data_7PBO # _model_server_result.job_id 24TVFX2Ac18R65YiQdTQyw _model_server_result.datetime_utc '2024-10-20 07:36:52' _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 7pbo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":401}' # _entry.id 7PBO # _exptl.entry_id 7PBO _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.247 _entity.id 7 _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 ? # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details decameric _pdbx_struct_assembly.oligomeric_count 10 _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 ? 7 L N N ? 7 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 B OG1 THR 48 B THR 66 1_555 M MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc2 L O2G AGS . B AGS 401 1_555 M MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.833 ? metalc ? metalc3 L O2B AGS . B AGS 401 1_555 M MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc4 C OG1 THR 48 C THR 66 1_555 O MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc5 N O2G AGS . C AGS 401 1_555 O MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc6 N O2B AGS . C AGS 401 1_555 O MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? hydrog WATSON-CRICK hydrog1 I N1 DG 1 U DG 1 1_555 J N3 DC 15 V DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 I N2 DG 1 U DG 1 1_555 J O2 DC 15 V DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 I O6 DG 1 U DG 1 1_555 J N4 DC 15 V DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 I N1 DA 2 U DA 2 1_555 J N3 DT 14 V DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 I N6 DA 2 U DA 2 1_555 J O4 DT 14 V DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 I N1 DA 3 U DA 3 1_555 J N3 DT 13 V DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 I N6 DA 3 U DA 3 1_555 J O4 DT 13 V DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 I N3 DC 4 U DC 4 1_555 J N1 DG 12 V DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 I N4 DC 4 U DC 4 1_555 J O6 DG 12 V DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 I O2 DC 4 U DC 4 1_555 J N2 DG 12 V DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 I N3 DC 5 U DC 5 1_555 J N1 DG 11 V DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 I N4 DC 5 U DC 5 1_555 J O6 DG 11 V DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 I O2 DC 5 U DC 5 1_555 J N2 DG 11 V DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 I N3 DT 6 U DT 6 1_555 J N1 DA 10 V DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 I O4 DT 6 U DT 6 1_555 J N6 DA 10 V DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 I N3 DT 7 U DT 7 1_555 J N1 DA 9 V DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 I O4 DT 7 U DT 7 1_555 J N6 DA 9 V DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 I N3 DC 8 U DC 8 1_555 J N1 DG 8 V DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 I N4 DC 8 U DC 8 1_555 J O6 DG 8 V DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 I O2 DC 8 U DC 8 1_555 J N2 DG 8 V DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 I N1 DG 9 U DG 9 1_555 J N3 DC 7 V DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 I N2 DG 9 U DG 9 1_555 J O2 DC 7 V DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 I O6 DG 9 U DG 9 1_555 J N4 DC 7 V DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 I N1 DA 10 U DA 10 1_555 J N3 DT 6 V DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 I N6 DA 10 U DA 10 1_555 J O4 DT 6 V DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 I N1 DG 11 U DG 11 1_555 J N3 DC 5 V DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 I N2 DG 11 U DG 11 1_555 J O2 DC 5 V DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 I O6 DG 11 U DG 11 1_555 J N4 DC 5 V DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 I N1 DG 12 U DG 12 1_555 J N3 DC 4 V DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 I N2 DG 12 U DG 12 1_555 J O2 DC 4 V DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 I O6 DG 12 U DG 12 1_555 J N4 DC 4 V DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 I N1 DA 13 U DA 13 1_555 J N3 DT 3 V DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 I N6 DA 13 U DA 13 1_555 J O4 DT 3 V DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 I N1 DA 14 U DA 14 1_555 J N3 DT 2 V DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 I N6 DA 