3.689 1 15.65 ? C6 RET 1274 A 1 HETATM 7 C C7 RET . . . J 3 20.627 6.873 -2.595 1 14.4 ? C7 RET 1274 A 1 HETATM 8 C C8 RET . . . J 3 19.587 6.122 -2.697 1 14.16 ? C8 RET 1274 A 1 HETATM 9 C C9 RET . . . J 3 19.12 5.322 -1.58 1 15.4 ? C9 RET 1274 A 1 HETATM 10 C C10 RET . . . J 3 18.047 4.565 -1.811 1 15.62 ? C10 RET 1274 A 1 HETATM 11 C C11 RET . . . J 3 17.391 3.657 -0.868 1 17.87 ? C11 RET 1274 A 1 HETATM 12 C C12 RET . . . J 3 16.339 2.975 -1.237 1 17.18 ? C12 RET 1274 A 1 HETATM 13 C C13 RET . . . J 3 15.609 1.982 -0.341 1 20.01 ? C13 RET 1274 A 1 HETATM 14 C C14 RET . . . J 3 14.577 1.298 -0.909 1 21.61 ? C14 RET 1274 A 1 HETATM 15 C C15 RET . . . J 3 13.779 0.43 -0.139 1 27.18 ? C15 RET 1274 A 1 HETATM 16 C C16 RET . . . J 3 20.576 6.27 -5.639 1 16.12 ? C16 RET 1274 A 1 HETATM 17 C C17 RET . . . J 3 19.117 8.241 -4.838 1 16.6 ? C17 RET 1274 A 1 HETATM 18 C C18 RET . . . J 3 22.894 8.507 -2.041 1 16.03 ? C18 RET 1274 A 1 HETATM 19 C C19 RET . . . J 3 19.822 5.366 -0.253 1 14.88 ? C19 RET 1274 A 1 HETATM 20 C C20 RET . . . J 3 16.063 1.735 1.085 1 17.61 ? C20 RET 1274 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 20 #