data_7PBN # _model_server_result.job_id p-O8s3FepbVM1MLap5ivKw _model_server_result.datetime_utc '2024-10-20 05:42:56' _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 7pbn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":401}' # _entry.id 7PBN # _exptl.entry_id 7PBN _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.247 _entity.id 8 _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,S _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 ? 8 M N N ? 8 O 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 L MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc2 K O1B ADP . A ADP 401 1_555 L MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc3 K O2B ADP . A ADP 401 1_555 L MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.895 ? metalc ? metalc4 B OG1 THR 48 B THR 66 1_555 N MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc5 M O2G AGS . B AGS 401 1_555 N MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.89 ? metalc ? metalc6 M O2B AGS . B AGS 401 1_555 N MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc7 C OG1 THR 48 C THR 66 1_555 P MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.933 ? metalc ? metalc8 O O2G AGS . C AGS 401 1_555 P MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? metalc ? metalc9 O O2B AGS . C AGS 401 1_555 P MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 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 'DC-DG PAIR' hydrog11 I O2 DC 5 U DC 5 1_555 J N2 DG 11 V DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 I N3 DT 6 U DT 6 1_555 J N1 DA 10 V DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 I O4 DT 6 U DT 6 1_555 J N6 DA 10 V DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 I N3 DT 7 U DT 7 1_555 J N1 DA 9 V DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 I O4 DT 7 U DT 7 1_555 J N6 DA 9 V DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 I N3 DC 8 U DC 8 1_555 J N1 DG 8 V DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 I N4 DC 8 U DC 8 1_555 J O6 DG 8 V DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 I O2 DC 8 U DC 8 1_555 J N2 DG 8 V DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog19 I N2 DG 9 U DG 9 1_555 J O2 DC 7 V DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 I N1 DA 10 U DA 10 1_555 J N3 DT 6 V DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 I N6 DA 10 U DA 10 1_555 J O4 DT 6 V DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 I N1 DG 11 U DG 11 1_555 J N3 DC 5 V DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 I N2 DG 11 U DG 11 1_555 J O2 DC 5 V DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 I O6 DG 11 U DG 11 1_555 J N4 DC 5 V DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 I N1 DG 12 U DG 12 1_555 J N3 DC 4 V DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 I N2 DG 12 U DG 12 1_555 J O2 DC 4 V DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 I O6 DG 12 U DG 12 1_555 J N4 DC 4 V DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 I N1 DA 13 U DA 13 1_555 J N3 DT 3 V DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 I N6 DA 13 U DA 13 1_555 J O4 DT 3 V DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 I N1 DA 14 U DA 14 1_555 J N3 DT 2 V DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 I N6 DA 14 U DA 14 1_555 J O4 DT 2 V DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 I N1 DG 15 U DG 15 1_555 J N3 DC 1 V DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 I N2 DG 15 U DG 15 1_555 J O2 DC 1 V DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 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 7PBN _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 1 401 600 ADP ADP . L 7 MG A 1 402 3 MG MG . M 8 AGS B 1 401 600 AGS AGS . N 7 MG B 1 402 2 MG MG . O 8 AGS C 1 401 600 AGS AGS . P 7 MG C 1 402 1 MG MG . Q 6 ADP D 1 600 600 ADP ADP . R 6 ADP E 1 600 600 ADP ADP . S 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 . . . O 8 166.202 186.995 190.824 1 42.34 ? PG AGS 401 C 1 HETATM 2 S S1G AGS . . . O 8 167.202 188.367 191.77 1 42.34 ? S1G AGS 401 C 1 HETATM 3 O O2G AGS . . . O 8 165.836 187.478 189.392 1 42.34 ? O2G AGS 401 C 1 HETATM 4 O O3G AGS . . . O 8 167.095 185.73 190.735 1 42.34 ? O3G AGS 401 C 1 HETATM 5 P PB AGS . . . O 8 163.522 187.339 191.298 1 42.34 ? PB AGS 401 C 1 HETATM 6 O O1B AGS . . . O 8 163.477 188.651 191.963 1 42.34 -1 O1B AGS 401 C 1 HETATM 7 O O2B AGS . . . O 8 163.423 187.477 189.78 1 42.34 ? O2B AGS 401 C 1 HETATM 8 O O3B AGS . . . O 8 164.897 186.609 191.57 1 42.34 ? O3B AGS 401 C 1 HETATM 9 P PA AGS . . . O 8 161.076 186.135 190.836 1 42.34 ? PA AGS 401 C 1 HETATM 10 O O1A AGS . . . O 8 160.302 187.359 190.629 1 42.34 -1 O1A AGS 401 C 1 HETATM 11 O O2A AGS . . . O 8 161.575 185.533 189.525 1 42.34 ? O2A AGS 401 C 1 HETATM 12 O O3A AGS . . . O 8 162.35 186.379 191.737 1 42.34 ? O3A AGS 401 C 1 HETATM 13 O O5' AGS . . . O 8 160.21 185.088 191.629 1 42.34 ? O5' AGS 401 C 1 HETATM 14 C C5' AGS . . . O 8 160.603 183.705 191.645 1 42.34 ? C5' AGS 401 C 1 HETATM 15 C C4' AGS . . . O 8 159.388 182.832 191.824 1 42.34 ? C4' AGS 401 C 1 HETATM 16 O O4' AGS . . . O 8 158.658 183.256 192.995 1 42.34 ? O4' AGS 401 C 1 HETATM 17 C C3' AGS . . . O 8 158.394 182.855 190.665 1 42.34 ? C3' AGS 401 C 1 HETATM 18 O O3' AGS . . . O 8 157.881 181.553 190.414 1 42.34 ? O3' AGS 401 C 1 HETATM 19 C C2' AGS . . . O 8 157.301 183.802 191.159 1 42.34 ? C2' AGS 401 C 1 HETATM 20 O O2' AGS . . . O 8 156.037 183.479 190.597 1 42.34 ? O2' AGS 401 C 1 HETATM 21 C C1' AGS . . . O 8 157.316 183.536 192.66 1 42.34 ? C1' AGS 401 C 1 HETATM 22 N N9 AGS . . . O 8 156.868 184.66 193.47 1 42.34 ? N9 AGS 401 C 1 HETATM 23 C C8 AGS . . . O 8 157.642 185.665 193.984 1 42.34 ? C8 AGS 401 C 1 HETATM 24 N N7 AGS . . . O 8 156.975 186.547 194.687 1 42.34 ? N7 AGS 401 C 1 HETATM 25 C C5 AGS . . . O 8 155.671 186.082 194.643 1 42.34 ? C5 AGS 401 C 1 HETATM 26 C C6 AGS . . . O 8 154.473 186.567 195.198 1 42.34 ? C6 AGS 401 C 1 HETATM 27 N N6 AGS . . . O 8 154.394 187.675 195.938 1 42.34 ? N6 AGS 401 C 1 HETATM 28 N N1 AGS . . . O 8 153.344 185.865 194.964 1 42.34 ? N1 AGS 401 C 1 HETATM 29 C C2 AGS . . . O 8 153.419 184.756 194.224 1 42.34 ? C2 AGS 401 C 1 HETATM 30 N N3 AGS . . . O 8 154.488 184.202 193.65 1 42.34 ? N3 AGS 401 C 1 HETATM 31 C C4 AGS . . . O 8 155.591 184.918 193.9 1 42.34 ? C4 AGS 401 C 1 HETATM 32 H HOG2 AGS . . . O 8 166.554 187.439 188.877 1 42.34 ? HOG2 AGS 401 C 1 HETATM 33 H H21 AGS . . . O 8 167.661 185.717 191.415 1 42.34 ? H21 AGS 401 C 1 HETATM 34 H "H5'1" AGS . . . O 8 161.223 183.549 192.379 1 42.34 ? "H5'1" AGS 401 C 1 HETATM 35 H "H5'2" AGS . . . O 8 161.036 183.48 190.803 1 42.34 ? "H5'2" AGS 401 C 1 HETATM 36 H H4' AGS . . . O 8 159.683 181.917 191.959 1 42.34 ? H4' AGS 401 C 1 HETATM 37 H H3' AGS . . . O 8 158.817 183.214 189.869 1 42.34 ? H3' AGS 401 C 1 HETATM 38 H HO3' AGS . . . O 8 157.013 181.606 190.236 1 42.34 ? HO3' AGS 401 C 1 HETATM 39 H H2' AGS . . . O 8 157.54 184.725 190.972 1 42.34 ? H2' AGS 401 C 1 HETATM 40 H HO2' AGS . . . O 8 155.393 183.698 191.167 1 42.34 ? HO2' AGS 401 C 1 HETATM 41 H H1' AGS . . . O 8 156.765 182.757 192.853 1 42.34 ? H1' AGS 401 C 1 HETATM 42 H H8 AGS . . . O 8 158.597 185.728 193.831 1 42.34 ? H8 AGS 401 C 1 HETATM 43 H HN61 AGS . . . O 8 155.14 188.171 196.091 1 42.34 ? HN61 AGS 401 C 1 HETATM 44 H HN62 AGS . . . O 8 153.597 187.934 196.289 1 42.34 ? HN62 AGS 401 C 1 HETATM 45 H H2 AGS . . . O 8 152.578 184.287 194.085 1 42.34 ? H2 AGS 401 C 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 45 #