data_7WAD # _model_server_result.job_id 61Ailu1lVVuWYreZc4z8TQ _model_server_result.datetime_utc '2024-10-19 22:38:18' _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 7wad # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1002}' # _entry.id 7WAD # _exptl.entry_id 7WAD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.247 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 8 _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 7WAD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7WAD _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,N,O,P _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 ? 3 F N N ? 3 G N N ? 3 I N N ? 3 J N N ? 3 L N N ? 3 M N N ? 3 O N N ? 3 P 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 metalc ? metalc1 A OG1 THR 500 A THR 500 1_555 E MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? metalc ? metalc2 E MG MG . A MG 1001 1_555 G O3G AGS . A AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc3 E MG MG . A MG 1001 1_555 G O2B AGS . A AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc4 E MG MG . A MG 1001 1_555 G O3B AGS . A AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc5 B OG1 THR 500 B THR 500 1_555 H MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc6 H MG MG . B MG 1001 1_555 J O2B AGS . B AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc7 H MG MG . B MG 1001 1_555 J O3G AGS . B AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc8 H MG MG . B MG 1001 1_555 J O3B AGS . B AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc9 C OG1 THR 500 C THR 500 1_555 K MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc10 K MG MG . C MG 1001 1_555 M O3G AGS . C AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc11 K MG MG . C MG 1001 1_555 M O2B AGS . C AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc12 K MG MG . C MG 1001 1_555 M O3B AGS . C AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc13 D OG1 THR 500 D THR 500 1_555 N MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? metalc ? metalc14 N MG MG . D MG 1001 1_555 P O2B AGS . D AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc15 N MG MG . D MG 1001 1_555 P O3G AGS . D AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc16 N MG MG . D MG 1001 1_555 P O3B AGS . D AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? # _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" # 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 PG S1G AGS doub 1 n n PG O2G AGS sing 2 n n PG O3G AGS sing 3 n n PG O3B AGS sing 4 n n PB O1B AGS doub 5 n n PB O2B AGS sing 6 n n PB O3B AGS sing 7 n n PB O3A AGS sing 8 n n PA O1A AGS doub 9 n n PA O2A AGS sing 10 n n PA O3A AGS sing 11 n n PA O5' AGS sing 12 n n O5' C5' AGS sing 13 n n C5' C4' AGS sing 14 n n C4' O4' AGS sing 15 n n C4' C3' AGS sing 16 n n O4' C1' AGS sing 17 n n C3' O3' AGS sing 18 n n C3' C2' AGS sing 19 n n C2' O2' AGS sing 20 n n C2' C1' AGS sing 21 n n C1' N9 AGS sing 22 n n N9 C8 AGS sing 23 n y N9 C4 AGS sing 24 n y C8 N7 AGS doub 25 n y N7 C5 AGS sing 26 n y C5 C6 AGS sing 27 n y C5 C4 AGS doub 28 n y C6 N6 AGS sing 29 n n C6 N1 AGS doub 30 n y N1 C2 AGS sing 31 n y C2 N3 AGS doub 32 n y N3 C4 AGS sing 33 n y O2G HOG2 AGS sing 34 n n O3G H21 AGS sing 35 n n O2B HOB2 AGS sing 36 n n O2A HOA2 AGS sing 37 n n C5' "H5'1" AGS sing 38 n n C5' "H5'2" AGS sing 39 n n C4' H4' AGS sing 40 n n C3' H3' AGS sing 41 n n O3' HO3' AGS sing 42 n n C2' H2' AGS sing 43 n n O2' HO2' AGS sing 44 n n C1' H1' AGS sing 45 n n C8 H8 AGS sing 46 n n N6 HN61 AGS sing 47 n n N6 HN62 AGS sing 48 n n C2 H2 AGS sing 49 n n # _atom_sites.entry_id 7WAD _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 E 2 MG A 1 1001 1 MG MG . F 3 AGS A 1 1002 2 AGS AGS . G 3 AGS A 1 1003 3 AGS AGS . H 2 MG B 1 1001 1 MG MG . I 3 AGS B 1 1002 2 AGS AGS . J 3 AGS B 1 1003 3 AGS AGS . K 2 MG C 1 1001 1 MG MG . L 3 AGS C 1 1002 2 AGS AGS . M 3 AGS C 1 1003 3 AGS AGS . N 2 MG D 1 1001 1 MG MG . O 3 AGS D 1 1002 2 AGS AGS . P 3 AGS D 1 1003 3 AGS AGS . # 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 3 93.617 130.716 102.757 1 144.25 ? PG AGS 1002 A 1 HETATM 2 S S1G AGS . . . F 3 95.428 130.424 103.412 1 144.25 ? S1G AGS 1002 A 1 HETATM 3 O O2G AGS . . . F 3 92.898 129.344 102.59 1 144.25 ? O2G AGS 1002 A 1 HETATM 4 O O3G AGS . . . F 3 93.671 131.441 101.379 1 144.25 ? O3G AGS 1002 A 1 HETATM 5 P PB AGS . . . F 3 91.277 131.343 103.987 1 144.25 ? PB AGS 1002 A 1 HETATM 6 O O1B AGS . . . F 3 90.569 132.625 104.208 1 144.25 ? O1B AGS 1002 A 1 HETATM 7 O O2B AGS . . . F 3 90.79 130.611 102.734 1 144.25 ? O2B AGS 1002 A 1 HETATM 8 O O3B AGS . . . F 3 92.827 131.588 103.777 1 144.25 ? O3B AGS 1002 A 1 HETATM 9 P PA AGS . . . F 3 92.271 129.901 106.104 1 144.25 ? PA AGS 1002 A 1 HETATM 10 O O1A AGS . . . F 3 93.081 131.064 106.53 1 144.25 ? O1A AGS 1002 A 1 HETATM 11 O O2A AGS . . . F 3 93.043 128.839 105.317 1 144.25 ? O2A AGS 1002 A 1 HETATM 12 O O3A AGS . . . F 3 91.045 130.354 105.203 1 144.25 ? O3A AGS 1002 A 1 HETATM 13 O O5' AGS . . . F 3 91.6 129.296 107.398 1 144.25 ? O5' AGS 1002 A 1 HETATM 14 C C5' AGS . . . F 3 91.323 130.132 108.536 1 144.25 ? C5' AGS 1002 A 1 HETATM 15 C C4' AGS . . . F 3 92.204 129.699 109.679 1 144.25 ? C4' AGS 1002 A 1 HETATM 16 O O4' AGS . . . F 3 91.737 130.313 110.9 1 144.25 ? O4' AGS 1002 A 1 HETATM 17 C C3' AGS . . . F 3 92.214 128.198 109.949 1 144.25 ? C3' AGS 1002 A 1 HETATM 18 O O3' AGS . . . F 3 93.244 127.558 109.206 1 144.25 ? O3' AGS 1002 A 1 HETATM 19 C C2' AGS . . . F 3 92.471 128.132 111.455 1 144.25 ? C2' AGS 1002 A 1 HETATM 20 O O2' AGS . . . F 3 93.856 128.24 111.761 1 144.25 ? O2' AGS 1002 A 1 HETATM 21 C C1' AGS . . . F 3 91.717 129.366 111.952 1 144.25 ? C1' AGS 1002 A 1 HETATM 22 N N9 AGS . . . F 3 90.327 129.113 112.313 1 144.25 ? N9 AGS 1002 A 1 HETATM 23 C C8 AGS . . . F 3 89.223 129.277 111.519 1 144.25 ? C8 AGS 1002 A 1 HETATM 24 N N7 AGS . . . F 3 88.092 128.976 112.109 1 144.25 ? N7 AGS 1002 A 1 HETATM 25 C C5 AGS . . . F 3 88.479 128.585 113.382 1 144.25 ? C5 AGS 1002 A 1 HETATM 26 C C6 AGS . . . F 3 87.749 128.143 114.501 1 144.25 ? C6 AGS 1002 A 1 HETATM 27 N N6 AGS . . . F 3 86.42 128.014 114.517 1 144.25 ? N6 AGS 1002 A 1 HETATM 28 N N1 AGS . . . F 3 88.442 127.833 115.619 1 144.25 ? N1 AGS 1002 A 1 HETATM 29 C C2 AGS . . . F 3 89.771 127.96 115.608 1 144.25 ? C2 AGS 1002 A 1 HETATM 30 N N3 AGS . . . F 3 90.566 128.366 114.615 1 144.25 ? N3 AGS 1002 A 1 HETATM 31 C C4 AGS . . . F 3 89.854 128.666 113.522 1 144.25 ? C4 AGS 1002 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 43 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 31 #