data_8DGT # _model_server_result.job_id naQg1ylyoKcL16RaC4cInA _model_server_result.datetime_utc '2024-12-23 05:39:06' _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 8dgt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":801}' # _entry.id 8DGT # _exptl.entry_id 8DGT _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.247 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 2 _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 8DGT _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DGT _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_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 _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 ? _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 F N N ? 5 J N 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 disulf ? disulf1 A SG CYS 275 A CYS 248 1_555 A SG CYS 278 A CYS 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.988 ? covale ? covale1 A C SER 391 A SER 364 1_555 A N SEP 392 A SEP 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 A C SEP 392 A SEP 365 1_555 A N ALA 393 A ALA 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 A C ALA 755 A ALA 728 1_555 A N SEP 756 A SEP 729 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale4 A C SEP 756 A SEP 729 1_555 A N GLU 757 A GLU 730 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale5 B NZ LYS 214 B LYS 192 1_555 J O2G AGS . B AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.304 ? metalc ? metalc1 A ND1 HIS 262 A HIS 235 1_555 H ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc2 A SG CYS 275 A CYS 248 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc3 A SG CYS 278 A CYS 251 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? metalc ? metalc4 A SG CYS 288 A CYS 261 1_555 H ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc5 A SG CYS 291 A CYS 264 1_555 H ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc6 A ND1 HIS 296 A HIS 269 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc7 A SG CYS 299 A CYS 272 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc8 A SG CYS 307 A CYS 280 1_555 H ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc9 B OD1 ASN 217 B ASN 195 1_555 I MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc10 B OD2 ASP 230 B ASP 208 1_555 I MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc11 I MG MG . B MG 401 1_555 J O3G AGS . B AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.846 ? metalc ? metalc12 I MG MG . B MG 401 1_555 J O3A AGS . B AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc13 I MG MG . B MG 401 1_555 J O1A AGS . B AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.969 ? metalc ? metalc14 I MG MG . B MG 401 1_555 J O5' AGS . B AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? metalc ? metalc15 E OG SER 39 F SER 17 1_555 L MG MG . F MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc16 E OG1 THR 57 F THR 35 1_555 L MG MG . F MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc17 L MG MG . F MG 201 1_555 M O2B GNP . F GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc18 L MG MG . F MG 201 1_555 M O2G GNP . F GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? # _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 8DGT _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 F 5 AGS A 1 801 801 AGS AGS . G 6 ZN A 1 802 901 ZN ZN . H 6 ZN A 1 803 902 ZN ZN . I 7 MG B 1 401 503 MG MG . J 5 AGS B 1 402 607 AGS AGS . K 8 LCJ B 1 403 803 LCJ LCJ . L 7 MG F 1 201 201 MG MG . M 9 GNP F 1 202 202 GNP GNP . # 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 P PG AGS . . . F 5 138.535 117.372 147.008 1 92.79 ? PG AGS 801 A 1 HETATM 2 S S1G AGS . . . F 5 137.931 119.22 147.14 1 92.79 ? S1G AGS 801 A 1 HETATM 3 O O2G AGS . . . F 5 138.723 116.993 145.512 1 92.79 ? O2G AGS 801 A 1 HETATM 4 O O3G AGS . . . F 5 137.468 116.447 147.653 1 92.79 ? O3G AGS 801 A 1 HETATM 5 P PB AGS . . . F 5 141.195 117.735 147.009 1 92.79 ? PB AGS 801 A 1 HETATM 6 O O1B AGS . . . F 5 141.066 117.496 145.556 1 92.79 ? O1B AGS 801 A 1 HETATM 7 O O2B AGS . . . F 5 141.337 119.211 147.388 1 92.79 ? O2B AGS 801 A 1 HETATM 8 O O3B AGS . . . F 5 139.897 117.214 147.739 1 92.79 ? O3B AGS 801 A 1 HETATM 9 P PA AGS . . . F 5 142.456 115.432 147.679 1 92.79 ? PA AGS 801 A 1 HETATM 10 O O1A AGS . . . F 5 142.291 114.826 146.35 1 92.79 ? O1A AGS 801 A 1 HETATM 11 O O2A AGS . . . F 5 141.335 115.081 148.66 1 92.79 ? O2A AGS 801 A 1 HETATM 12 O O3A AGS . . . F 5 142.478 117.007 147.569 1 92.79 ? O3A AGS 801 A 1 HETATM 13 O O5' AGS . . . F 5 143.879 115.03 148.24 1 92.79 ? O5' AGS 801 A 1 HETATM 14 C C5' AGS . . . F 5 144.993 115.943 148.169 1 92.79 ? C5' AGS 801 A 1 HETATM 15 C C4' AGS . . . F 5 145.983 115.435 147.149 1 92.79 ? C4' AGS 801 A 1 HETATM 16 O O4' AGS . . . F 5 145.545 114.165 146.64 1 92.79 ? O4' AGS 801 A 1 HETATM 17 C C3' AGS . . . F 5 146.145 116.295 145.901 1 92.79 ? C3' AGS 801 A 1 HETATM 18 O O3' AGS . . . F 5 147.093 117.335 146.12 1 92.79 ? O3' AGS 801 A 1 HETATM 19 C C2' AGS . . . F 5 146.645 115.287 144.852 1 92.79 ? C2' AGS 801 A 1 HETATM 20 O O2' AGS . . . F 5 148.061 115.317 144.723 1 92.79 ? O2' AGS 801 A 1 HETATM 21 C C1' AGS . . . F 5 146.197 113.928 145.41 1 92.79 ? C1' AGS 801 A 1 HETATM 22 N N9 AGS . . . F 5 145.293 113.188 144.541 1 92.79 ? N9 AGS 801 A 1 HETATM 23 C C8 AGS . . . F 5 143.925 113.23 144.547 1 92.79 ? C8 AGS 801 A 1 HETATM 24 N N7 AGS . . . F 5 143.36 112.451 143.654 1 92.79 ? N7 AGS 801 A 1 HETATM 25 C C5 AGS . . . F 5 144.435 111.854 143.015 1 92.79 ? C5 AGS 801 A 1 HETATM 26 C C6 AGS . . . F 5 144.511 110.921 141.967 1 92.79 ? C6 AGS 801 A 1 HETATM 27 N N6 AGS . . . F 5 143.445 110.404 141.352 1 92.79 ? N6 AGS 801 A 1 HETATM 28 N N1 AGS . . . F 5 145.742 110.531 141.566 1 92.79 ? N1 AGS 801 A 1 HETATM 29 C C2 AGS . . . F 5 146.814 111.043 142.176 1 92.79 ? C2 AGS 801 A 1 HETATM 30 N N3 AGS . . . F 5 146.864 111.928 143.173 1 92.79 ? N3 AGS 801 A 1 HETATM 31 C C4 AGS . . . F 5 145.631 112.297 143.55 1 92.79 ? C4 AGS 801 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #