data_9CDG # _model_server_result.job_id B2xzMfyyJspNmYaRdV2dIA _model_server_result.datetime_utc '2025-08-21 03:01:51' _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 9cdg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1102}' # _entry.id 9CDG # _exptl.entry_id 9CDG _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 9CDG _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9CDG _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 3 D N N ? 3 G 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 OD1 ASN 39 A ASN 39 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc2 A SG CYS 499 A CYS 499 1_555 C ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc3 A SG CYS 502 A CYS 502 1_555 C ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc4 A SG CYS 525 A CYS 525 1_555 C ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc5 A SG CYS 536 A CYS 536 1_555 C ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc6 D O2G ATP . A ATP 1102 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc7 D O2B ATP . A ATP 1102 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc8 D O3B ATP . A ATP 1102 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc9 D O2A ATP . A ATP 1102 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc10 D O3A ATP . A ATP 1102 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? metalc ? metalc11 B OD1 ASN 39 B ASN 39 1_555 H MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.815 ? metalc ? metalc12 B O ASP 69 B ASP 69 1_555 I MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc13 B O GLY 70 B GLY 70 1_555 I MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc14 B O SER 195 B SER 195 1_555 I MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc15 B OG SER 195 B SER 195 1_555 I MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc16 B SG CYS 499 B CYS 499 1_555 F ZN ZN . B ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc17 B SG CYS 502 B CYS 502 1_555 F ZN ZN . B ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc18 B SG CYS 525 B CYS 525 1_555 F ZN ZN . B ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc19 B SG CYS 536 B CYS 536 1_555 F ZN ZN . B ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc20 G O1G ATP . B ATP 1102 1_555 H MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc21 G O2B ATP . B ATP 1102 1_555 H MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc22 G O3B ATP . B ATP 1102 1_555 H MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc23 G O2A ATP . B ATP 1102 1_555 H MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc24 G O3A ATP . B ATP 1102 1_555 H MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.751 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 9CDG _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 C 2 ZN A 1 1101 701 ZN ZN . D 3 ATP A 1 1102 702 ATP ATP . E 4 MG A 1 1103 703 MG MG . F 2 ZN B 1 1101 701 ZN ZN . G 3 ATP B 1 1102 702 ATP ATP . H 4 MG B 1 1103 703 MG MG . I 4 MG B 1 1104 704 MG MG . # 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 ATP . . . D 3 114.249 129.844 113.648 1 82.73 ? PG ATP 1102 A 1 HETATM 2 O O1G ATP . . . D 3 114.894 128.532 113.899 1 81.05 ? O1G ATP 1102 A 1 HETATM 3 O O2G ATP . . . D 3 112.914 130.029 114.352 1 88.42 ? O2G ATP 1102 A 1 HETATM 4 O O3G ATP . . . D 3 115.153 131.023 113.975 1 82.98 ? O3G ATP 1102 A 1 HETATM 5 P PB ATP . . . D 3 112.881 130.746 111.162 1 84.17 ? PB ATP 1102 A 1 HETATM 6 O O1B ATP . . . D 3 113.457 131.943 110.529 1 83.36 ? O1B ATP 1102 A 1 HETATM 7 O O2B ATP . . . D 3 111.6 130.967 111.953 1 85.97 ? O2B ATP 1102 A 1 HETATM 8 O O3B ATP . . . D 3 113.915 130.013 112.107 1 85.14 ? O3B ATP 1102 A 1 HETATM 9 P PA ATP . . . D 3 111.823 128.23 110.045 1 85.24 ? PA ATP 1102 A 1 HETATM 10 O O1A ATP . . . D 3 112.734 127.077 109.92 1 89.38 ? O1A ATP 1102 A 1 HETATM 11 O O2A ATP . . . D 3 110.904 128.18 111.249 1 74.35 ? O2A ATP 1102 A 1 HETATM 12 O O3A ATP . . . D 3 112.585 129.613 110.087 1 84.31 ? O3A ATP 1102 A 1 HETATM 13 O O5' ATP . . . D 3 110.967 128.408 108.733 1 81.28 ? O5' ATP 1102 A 1 HETATM 14 C C5' ATP . . . D 3 111.471 129.163 107.613 1 85.37 ? C5' ATP 1102 A 1 HETATM 15 C C4' ATP . . . D 3 110.47 130.245 107.317 1 82.85 ? C4' ATP 1102 A 1 HETATM 16 O O4' ATP . . . D 3 109.155 129.703 107.511 1 82.69 ? O4' ATP 1102 A 1 HETATM 17 C C3' ATP . . . D 3 110.564 131.474 108.222 1 83.52 ? C3' ATP 1102 A 1 HETATM 18 O O3' ATP . . . D 3 111.132 132.577 107.526 1 84.35 ? O3' ATP 1102 A 1 HETATM 19 C C2' ATP . . . D 3 109.113 131.761 108.642 1 83.72 ? C2' ATP 1102 A 1 HETATM 20 O O2' ATP . . . D 3 108.734 133.088 108.295 1 83.37 ? O2' ATP 1102 A 1 HETATM 21 C C1' ATP . . . D 3 108.289 130.755 107.838 1 83.01 ? C1' ATP 1102 A 1 HETATM 22 N N9 ATP . . . D 3 107.172 130.185 108.574 1 78.45 ? N9 ATP 1102 A 1 HETATM 23 C C8 ATP . . . D 3 107.135 128.965 109.195 1 76.92 ? C8 ATP 1102 A 1 HETATM 24 N N7 ATP . . . D 3 105.993 128.697 109.779 1 75.89 ? N7 ATP 1102 A 1 HETATM 25 C C5 ATP . . . D 3 105.227 129.825 109.53 1 75.92 ? C5 ATP 1102 A 1 HETATM 26 C C6 ATP . . . D 3 103.912 130.177 109.883 1 78.47 ? C6 ATP 1102 A 1 HETATM 27 N N6 ATP . . . D 3 103.1 129.395 110.599 1 80.53 ? N6 ATP 1102 A 1 HETATM 28 N N1 ATP . . . D 3 103.45 131.375 109.467 1 79.36 ? N1 ATP 1102 A 1 HETATM 29 C C2 ATP . . . D 3 104.255 132.161 108.748 1 78.77 ? C2 ATP 1102 A 1 HETATM 30 N N3 ATP . . . D 3 105.515 131.945 108.373 1 79.28 ? N3 ATP 1102 A 1 HETATM 31 C C4 ATP . . . D 3 105.941 130.749 108.786 1 76.68 ? C4 ATP 1102 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 205 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #