data_6QS8 # _model_server_result.job_id gqZWPPvwvI-EAEsWjaQeOw _model_server_result.datetime_utc '2024-10-19 22:39:48' _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 6qs8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1001}' # _entry.id 6QS8 # _exptl.entry_id 6QS8 _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 10 _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 6QS8 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QS8 _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 PISA _pdbx_struct_assembly.oligomeric_details heptameric _pdbx_struct_assembly.oligomeric_count 7 _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,O,P,Q,R,S,T,U,V,W,X,Y,Z _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 H N N ? 3 J N N ? 3 K N N ? 3 N N N ? 3 O N N ? 3 R N N ? 3 S N N ? 3 V N N ? 3 W N N ? 3 Z 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 213 A THR 213 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc2 H O2G AGS . A AGS 1001 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc3 B OG1 THR 213 B THR 213 1_555 L MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc4 B OG1 THR 612 B THR 612 1_555 M MG MG . B MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc5 J O2G AGS . B AGS 1001 1_555 L MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc6 J O1B AGS . B AGS 1001 1_555 L MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc7 K O2G AGS . B AGS 1002 1_555 M MG MG . B MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc8 K O1B AGS . B AGS 1002 1_555 M MG MG . B MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc9 C OG1 THR 213 C THR 213 1_555 P MG MG . C MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc10 C OG1 THR 612 C THR 612 1_555 Q MG MG . C MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc11 N O2G AGS . C AGS 1001 1_555 P MG MG . C MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc12 N O1B AGS . C AGS 1001 1_555 P MG MG . C MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc13 O O2G AGS . C AGS 1002 1_555 Q MG MG . C MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc14 O O1B AGS . C AGS 1002 1_555 Q MG MG . C MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc15 D OG1 THR 213 D THR 213 1_555 T MG MG . D MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc16 D OG1 THR 612 D THR 612 1_555 U MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc17 D OD1 ASP 677 D ASP 677 1_555 U MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.873 ? metalc ? metalc18 R O2G AGS . D AGS 901 1_555 T MG MG . D MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc19 R O1B AGS . D AGS 901 1_555 T MG MG . D MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc20 S O1B AGS . D AGS 902 1_555 U MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc21 W O2G AGS . E AGS 1002 1_555 X MG MG . E MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? # _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 45 n n PG O2G AGS sing 46 n n PG O3G AGS sing 47 n n PG O3B AGS sing 48 n n PB O1B AGS doub 49 n n PB O2B AGS sing 50 n n PB O3B AGS sing 51 n n PB O3A AGS sing 52 n n PA O1A AGS doub 53 n n PA O2A AGS sing 54 n n PA O3A AGS sing 55 n n PA O5' AGS sing 56 n n O5' C5' AGS sing 57 n n C5' C4' AGS sing 58 n n C4' O4' AGS sing 59 n n C4' C3' AGS sing 60 n n O4' C1' AGS sing 61 n n C3' O3' AGS sing 62 n n C3' C2' AGS sing 63 n n C2' O2' AGS sing 64 n n C2' C1' AGS sing 65 n n C1' N9 AGS sing 66 n n N9 C8 AGS sing 67 n y N9 C4 AGS sing 68 n y C8 N7 AGS doub 69 n y N7 C5 AGS sing 70 n y C5 C6 AGS sing 71 n y C5 C4 AGS doub 72 n y C6 N6 AGS sing 73 n n C6 N1 AGS doub 74 n y N1 C2 AGS sing 