data_2JAG # _model_server_result.job_id Sm5-EQUcCrBBKnAKMvSpXw _model_server_result.datetime_utc '2024-10-18 20:33:50' _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 2jag # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":900}' # _entry.id 2JAG # _exptl.entry_id 2JAG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 5 _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 2JAG _cell.length_a 95.042 _cell.length_b 95.042 _cell.length_c 157.674 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2JAG _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,G _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' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 95.042 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 47.521 82.308786 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _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 242 _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 F _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 B _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id B _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 1.438 _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 374 n n C1 C6 RET sing 375 n n C1 C16 RET sing 376 n n C1 C17 RET sing 377 n n C2 C3 RET sing 378 n n C2 H21 RET sing 379 n n C2 H22 RET sing 380 n n C3 C4 RET sing 381 n n C3 H31 RET sing 382 n n C3 H32 RET sing 383 n n C4 C5 RET sing 384 n n C4 H41 RET sing 385 n n C4 H42 RET sing 386 n n C5 C6 RET doub 387 n n C5 C18 RET sing 388 n n C6 C7 RET sing 389 n n C7 C8 RET doub 390 e n C7 H7 RET sing 391 n n C8 C9 RET sing 392 n n C8 H8 RET sing 393 n n C9 C10 RET doub 394 e n C9 C19 RET sing 395 n n C10 C11 RET sing 396 n n C10 H10 RET sing 397 n n C11 C12 RET doub 398 e n C11 H11 RET sing 399 n n C12 C13 RET sing 400 n n C12 H12 RET sing 401 n n C13 C14 RET doub 402 e n C13 C20 RET sing 403 n n C14 C15 RET sing 404 n n C14 H14 RET sing 405 n n C15 O1 RET doub 406 n n C15 H15 RET sing 407 n n C16 H161 RET sing 408 n n C16 H162 RET sing 409 n n C16 H163 RET sing 410 n n C17 H171 RET sing 411 n n C17 H172 RET sing 412 n n C17 H173 RET sing 413 n n C18 H181 RET sing 414 n n C18 H182 RET sing 415 n n C18 H183 RET sing 416 n n C19 H191 RET sing 417 n n C19 H192 RET sing 418 n n C19 H193 RET sing 419 n n C20 H201 RET sing 420 n n C20 H202 RET sing 421 n n C20 H203 RET sing 422 n n # _atom_sites.entry_id 2JAG _atom_sites.fract_transf_matrix[1][1] 0.010522 _atom_sites.fract_transf_matrix[1][2] 0.006075 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012149 _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] 0.006342 _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 CL A 1 501 501 CL CL . C 2 CL A 1 502 502 CL CL . D 3 PLM A 1 700 700 PLM PLM . E 4 BOG A 1 801 801 BOG BOG . F 5 RET A 1 900 900 RET RET . G 6 HOH A 1 2001 2001 HOH HOH . G 6 HOH A 2 2002 2002 HOH HOH . G 6 HOH A 3 2003 2003 HOH HOH . G 6 HOH A 4 2004 2004 HOH HOH . G 6 HOH A 5 2005 2005 HOH HOH . G 6 HOH A 6 2006 2006 HOH HOH . G 6 HOH A 7 2007 2007 HOH HOH . G 6 HOH A 8 2008 2008 HOH HOH . G 6 HOH A 9 2009 2009 HOH HOH . G 6 HOH A 10 2010 2010 HOH HOH . G 6 HOH A 11 2011 2011 HOH HOH . G 6 HOH A 12 2012 2012 HOH HOH . G 6 HOH A 13 2013 2013 HOH HOH . G 6 HOH A 14 2014 2014 HOH HOH . G 6 HOH A 15 2015 2015 HOH HOH . G 6 HOH A 16 2016 2016 HOH HOH . G 6 HOH A 17 2017 2017 HOH HOH . G 6 HOH A 18 2018 2018 HOH HOH . G 6 HOH A 19 2019 2019 HOH HOH . G 6 HOH A 20 2020 2020 HOH HOH . G 6 HOH A 21 2021 2021 HOH HOH . G 6 HOH A 22 2022 2022 HOH HOH . G 6 HOH A 23 2023 2023 HOH HOH . G 6 HOH A 24 2024 2024 HOH HOH . G 6 HOH A 25 2025 2025 HOH HOH . G 6 HOH A 26 2026 2026 HOH HOH . G 6 HOH A 27 2027 2027 HOH HOH . G 6 HOH A 28 2028 2028 HOH HOH . G 6 HOH A 29 2029 2029 HOH HOH . G 6 HOH A 30 2030 2030 HOH HOH . G 6 HOH A 31 2031 2031 HOH HOH . G 6 HOH A 32 2032 2032 HOH HOH . G 6 HOH A 33 2033 2033 HOH HOH . G 6 HOH A 34 2034 2034 HOH HOH . G 6 HOH A 35 2035 2035 HOH HOH . G 6 HOH A 36 2036 2036 HOH HOH . G 6 HOH A 37 2037 2037 HOH HOH . G 6 HOH A 38 2038 2038 HOH HOH . G 6 HOH A 39 2039 2039 HOH HOH . G 6 HOH A 40 2040 2040 HOH HOH . G 6 HOH A 41 2041 2041 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 . A . F 5 34.908 14.978 30.594 0.4 17.18 ? C1 RET 900 A 1 HETATM 2 C C1 RET . B . F 5 34.988 15.058 30.702 0.6 26.33 ? C1 RET 900 A 1 HETATM 3 C C2 RET . A . F 5 33.813 15.48 31.64 0.4 17.59 ? C2 RET 900 A 1 HETATM 4 C C2 RET . B . F 5 33.879 15.496 31.812 0.6 26.77 ? C2 RET 900 A 1 HETATM 5 C C3 RET . A . F 5 32.824 16.582 31.134 0.4 17.85 ? C3 RET 900 A 1 HETATM 6 C C3 RET . B . F 5 32.766 16.49 31.277 0.6 26.5 ? C3 RET 900 A 1 HETATM 7 C C4 RET . A . F 5 32.005 16.067 29.867 0.4 16.83 ? C4 RET 900 A 1 HETATM 8 C C4 RET . B . F 5 31.99 15.881 30.012 0.6 25.4 ? C4 RET 900 A 1 HETATM 9 C C5 RET . A . F 5 32.908 15.458 28.717 0.4 17.38 ? C5 RET 900 A 1 HETATM 10 C C5 RET . B . F 5 33.006 15.487 28.806 0.6 26.1 ? C5 RET 900 A 1 HETATM 11 C C6 RET . A . F 5 34.336 14.915 29.037 0.4 17.38 ? C6 RET 900 A 1 HETATM 12 C C6 RET . B . F 5 34.397 14.965 29.101 0.6 26.83 ? C6 RET 900 A 1 HETATM 13 C C7 RET . A . F 5 35.158 14.432 27.888 0.4 15.89 ? C7 RET 900 A 1 HETATM 14 C C7 RET . B . F 5 35.193 14.426 27.906 0.6 26.41 ? C7 RET 900 A 1 HETATM 15 C C8 RET . A . F 5 36.449 14.015 27.792 0.4 15.89 ? C8 RET 900 A 1 HETATM 16 C C8 RET . B . F 5 36.496 14.048 27.767 0.6 27.98 ? C8 RET 900 A 1 HETATM 17 C C9 RET . A . F 5 37.021 13.374 26.644 0.4 16.69 ? C9 RET 900 A 1 HETATM 18 C C9 RET . B . F 5 37.077 13.347 26.61 0.6 29.69 ? C9 RET 900 A 1 HETATM 19 C C10 RET . A . F 5 38.32 12.962 26.924 0.4 17.4 ? C10 RET 900 A 1 HETATM 20 C C10 RET . B . F 5 38.455 13.06 26.781 0.6 31.61 ? C10 RET 900 A 1 HETATM 21 C C11 RET . A . F 5 39.145 12.289 26.05 0.4 18.43 ? C11 RET 900 A 1 HETATM 22 C C11 RET . B . F 5 39.214 12.274 25.871 0.6 33.17 ? C11 RET 900 A 1 HETATM 23 C C12 RET . A . F 5 40.42 11.87 26.472 0.4 17.24 ? C12 RET 900 A 1 HETATM 24 C C12 RET . B . F 5 40.597 11.997 25.984 0.6 34.76 ? C12 RET 900 A 1 HETATM 25 C C13 RET . A . F 5 41.369 11.222 25.583 0.4 19.47 ? C13 RET 900 A 1 HETATM 26 C C13 RET . B . F 5 41.302 11.084 24.997 0.6 36 ? C13 RET 900 A 1 HETATM 27 C C14 RET . A . F 5 42.609 10.944 26.214 0.4 20.55 ? C14 RET 900 A 1 HETATM 28 C C14 RET . B . F 5 42.628 10.717 25.121 0.6 36.03 ? C14 RET 900 A 1 HETATM 29 C C15 RET . A . F 5 43.772 10.529 25.599 0.4 21.99 ? C15 RET 900 A 1 HETATM 30 C C15 RET . B . F 5 43.679 11.137 25.943 0.6 35.91 ? C15 RET 900 A 1 HETATM 31 C C16 RET . A . F 5 36.068 16.044 30.727 0.4 18.36 ? C16 RET 900 A 1 HETATM 32 C C16 RET . B . F 5 36.113 16.08 30.801 0.6 27.55 ? C16 RET 900 A 1 HETATM 33 C C17 RET . A . F 5 35.391 13.519 31.13 0.4 17.67 ? C17 RET 900 A 1 HETATM 34 C C17 RET . B . F 5 35.483 13.684 31.239 0.6 26.61 ? C17 RET 900 A 1 HETATM 35 C C18 RET . A . F 5 32.266 15.423 27.323 0.4 18.12 ? C18 RET 900 A 1 HETATM 36 C C18 RET . B . F 5 32.423 15.721 27.383 0.6 26.64 ? C18 RET 900 A 1 HETATM 37 C C19 RET . A . F 5 36.155 13.023 25.306 0.4 15.82 ? C19 RET 900 A 1 HETATM 38 C C19 RET . B . F 5 36.221 12.964 25.312 0.6 28.73 ? C19 RET 900 A 1 HETATM 39 C C20 RET . A . F 5 41.036 10.852 24.131 0.4 19.96 ? C20 RET 900 A 1 HETATM 40 C C20 RET . B . F 5 40.62 10.279 24.04 0.6 36.12 ? C20 RET 900 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 40 #