14 U DA 14 1_555 J O4 DT 2 V DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 I N1 DG 15 U DG 15 1_555 J N3 DC 1 V DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 I N2 DG 15 U DG 15 1_555 J O2 DC 1 V DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 I O6 DG 15 U DG 15 1_555 J 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 7PBO _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 K 6 ADP A 1 600 600 ADP ADP . L 7 AGS B 1 401 600 AGS AGS . M 8 MG B 1 402 2 MG MG . N 7 AGS C 1 401 600 AGS AGS . O 8 MG C 1 402 1 MG MG . P 6 ADP D 1 600 600 ADP ADP . Q 6 ADP E 1 600 600 ADP ADP . R 6 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 . . . L 7 186.679 164.803 190.75 1 56.51 ? PG AGS 401 B 1 HETATM 2 S S1G AGS . . . L 7 186.202 166.226 191.984 1 56.51 ? S1G AGS 401 B 1 HETATM 3 O O2G AGS . . . L 7 185.961 164.99 189.385 1 56.51 ? O2G AGS 401 B 1 HETATM 4 O O3G AGS . . . L 7 188.211 164.854 190.541 1 56.51 ? O3G AGS 401 B 1 HETATM 5 P PB AGS . . . L 7 185.027 162.628 190.918 1 56.51 ? PB AGS 401 B 1 HETATM 6 O O1B AGS . . . L 7 183.866 163.119 191.679 1 56.51 -1 O1B AGS 401 B 1 HETATM 7 O O2B AGS . . . L 7 184.855 162.86 189.419 1 56.51 ? O2B AGS 401 B 1 HETATM 8 O O3B AGS . . . L 7 186.342 163.398 191.311 1 56.51 ? O3B AGS 401 B 1 HETATM 9 P PA AGS . . . L 7 185.235 160.109 189.879 1 56.51 ? PA AGS 401 B 1 HETATM 10 O O1A AGS . . . L 7 183.925 160.119 189.231 1 56.51 -1 O1A AGS 401 B 1 HETATM 11 O O2A AGS . . . L 7 186.32 160.573 188.911 1 56.51 ? O2A AGS 401 B 1 HETATM 12 O O3A AGS . . . L 7 185.3 161.094 191.103 1 56.51 ? O3A AGS 401 B 1 HETATM 13 O O5' AGS . . . L 7 185.57 158.698 190.484 1 56.51 ? O5' AGS 401 B 1 HETATM 14 C C5' AGS . . . L 7 186.814 158.046 190.165 1 56.51 ? C5' AGS 401 B 1 HETATM 15 C C4' AGS . . . L 7 186.606 156.555 190.126 1 56.51 ? C4' AGS 401 B 1 HETATM 16 O O4' AGS . . . L 7 185.915 156.142 191.313 1 56.51 ? O4' AGS 401 B 1 HETATM 17 C C3' AGS . . . L 7 185.762 156.043 188.966 1 56.51 ? C3' AGS 401 B 1 HETATM 18 O O3' AGS . . . L 7 186.597 155.716 187.863 1 56.51 ? O3' AGS 401 B 1 HETATM 19 C C2' AGS . . . L 7 185.064 154.8 189.536 1 56.51 ? C2' AGS 401 B 1 HETATM 20 O O2' AGS . . . L 7 185.696 153.598 189.113 1 56.51 ? O2' AGS 401 B 1 HETATM 21 C C1' AGS . . . L 7 185.182 154.964 191.057 1 56.51 ? C1' AGS 401 B 1 HETATM 22 N N9 AGS . . . L 7 183.91 155.045 191.761 1 56.51 ? N9 AGS 401 B 1 HETATM 23 C C8 AGS . . . L 7 183.363 156.147 192.362 1 56.51 ? C8 AGS 401 B 1 HETATM 24 N N7 AGS . . . L 7 182.217 155.918 192.953 1 56.51 ? N7 AGS 401 B 1 HETATM 25 C C5 AGS . . . L 7 182.009 154.562 192.752 1 56.51 ? C5 AGS 401 B 1 HETATM 26 C C6 AGS . . . L 7 180.97 153.696 193.137 1 56.51 ? C6 AGS 401 B 1 HETATM 27 N N6 AGS . . . L 7 179.903 154.081 193.838 1 56.51 ? N6 AGS 401 B 1 HETATM 28 N N1 AGS . . . L 7 181.069 152.4 192.773 1 56.51 ? N1 AGS 401 B 1 HETATM 29 C C2 AGS . . . L 7 182.134 152.008 192.07 1 56.51 ? C2 AGS 401 B 1 HETATM 30 N N3 AGS . . . L 7 183.174 152.732 191.653 1 56.51 ? N3 AGS 401 B 1 HETATM 31 C C4 AGS . . . L 7 183.049 154.01 192.026 1 56.51 ? C4 AGS 401 B 1 HETATM 32 H HOG2 AGS . . . L 7 186.34 165.656 188.942 1 56.51 ? HOG2 AGS 401 B 1 HETATM 33 H H21 AGS . . . L 7 188.584 165.311 191.2 1 56.51 ? H21 AGS 401 B 1 HETATM 34 H "H5'1" AGS . . . L 7 187.479 158.263 190.841 1 56.51 ? "H5'1" AGS 401 B 1 HETATM 35 H "H5'2" AGS . . . L 7 187.127 158.346 189.294 1 56.51 ? "H5'2" AGS 401 B 1 HETATM 36 H H4' AGS . . . L 7 187.473 156.118 190.1 1 56.51 ? H4' AGS 401 B 1 HETATM 37 H H3' AGS . . . L 7 185.104 156.71 188.71 1 56.51 ? H3' AGS 401 B 1 HETATM 38 H HO3' AGS . . . L 7 186.96 154.917 187.993 1 56.51 ? HO3' AGS 401 B 1 HETATM 39 H H2' AGS . . . L 7 184.129 154.797 189.274 1 56.51 ? H2' AGS 401 B 1 HETATM 40 H HO2' AGS . . . L 7 185.13 153.118 188.627 1 56.51 ? HO2' AGS 401 B 1 HETATM 41 H H1' AGS . . . L 7 185.682 154.206 191.407 1 56.51 ? H1' AGS 401 B 1 HETATM 42 H H8 AGS . . . L 7 183.774 157.024 192.331 1 56.51 ? H8 AGS 401 B 1 HETATM 43 H HN61 AGS . . . L 7 179.794 154.958 194.052 1 56.51 ? HN61 AGS 401 B 1 HETATM 44 H HN62 AGS . . . L 7 179.285 153.469 194.101 1 56.51 ? HN62 AGS 401 B 1 HETATM 45 H H2 AGS . . . L 7 182.158 151.065 191.834 1 56.51 ? H2 AGS 401 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 51 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 45 #