75 n y C2 N3 AGS doub 76 n y N3 C4 AGS sing 77 n y O2G HOG2 AGS sing 78 n n O3G H21 AGS sing 79 n n O2B HOB2 AGS sing 80 n n O2A HOA2 AGS sing 81 n n C5' "H5'1" AGS sing 82 n n C5' "H5'2" AGS sing 83 n n C4' H4' AGS sing 84 n n C3' H3' AGS sing 85 n n O3' HO3' AGS sing 86 n n C2' H2' AGS sing 87 n n O2' HO2' AGS sing 88 n n C1' H1' AGS sing 89 n n C8 H8 AGS sing 90 n n N6 HN61 AGS sing 91 n n N6 HN62 AGS sing 92 n n C2 H2 AGS sing 93 n n # _atom_sites.entry_id 6QS8 _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 H 3 AGS A 1 1001 1001 AGS AGS . I 4 MG A 1 1002 1 MG MG . J 3 AGS B 1 1001 1001 AGS AGS . K 3 AGS B 1 1002 1002 AGS AGS . L 4 MG B 1 1003 1 MG MG . M 4 MG B 1 1004 4 MG MG . N 3 AGS C 1 1001 1001 AGS AGS . O 3 AGS C 1 1002 1002 AGS AGS . P 4 MG C 1 1003 2 MG MG . Q 4 MG C 1 1004 5 MG MG . R 3 AGS D 1 901 1001 AGS AGS . S 3 AGS D 1 902 1002 AGS AGS . T 4 MG D 1 903 3 MG MG . U 4 MG D 1 904 6 MG MG . V 3 AGS E 1 1001 1001 AGS AGS . W 3 AGS E 1 1002 1002 AGS AGS . X 4 MG E 1 1003 7 MG MG . Y 5 ADP F 1 1001 1001 ADP ADP . Z 3 AGS F 1 1002 1001 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 . . . H 3 138.801 126.034 168.884 1 39.97 ? PG AGS 1001 A 1 HETATM 2 S S1G AGS . . . H 3 139.455 124.462 167.941 1 39.97 ? S1G AGS 1001 A 1 HETATM 3 O O2G AGS . . . H 3 137.28 126.2 168.631 1 39.97 ? O2G AGS 1001 A 1 HETATM 4 O O3G AGS . . . H 3 139.57 127.264 168.326 1 39.97 ? O3G AGS 1001 A 1 HETATM 5 P PB AGS . . . H 3 137.778 125.317 171.259 1 39.97 ? PB AGS 1001 A 1 HETATM 6 O O1B AGS . . . H 3 136.573 126.07 170.875 1 39.97 ? O1B AGS 1001 A 1 HETATM 7 O O2B AGS . . . H 3 138.113 125.302 172.759 1 39.97 ? O2B AGS 1001 A 1 HETATM 8 O O3B AGS . . . H 3 139 125.878 170.419 1 39.97 ? O3B AGS 1001 A 1 HETATM 9 P PA AGS . . . H 3 136.223 123.474 170.205 1 39.97 ? PA AGS 1001 A 1 HETATM 10 O O1A AGS . . . H 3 136.195 124.033 168.848 1 39.97 ? O1A AGS 1001 A 1 HETATM 11 O O2A AGS . . . H 3 135.107 123.931 171.136 1 39.97 ? O2A AGS 1001 A 1 HETATM 12 O O3A AGS . . . H 3 137.558 123.821 170.918 1 39.97 ? O3A AGS 1001 A 1 HETATM 13 O O5' AGS . . . H 3 136.269 121.922 170.138 1 39.97 ? O5' AGS 1001 A 1 HETATM 14 C C5' AGS . . . H 3 137.077 121.236 171.094 1 39.97 ? C5' AGS 1001 A 1 HETATM 15 C C4' AGS . . . H 3 136.531 119.851 171.294 1 39.97 ? C4' AGS 1001 A 1 HETATM 16 O O4' AGS . . . H 3 136.562 119.539 172.7 1 39.97 ? O4' AGS 1001 A 1 HETATM 17 C C3' AGS . . . H 3 135.09 119.644 170.841 1 39.97 ? C3' AGS 1001 A 1 HETATM 18 O O3' AGS . . . H 3 134.91 118.34 170.305 1 39.97 ? O3' AGS 1001 A 1 HETATM 19 C C2' AGS . . . H 3 134.291 119.825 172.129 1 39.97 ? C2' AGS 1001 A 1 HETATM 20 O O2' AGS . . . H 3 133.116 119.026 172.115 1 39.97 ? O2' AGS 1001 A 1 HETATM 21 C C1' AGS . . . H 3 135.258 119.29 173.177 1 39.97 ? C1' AGS 1001 A 1 HETATM 22 N N9 AGS . . . H 3 135.127 119.93 174.471 1 39.97 ? N9 AGS 1001 A 1 HETATM 23 C C8 AGS . . . H 3 135.943 120.89 175.002 1 39.97 ? C8 AGS 1001 A 1 HETATM 24 N N7 AGS . . . H 3 135.584 121.296 176.193 1 39.97 ? N7 AGS 1001 A 1 HETATM 25 C C5 AGS . . . H 3 134.442 120.561 176.459 1 39.97 ? C5 AGS 1001 A 1 HETATM 26 C C6 AGS . . . H 3 133.574 120.526 177.563 1 39.97 ? C6 AGS 1001 A 1 HETATM 27 N N6 AGS . . . H 3 133.732 121.278 178.653 1 39.97 ? N6 AGS 1001 A 1 HETATM 28 N N1 AGS . . . H 3 132.527 119.674 177.511 1 39.97 ? N1 AGS 1001 A 1 HETATM 29 C C2 AGS . . . H 3 132.368 118.916 176.423 1 39.97 ? C2 AGS 1001 A 1 HETATM 30 N N3 AGS . . . H 3 133.119 118.866 175.322 1 39.97 ? N3 AGS 1001 A 1 HETATM 31 C C4 AGS . . . H 3 134.148 119.716 175.405 1 39.97 ? C4 AGS 1001 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #