data_7PBT # _model_server_result.job_id v_00V4F95n3-uBnqRPeGag _model_server_result.datetime_utc '2024-11-19 13:28:02' _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":"P","auth_seq_id":600}' # _entry.id 7PBT # _exptl.entry_id 7PBT _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 ? 7 P N N ? 7 Q N N ? 7 R 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 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _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 PB ADP . . . P 7 176.987 220.96 188.475 1 86.38 ? PB ADP 600 D 1 HETATM 2 O O1B ADP . . . P 7 177.229 221.442 187.066 1 86.38 -1 O1B ADP 600 D 1 HETATM 3 O O2B ADP . . . P 7 178.196 220.367 189.157 1 86.38 ? O2B ADP 600 D 1 HETATM 4 O O3B ADP . . . P 7 175.721 220.161 188.654 1 86.38 ? O3B ADP 600 D 1 HETATM 5 P PA ADP . . . P 7 175.463 223.274 188.963 1 86.38 ? PA ADP 600 D 1 HETATM 6 O O1A ADP . . . P 7 174.626 222.699 187.855 1 86.38 ? O1A ADP 600 D 1 HETATM 7 O O2A ADP . . . P 7 176.005 224.664 188.758 1 86.38 -1 O2A ADP 600 D 1 HETATM 8 O O3A ADP . . . P 7 176.712 222.314 189.294 1 86.38 ? O3A ADP 600 D 1 HETATM 9 O O5' ADP . . . P 7 174.671 223.235 190.367 1 86.38 ? O5' ADP 600 D 1 HETATM 10 C C5' ADP . . . P 7 173.89 222.108 190.77 1 86.38 ? C5' ADP 600 D 1 HETATM 11 C C4' ADP . . . P 7 172.377 222.302 190.608 1 86.38 ? C4' ADP 600 D 1 HETATM 12 O O4' ADP . . . P 7 171.792 222.695 191.86 1 86.38 ? O4' ADP 600 D 1 HETATM 13 C C3' ADP . . . P 7 171.948 223.362 189.603 1 86.38 ? C3' ADP 600 D 1 HETATM 14 O O3' ADP . . . P 7 171.662 222.813 188.314 1 86.38 ? O3' ADP 600 D 1 HETATM 15 C C2' ADP . . . P 7 170.662 223.866 190.223 1 86.38 ? C2' ADP 600 D 1 HETATM 16 O O2' ADP . . . P 7 169.528 223.025 189.981 1 86.38 ? O2' ADP 600 D 1 HETATM 17 C C1' ADP . . . P 7 170.986 223.868 191.705 1 86.38 ? C1' ADP 600 D 1 HETATM 18 N N9 ADP . . . P 7 171.749 225.054 192.169 1 86.38 ? N9 ADP 600 D 1 HETATM 19 C C8 ADP . . . P 7 173.054 225.069 192.499 1 86.38 ? C8 ADP 600 D 1 HETATM 20 N N7 ADP . . . P 7 173.434 226.31 192.893 1 86.38 ? N7 ADP 600 D 1 HETATM 21 C C5 ADP . . . P 7 172.359 227.112 192.825 1 86.38 ? C5 ADP 600 D 1 HETATM 22 C C6 ADP . . . P 7 172.071 228.536 193.101 1 86.38 ? C6 ADP 600 D 1 HETATM 23 N N6 ADP . . . P 7 173.036 229.376 193.541 1 86.38 ? N6 ADP 600 D 1 HETATM 24 N N1 ADP . . . P 7 170.813 228.975 192.899 1 86.38 ? N1 ADP 600 D 1 HETATM 25 C C2 ADP . . . P 7 169.839 228.158 192.462 1 86.38 ? C2 ADP 600 D 1 HETATM 26 N N3 ADP . . . P 7 170.035 226.853 192.194 1 86.38 ? N3 ADP 600 D 1 HETATM 27 C C4 ADP . . . P 7 171.25 226.28 192.349 1 86.38 ? C4 ADP 600 D 1 HETATM 28 H "H5'1" ADP . . . P 7 174.106 221.886 191.817 1 86.38 ? "H5'1" ADP 600 D 1 HETATM 29 H "H5'2" ADP . . . P 7 174.196 221.239 190.184 1 86.38 ? "H5'2" ADP 600 D 1 HETATM 30 H H4' ADP . . . P 7 171.944 221.343 190.294 1 86.38 ? H4' ADP 600 D 1 HETATM 31 H H3' ADP . . . P 7 172.685 224.175 189.547 1 86.38 ? H3' ADP 600 D 1 HETATM 32 H HO3' ADP . . . P 7 172.466 222.522 187.876 1 86.38 ? HO3' ADP 600 D 1 HETATM 33 H H2' ADP . . . P 7 170.466 224.894 189.887 1 86.38 ? H2' ADP 600 D 1 HETATM 34 H HO2' ADP . . . P 7 169.618 222.549 189.146 1 86.38 ? HO2' ADP 600 D 1 HETATM 35 H H1' ADP . . . P 7 170.053 223.766 192.277 1 86.38 ? H1' ADP 600 D 1 HETATM 36 H H8 ADP . . . P 7 173.713 224.212 192.452 1 86.38 ? H8 ADP 600 D 1 HETATM 37 H HN61 ADP . . . P 7 172.818 230.345 193.723 1 86.38 ? HN61 ADP 600 D 1 HETATM 38 H HN62 ADP . . . P 7 173.975 229.034 193.687 1 86.38 ? HN62 ADP 600 D 1 HETATM 39 H H2 ADP . . . P 7 168.85 228.572 192.32 1 86.38 ? H2 ADP 600 D 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 59 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 39 #