data_7PBT # _model_server_result.job_id q5AS7injqnPDIj6A8iS6Sg _model_server_result.datetime_utc '2024-11-19 13:39:20' _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 7pbt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":401}' # _entry.id 7PBT # _exptl.entry_id 7PBT _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 _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 _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 J N N ? 5 L N N ? 5 N 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 48 A THR 66 1_555 K MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc2 J O2G AGS . A AGS 401 1_555 K MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.83 ? metalc ? metalc3 J O2B AGS . A AGS 401 1_555 K MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? metalc ? metalc4 B OG1 THR 48 B THR 66 1_555 M MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? metalc ? metalc5 L O2G AGS . B AGS 401 1_555 M MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc6 L O2B AGS . B AGS 401 1_555 M MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc7 C OG1 THR 48 C THR 66 1_555 O MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc8 N O2G AGS . C AGS 401 1_555 O MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? metalc ? metalc9 N O2B AGS . C AGS 401 1_555 O MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? hydrog WATSON-CRICK hydrog1 H N1 DG 1 U DG 1 1_555 I N3 DC 15 V DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 H N2 DG 1 U DG 1 1_555 I O2 DC 15 V DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 H O6 DG 1 U DG 1 1_555 I N4 DC 15 V DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 H N1 DA 2 U DA 2 1_555 I N3 DT 14 V DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 H N6 DA 2 U DA 2 1_555 I O4 DT 14 V DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 H N1 DA 3 U DA 3 1_555 I N3 DT 13 V DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 H N6 DA 3 U DA 3 1_555 I O4 DT 13 V DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 H N3 DC 4 U DC 4 1_555 I N1 DG 12 V DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 H N4 DC 4 U DC 4 1_555 I O6 DG 12 V DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 H O2 DC 4 U DC 4 1_555 I N2 DG 12 V DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog11 H O2 DC 5 U DC 5 1_555 I N2 DG 11 V DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 H N3 DT 6 U DT 6 1_555 I N1 DA 10 V DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 H O4 DT 6 U DT 6 1_555 I N6 DA 10 V DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 H N3 DT 7 U DT 7 1_555 I N1 DA 9 V DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 H O4 DT 7 U DT 7 1_555 I N6 DA 9 V DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog16 H O2 DC 8 U DC 8 1_555 I N2 DG 8 V DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog17 H N2 DG 9 U DG 9 1_555 I O2 DC 7 V DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 H N1 DA 10 U DA 10 1_555 I N3 DT 6 V DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 H N6 DA 10 U DA 10 1_555 I O4 DT 6 V DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog20 H N1 DG 11 U DG 11 1_555 I O2 DC 5 V DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog21 H N2 DG 11 U DG 11 1_555 I N3 DC 5 V DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 H N1 DG 12 U DG 12 1_555 I N3 DC 4 V DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 H N2 DG 12 U DG 12 1_555 I O2 DC 4 V DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 H O6 DG 12 U DG 12 1_555 I N4 DC 4 V DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 H N1 DA 13 U DA 13 1_555 I N3 DT 3 V DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 H N6 DA 13 U DA 13 1_555 I O4 DT 3 V DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog27 H N1 DA 14 U DA 14 1_555 I N3 DT 2 V DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 H N1 DG 15 U DG 15 1_555 I N3 DC 1 V DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 H N2 DG 15 U DG 15 1_555 I O2 DC 1 V DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 H O6 DG 15 U DG 15 1_555 I N4 DC 1 V DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 7PBT _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 J 5 AGS A 1 401 600 AGS AGS . K 6 MG A 1 402 3 MG MG . L 5 AGS B 1 401 600 AGS AGS . M 6 MG B 1 402 2 MG MG . N 5 AGS C 1 401 600 AGS AGS . O 6 MG C 1 402 1 MG MG . P 7 ADP D 1 600 600 ADP ADP . Q 7 ADP E 1 600 600 ADP ADP . R 7 ADP F 1 600 600 ADP ADP . # 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 . . . J 5 217.439 173.881 194.277 1 60.37 ? PG AGS 401 A 1 HETATM 2 S S1G AGS . . . J 5 215.915 173.321 195.346 1 60.37 ? S1G AGS 401 A 1 HETATM 3 O O2G AGS . . . J 5 217.067 173.794 192.771 1 60.37 ? O2G AGS 401 A 1 HETATM 4 O O3G AGS . . . J 5 217.799 175.348 194.651 1 60.37 ? O3G AGS 401 A 1 HETATM 5 P PB AGS . . . J 5 218.743 171.501 193.973 1 60.37 ? PB AGS 401 A 1 HETATM 6 O O1B AGS . . . J 5 217.823 170.604 194.699 1 60.37 -1 O1B AGS 401 A 1 HETATM 7 O O2B AGS . . . J 5 218.418 171.611 192.484 1 60.37 ? O2B AGS 401 A 1 HETATM 8 O O3B AGS . . . J 5 218.671 172.97 194.549 1 60.37 ? O3B AGS 401 A 1 HETATM 9 P PA AGS . . . J 5 220.92 170.354 192.795 1 60.37 ? PA AGS 401 A 1 HETATM 10 O O1A AGS . . . J 5 220.175 169.189 192.305 1 60.37 -1 O1A AGS 401 A 1 HETATM 11 O O2A AGS . . . J 5 221.025 171.469 191.756 1 60.37 ? O2A AGS 401 A 1 HETATM 12 O O3A AGS . . . J 5 220.23 170.998 194.054 1 60.37 ? O3A AGS 401 A 1 HETATM 13 O O5' AGS . . . J 5 222.345 169.913 193.297 1 60.37 ? O5' AGS 401 A 1 HETATM 14 C C5' AGS . . . J 5 223.339 170.926 193.525 1 60.37 ? C5' AGS 401 A 1 HETATM 15 C C4' AGS . . . J 5 224.708 170.341 193.304 1 60.37 ? C4' AGS 401 A 1 HETATM 16 O O4' AGS . . . J 5 224.884 169.188 194.158 1 60.37 ? O4' AGS 401 A 1 HETATM 17 C C3' AGS . . . J 5 224.978 169.865 191.877 1 60.37 ? C3' AGS 401 A 1 HETATM 18 O O3' AGS . . . J 5 226.29 170.224 191.462 1 60.37 ? O3' AGS 401 A 1 HETATM 19 C C2' AGS . . . J 5 224.808 168.349 191.979 1 60.37 ? C2' AGS 401 A 1 HETATM 20 O O2' AGS . . . J 5 225.599 167.658 191.022 1 60.37 ? O2' AGS 401 A 1 HETATM 21 C C1' AGS . . . J 5 225.32 168.089 193.388 1 60.37 ? C1' AGS 401 A 1 HETATM 22 N N9 AGS . . . J 5 224.807 166.87 193.998 1 60.37 ? N9 AGS 401 A 1 HETATM 23 C C8 AGS . . . J 5 223.595 166.699 194.611 1 60.37 ? C8 AGS 401 A 1 HETATM 24 N N7 AGS . . . J 5 223.397 165.491 195.077 1 60.37 ? N7 AGS 401 A 1 HETATM 25 C C5 AGS . . . J 5 224.565 164.82 194.752 1 60.37 ? C5 AGS 401 A 1 HETATM 26 C C6 AGS . . . J 5 224.989 163.497 194.972 1 60.37 ? C6 AGS 401 A 1 HETATM 27 N N6 AGS . . . J 5 224.254 162.577 195.6 1 60.37 ? N6 AGS 401 A 1 HETATM 28 N N1 AGS . . . J 5 226.213 163.148 194.52 1 60.37 ? N1 AGS 401 A 1 HETATM 29 C C2 AGS . . . J 5 226.952 164.065 193.893 1 60.37 ? C2 AGS 401 A 1 HETATM 30 N N3 AGS . . . J 5 226.659 165.34 193.629 1 60.37 ? N3 AGS 401 A 1 HETATM 31 C C4 AGS . . . J 5 225.443 165.657 194.089 1 60.37 ? C4 AGS 401 A 1 HETATM 32 H HOG2 AGS . . . J 5 216.393 174.341 192.6 1 60.37 ? HOG2 AGS 401 A 1 HETATM 33 H H21 AGS . . . J 5 217.14 175.702 195.124 1 60.37 ? H21 AGS 401 A 1 HETATM 34 H "H5'1" AGS . . . J 5 223.27 171.253 194.439 1 60.37 ? "H5'1" AGS 401 A 1 HETATM 35 H "H5'2" AGS . . . J 5 223.201 171.661 192.904 1 60.37 ? "H5'2" AGS 401 A 1 HETATM 36 H H4' AGS . . . J 5 225.373 171.007 193.542 1 60.37 ? H4' AGS 401 A 1 HETATM 37 H H3' AGS . . . J 5 224.316 170.236 191.272 1 60.37 ? H3' AGS 401 A 1 HETATM 38 H HO3' AGS . . . J 5 226.277 171.043 191.121 1 60.37 ? HO3' AGS 401 A 1 HETATM 39 H H2' AGS . . . J 5 223.872 168.104 191.902 1 60.37 ? H2' AGS 401 A 1 HETATM 40 H HO2' AGS . . . J 5 226.282 168.167 190.775 1 60.37 ? HO2' AGS 401 A 1 HETATM 41 H H1' AGS . . . J 5 226.293 168.065 193.379 1 60.37 ? H1' AGS 401 A 1 HETATM 42 H H8 AGS . . . J 5 222.939 167.408 194.69 1 60.37 ? H8 AGS 401 A 1 HETATM 43 H HN61 AGS . . . J 5 223.402 162.773 195.85 1 60.37 ? HN61 AGS 401 A 1 HETATM 44 H HN62 AGS . . . J 5 224.602 161.756 195.777 1 60.37 ? HN62 AGS 401 A 1 HETATM 45 H H2 AGS . . . J 5 227.826 163.764 193.587 1 60.37 ? H2 AGS 401 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 355 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 45 #