data_1QHY # _model_server_result.job_id zvwRhXhswiXybWM0X-kKHw _model_server_result.datetime_utc '2024-11-04 22:42:10' _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 1qhy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 1QHY # _exptl.entry_id 1QHY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _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 90 _cell.entry_id 1QHY _cell.length_a 200 _cell.length_b 200 _cell.length_c 200 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1QHY _symmetry.cell_setting ? _symmetry.Int_Tables_number 214 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 41 3 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 1,2,3,4 # 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' 13_455 y-1/4,x+1/4,-z+1/4 0 1 0 1 0 0 0 0 -1 -50 50 50 3 'crystal symmetry operation' 26_555 -x,-y+1/2,z -1 0 0 0 -1 0 0 0 1 0 100 0 4 'crystal symmetry operation' 38_555 -y+1/4,-x+1/4,-z+1/4 0 -1 0 -1 0 0 0 0 -1 50 50 50 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 A OG SER 17 A SER 17 1_555 C MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc2 A OD2 ASP 92 A ASP 92 1_555 C MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc3 C MG MG . A MG 500 1_555 D O2B AGS . A AGS 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? metalc ? metalc4 C MG MG . A MG 500 1_555 D O2G AGS . A AGS 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? # _chem_comp.formula 'C10 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id AGS _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" # _atom_sites.entry_id 1QHY _atom_sites.fract_transf_matrix[1][1] 0.005 _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] 0.005 _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] 0.005 _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 SO4 A 1 602 602 SO4 SO4 . C 3 MG A 1 500 500 MG MG . D 4 AGS A 1 501 501 AGS AGS . E 5 CLM A 1 999 999 CLM CLM . F 5 CLM A 1 888 888 CLM CLM . G 6 HOH A 1 1000 1 HOH HOH . G 6 HOH A 2 1001 2 HOH HOH . G 6 HOH A 3 1002 3 HOH HOH . G 6 HOH A 4 1003 4 HOH HOH . G 6 HOH A 5 1004 5 HOH HOH . G 6 HOH A 6 1005 6 HOH HOH . G 6 HOH A 7 1006 7 HOH HOH . G 6 HOH A 8 1007 8 HOH HOH . G 6 HOH A 9 1008 9 HOH HOH . G 6 HOH A 10 1009 10 HOH HOH . G 6 HOH A 11 1010 11 HOH HOH . G 6 HOH A 12 1011 12 HOH HOH . G 6 HOH A 13 1012 13 HOH HOH . G 6 HOH A 14 1013 14 HOH HOH . G 6 HOH A 15 1014 15 HOH HOH . G 6 HOH A 16 1015 16 HOH HOH . G 6 HOH A 17 1016 17 HOH HOH . G 6 HOH A 18 1017 18 HOH HOH . G 6 HOH A 19 1018 19 HOH HOH . G 6 HOH A 20 1019 20 HOH HOH . G 6 HOH A 21 1020 21 HOH HOH . G 6 HOH A 22 1021 22 HOH HOH . G 6 HOH A 23 1022 23 HOH HOH . G 6 HOH A 24 1023 24 HOH HOH . G 6 HOH A 25 1024 25 HOH HOH . G 6 HOH A 26 1025 26 HOH HOH . G 6 HOH A 27 1026 27 HOH HOH . G 6 HOH A 28 1027 28 HOH HOH . G 6 HOH A 29 1028 29 HOH HOH . G 6 HOH A 30 1029 30 HOH HOH . G 6 HOH A 31 1030 31 HOH HOH . G 6 HOH A 32 1031 32 HOH HOH . G 6 HOH A 33 1032 33 HOH HOH . G 6 HOH A 34 1033 34 HOH HOH . G 6 HOH A 35 1034 35 HOH HOH . G 6 HOH A 36 1035 36 HOH HOH . G 6 HOH A 37 1036 37 HOH HOH . G 6 HOH A 38 1037 38 HOH HOH . G 6 HOH A 39 1038 39 HOH HOH . G 6 HOH A 40 1039 40 HOH HOH . G 6 HOH A 41 1040 41 HOH HOH . G 6 HOH A 42 1041 42 HOH HOH . G 6 HOH A 43 1042 43 HOH HOH . G 6 HOH A 44 1043 44 HOH HOH . G 6 HOH A 45 1044 45 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 S S1G AGS . . . D 4 13.247 47.788 31.66 0.5 59.05 ? S1G AGS 501 A 1 HETATM 2 O O2G AGS . . . D 4 11.538 46.751 33.324 0.5 59.05 ? O2G AGS 501 A 1 HETATM 3 O O3G AGS . . . D 4 14.106 47.024 33.813 0.5 59.05 ? O3G AGS 501 A 1 HETATM 4 P PB AGS . . . D 4 12.72 43.88 32.359 1 59.05 ? PB AGS 501 A 1 HETATM 5 O O1B AGS . . . D 4 13.477 43.281 33.485 1 59.05 ? O1B AGS 501 A 1 HETATM 6 O O2B AGS . . . D 4 11.343 44.039 32.482 1 59.05 ? O2B AGS 501 A 1 HETATM 7 O O3B AGS . . . D 4 13.302 45.349 31.962 1 59.05 ? O3B AGS 501 A 1 HETATM 8 P PA AGS . . . D 4 11.867 42.392 30.197 0.5 59.05 ? PA AGS 501 A 1 HETATM 9 O O1A AGS . . . D 4 11.179 41.281 30.946 0.5 59.05 ? O1A AGS 501 A 1 HETATM 10 O O2A AGS . . . D 4 10.872 43.421 29.616 0.5 59.05 ? O2A AGS 501 A 1 HETATM 11 O O3A AGS . . . D 4 12.982 43.081 31.141 0.5 59.05 ? O3A AGS 501 A 1 HETATM 12 O O5' AGS . . . D 4 12.792 41.772 29.087 0.5 59.05 ? O5' AGS 501 A 1 HETATM 13 C C5' AGS . . . D 4 13.077 42.555 27.887 0.5 59.05 ? C5' AGS 501 A 1 HETATM 14 C C4' AGS . . . D 4 12.641 41.916 26.788 0.5 59.05 ? C4' AGS 501 A 1 HETATM 15 O O4' AGS . . . D 4 13.358 40.664 26.703 0.5 59.05 ? O4' AGS 501 A 1 HETATM 16 C C3' AGS . . . D 4 11.151 41.585 26.767 0.5 59.05 ? C3' AGS 501 A 1 HETATM 17 O O3' AGS . . . D 4 10.653 42.03 25.488 0.5 59.05 ? O3' AGS 501 A 1 HETATM 18 C C2' AGS . . . D 4 11.095 40.082 26.974 0.5 59.05 ? C2' AGS 501 A 1 HETATM 19 O O2' AGS . . . D 4 10.099 39.438 26.194 0.5 59.05 ? O2' AGS 501 A 1 HETATM 20 C C1' AGS . . . D 4 12.488 39.531 26.592 0.5 59.05 ? C1' AGS 501 A 1 HETATM 21 N N9 AGS . . . D 4 13.006 38.451 27.456 0.5 59.05 ? N9 AGS 501 A 1 HETATM 22 C C8 AGS . . . D 4 12.723 38.292 28.793 0.5 59.05 ? C8 AGS 501 A 1 HETATM 23 N N7 AGS . . . D 4 13.298 37.269 29.357 0.5 59.05 ? N7 AGS 501 A 1 HETATM 24 C C5 AGS . . . D 4 14.01 36.712 28.307 0.5 59.05 ? C5 AGS 501 A 1 HETATM 25 C C6 AGS . . . D 4 14.87 35.579 28.221 0.5 59.05 ? C6 AGS 501 A 1 HETATM 26 N N6 AGS . . . D 4 15.094 34.819 29.276 0.5 59.05 ? N6 AGS 501 A 1 HETATM 27 N N1 AGS . . . D 4 15.445 35.277 27.024 0.5 59.05 ? N1 AGS 501 A 1 HETATM 28 C C2 AGS . . . D 4 15.2 36.061 25.961 0.5 59.05 ? C2 AGS 501 A 1 HETATM 29 N N3 AGS . . . D 4 14.415 37.162 25.905 0.5 59.05 ? N3 AGS 501 A 1 HETATM 30 C C4 AGS . . . D 4 13.85 37.435 27.142 0.5 59.05 ? C4 AGS 501 A 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 30 #