data_8VAT # _model_server_result.job_id rA_astMCfuvmE9l-k2BZzA _model_server_result.datetime_utc '2025-09-04 15:25:39' _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 8vat # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":402}' # _entry.id 8VAT # _exptl.entry_id 8VAT _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 8 _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 ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 8VAT _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VAT _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 ? _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 _pdbx_struct_assembly.details author_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 _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 K N N ? 8 O N N ? 8 S 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 55 B THR 52 1_555 M MG MG . B MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? metalc ? metalc2 B SG CYS 67 B CYS 64 1_555 J ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc3 B SG CYS 76 B CYS 73 1_555 J ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc4 B SG CYS 79 B CYS 76 1_555 J ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc5 B SG CYS 82 B CYS 79 1_555 J ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc6 K O3B ADP . B ADP 402 1_555 L BE BEF . B BEF 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.653 ? metalc ? metalc7 K O1B ADP . B ADP 402 1_555 M MG MG . B MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc8 C OG1 THR 55 C THR 52 1_555 Q MG MG . C MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc9 C SG CYS 67 C CYS 64 1_555 N ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc10 C SG CYS 79 C CYS 76 1_555 N ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc11 C SG CYS 82 C CYS 79 1_555 N ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc12 O O3B ADP . C ADP 402 1_555 P BE BEF . C BEF 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.644 ? metalc ? metalc13 O O1B ADP . C ADP 402 1_555 Q MG MG . C MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.849 ? metalc ? metalc14 D OG1 THR 55 D THR 52 1_555 U MG MG . D MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.818 ? metalc ? metalc15 D SG CYS 67 D CYS 64 1_555 R ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc16 D SG CYS 76 D CYS 73 1_555 R ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc17 D SG CYS 79 D CYS 76 1_555 R ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc18 D SG CYS 82 D CYS 79 1_555 R ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc19 S O3B ADP . D ADP 402 1_555 T BE BEF . D BEF 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.641 ? metalc ? metalc20 S O1B ADP . D ADP 402 1_555 U MG MG . D MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc21 E SG CYS 53 E CYS 50 1_555 V ZN ZN . E ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc22 E SG CYS 62 E CYS 59 1_555 V ZN ZN . E ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc23 E SG CYS 65 E CYS 62 1_555 V ZN ZN . E ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc24 E SG CYS 68 E CYS 65 1_555 V ZN ZN . E ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? hydrog WATSON-CRICK hydrog1 H N1 A 1 H A 1 1_555 I N3 DT 21 I DT 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 H N6 A 1 H A 1 1_555 I O4 DT 21 I DT 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_8_PAIR hydrog3 H N1 G 2 H G 2 1_555 I N1 DA 19 I DA 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_8_PAIR hydrog4 H O6 G 2 H G 2 1_555 I N6 DA 19 I DA 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 H N1 G 2 H G 2 1_555 I N3 DC 20 I DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 H N2 G 2 H G 2 1_555 I O2 DC 20 I DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 H O6 G 2 H G 2 1_555 I N4 DC 20 I DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 H N3 U 3 H U 3 1_555 I N1 DA 19 I DA 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 H O4 U 3 H U 3 1_555 I N6 DA 19 I DA 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 H N1 G 4 H G 4 1_555 I N3 DC 18 I DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 H N2 G 4 H G 4 1_555 I O2 DC 18 I DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 H O6 G 4 H G 4 1_555 I N4 DC 18 I DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 H N1 G 5 H G 5 1_555 I N3 DC 17 I DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 H N2 G 5 H G 5 1_555 I O2 DC 17 I DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 H O6 G 5 H G 5 1_555 I N4 DC 17 I DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 H N3 U 6 H U 6 1_555 I N1 DA 16 I DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 H O4 U 6 H U 6 1_555 I N6 DA 16 I DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 H N1 G 7 H G 7 1_555 I N3 DC 15 I DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 H N2 G 7 H G 7 1_555 I O2 DC 15 I DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 H O6 G 7 H G 7 1_555 I N4 DC 15 I DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 H N3 U 8 H U 8 1_555 I N1 DA 14 I DA 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 H O4 U 8 H U 8 1_555 I N6 DA 14 I DA 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 H N3 C 9 H C 9 1_555 I N1 DG 13 I DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 H N4 C 9 H C 9 1_555 I O6 DG 13 I DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 H O2 C 9 H C 9 1_555 I N2 DG 13 I DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 H N3 U 10 H U 10 1_555 I N1 DA 12 I DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 H O4 U 10 H U 10 1_555 I N6 DA 12 I DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 H N1 G 11 H G 11 1_555 I N3 DC 11 I DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 H N2 G 11 H G 11 1_555 I O2 DC 11 I DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 H O6 G 11 H G 11 1_555 I N4 DC 11 I DC 11 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 40 n n PB O2B ADP sing 41 n n PB O3B ADP sing 42 n n PB O3A ADP sing 43 n n O2B HOB2 ADP sing 44 n n O3B HOB3 ADP sing 45 n n PA O1A ADP doub 46 n n PA O2A ADP sing 47 n n PA O3A ADP sing 48 n n PA O5' ADP sing 49 n n O2A HOA2 ADP sing 50 n n O5' C5' ADP sing 51 n n C5' C4' ADP sing 52 n n C5' "H5'1" ADP sing 53 n n C5' "H5'2" ADP sing 54 n n C4' O4' ADP sing 55 n n C4' C3' ADP sing 56 n n C4' H4' ADP sing 57 n n O4' C1' ADP sing 58 n n C3' O3' ADP sing 59 n n C3' C2' ADP sing 60 n n C3' H3' ADP sing 61 n n O3' HO3' ADP sing 62 n n C2' O2' ADP sing 63 n n C2' C1' ADP sing 64 n n C2' H2' ADP sing 65 n n O2' HO2' ADP sing 66 n n C1' N9 ADP sing 67 n n C1' H1' ADP sing 68 n n N9 C8 ADP sing 69 n y N9 C4 ADP sing 70 n y C8 N7 ADP doub 71 n y C8 H8 ADP sing 72 n n N7 C5 ADP sing 73 n y C5 C6 ADP sing 74 n y C5 C4 ADP doub 75 n y C6 N6 ADP sing 76 n n C6 N1 ADP doub 77 n y N6 HN61 ADP sing 78 n n N6 HN62 ADP sing 79 n n N1 C2 ADP sing 80 n y C2 N3 ADP doub 81 n y C2 H2 ADP sing 82 n n N3 C4 ADP sing 83 n y # _atom_sites.entry_id 8VAT _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 7 ZN B 1 401 418 ZN ZN . K 8 ADP B 1 402 400 ADP ADP . L 9 BEF B 1 403 401 BEF BEF . M 10 MG B 1 404 412 MG MG . N 7 ZN C 1 401 419 ZN ZN . O 8 ADP C 1 402 402 ADP ADP . P 9 BEF C 1 403 403 BEF BEF . Q 10 MG C 1 404 413 MG MG . R 7 ZN D 1 401 420 ZN ZN . S 8 ADP D 1 402 404 ADP ADP . T 9 BEF D 1 403 405 BEF BEF . U 10 MG D 1 404 414 MG MG . V 7 ZN E 1 401 421 ZN ZN . # 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 . . . S 8 132.308 116.664 107.298 1 5335.94 ? PB ADP 402 D 1 HETATM 2 O O1B ADP . . . S 8 131.63 116.253 108.641 1 5598.61 ? O1B ADP 402 D 1 HETATM 3 O O2B ADP . . . S 8 133.773 116.872 107.194 1 5301.81 ? O2B ADP 402 D 1 HETATM 4 O O3B ADP . . . S 8 131.837 118.105 106.846 1 5475.33 ? O3B ADP 402 D 1 HETATM 5 P PA ADP . . . S 8 131.376 114.216 106.351 1 5399.93 ? PA ADP 402 D 1 HETATM 6 O O1A ADP . . . S 8 132.616 113.36 106.473 1 5512.09 ? O1A ADP 402 D 1 HETATM 7 O O2A ADP . . . S 8 130.396 114.222 107.509 1 5529.74 ? O2A ADP 402 D 1 HETATM 8 O O3A ADP . . . S 8 131.851 115.734 106.085 1 5512.77 ? O3A ADP 402 D 1 HETATM 9 O O5' ADP . . . S 8 130.711 113.656 104.998 1 5671.36 ? O5' ADP 402 D 1 HETATM 10 C C5' ADP . . . S 8 129.31 113.699 104.783 1 5693.84 ? C5' ADP 402 D 1 HETATM 11 C C4' ADP . . . S 8 129.027 112.952 103.494 1 5719.31 ? C4' ADP 402 D 1 HETATM 12 O O4' ADP . . . S 8 129.839 113.497 102.488 1 5748.2 ? O4' ADP 402 D 1 HETATM 13 C C3' ADP . . . S 8 129.541 111.553 103.602 1 5732.84 ? C3' ADP 402 D 1 HETATM 14 O O3' ADP . . . S 8 128.411 110.814 104.036 1 5573.15 ? O3' ADP 402 D 1 HETATM 15 C C2' ADP . . . S 8 130.025 111.189 102.215 1 5777.78 ? C2' ADP 402 D 1 HETATM 16 O O2' ADP . . . S 8 128.93 110.807 101.402 1 5686.22 ? O2' ADP 402 D 1 HETATM 17 C C1' ADP . . . S 8 130.405 112.51 101.64 1 5778.26 ? C1' ADP 402 D 1 HETATM 18 N N9 ADP . . . S 8 131.862 112.698 101.635 1 5777.67 ? N9 ADP 402 D 1 HETATM 19 C C8 ADP . . . S 8 132.504 113.758 102.134 1 5649.31 ? C8 ADP 402 D 1 HETATM 20 N N7 ADP . . . S 8 133.833 113.661 101.953 1 5546.43 ? N7 ADP 402 D 1 HETATM 21 C C5 ADP . . . S 8 134.033 112.512 101.326 1 5595.66 ? C5 ADP 402 D 1 HETATM 22 C C6 ADP . . . S 8 135.211 111.816 100.863 1 5544.57 ? C6 ADP 402 D 1 HETATM 23 N N6 ADP . . . S 8 136.427 112.359 101.032 1 5419.2 ? N6 ADP 402 D 1 HETATM 24 N N1 ADP . . . S 8 134.996 110.636 100.278 1 5469.36 ? N1 ADP 402 D 1 HETATM 25 C C2 ADP . . . S 8 133.762 110.114 100.107 1 5570.73 ? C2 ADP 402 D 1 HETATM 26 N N3 ADP . . . S 8 132.631 110.7 100.502 1 5751.68 ? N3 ADP 402 D 1 HETATM 27 C C4 ADP . . . S 8 132.733 111.879 101.111 1 5842 ? C4 ADP 402 D 1 # _model_server_stats.io_time_ms 90 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #