data_9BYT # _model_server_result.job_id gpHbJa4v3SgNcAJfg5cVyg _model_server_result.datetime_utc '2025-09-30 16:25:12' _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 9byt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":801}' # _entry.id 9BYT # _exptl.entry_id 9BYT _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 ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 E N N ? 3 K 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 G O2A TTP . A TTP 803 1_555 H MG MG . A MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc2 G O1B TTP . A TTP 803 1_555 H MG MG . A MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.849 ? metalc ? metalc3 G O1G TTP . A TTP 803 1_555 H MG MG . A MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc4 I O2A TTP . B TTP 801 1_555 J MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc5 I O1B TTP . B TTP 801 1_555 J MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc6 I O3G TTP . B TTP 801 1_555 J MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc7 C OD1 ASP 87 C ASP 66 1_555 N MN MN . C MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc8 C OE2 GLU 118 C GLU 97 1_555 M MN MN . C MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc9 C OE1 GLU 118 C GLU 97 1_555 N MN MN . C MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc10 C ND1 HIS 122 C HIS 101 1_555 N MN MN . C MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc11 C OE1 GLU 185 C GLU 164 1_555 M MN MN . C MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc12 C OE2 GLU 185 C GLU 164 1_555 M MN MN . C MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? metalc ? metalc13 C OE1 GLU 219 C GLU 198 1_555 M MN MN . C MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc14 C OE1 GLU 219 C GLU 198 1_555 N MN MN . C MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc15 C OE2 GLU 219 C GLU 198 1_555 N MN MN . C MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc16 C ND1 HIS 222 C HIS 201 1_555 M MN MN . C MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc17 D OD1 ASP 87 D ASP 66 1_555 P MN MN . D MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc18 D OD2 ASP 87 D ASP 66 1_555 P MN MN . D MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc19 D OE2 GLU 118 D GLU 97 1_555 O MN MN . D MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.911 ? metalc ? metalc20 D OE1 GLU 118 D GLU 97 1_555 P MN MN . D MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc21 D ND1 HIS 122 D HIS 101 1_555 P MN MN . D MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc22 D OE1 GLU 185 D GLU 164 1_555 O MN MN . D MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc23 D OE2 GLU 185 D GLU 164 1_555 O MN MN . D MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc24 D OE1 GLU 219 D GLU 198 1_555 O MN MN . D MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc25 D OE2 GLU 219 D GLU 198 1_555 P MN MN . D MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc26 D ND1 HIS 222 D HIS 201 1_555 O MN MN . D MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? # _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 9BYT _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 E 3 ATP A 1 801 701 ATP ATP . F 4 GDP A 1 802 702 GDP GDP . G 5 TTP A 1 803 703 TTP TTP . H 6 MG A 1 804 704 MG MG . I 5 TTP B 1 801 701 TTP TTP . J 6 MG B 1 802 702 MG MG . K 3 ATP B 1 803 703 ATP ATP . L 4 GDP B 1 804 704 GDP GDP . M 7 MN C 1 401 401 MN MN . N 7 MN C 1 402 402 MN MN . O 7 MN D 1 401 401 MN MN . P 7 MN D 1 402 402 MN MN . # 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 . . . E 3 104.397 141.997 82.591 1 68.91 ? PG ATP 801 A 1 HETATM 2 O O1G ATP . . . E 3 103.142 142.395 81.888 1 61.99 ? O1G ATP 801 A 1 HETATM 3 O O2G ATP . . . E 3 105.542 143.002 82.42 1 61.48 -1 O2G ATP 801 A 1 HETATM 4 O O3G ATP . . . E 3 104.201 141.71 84.083 1 57.91 ? O3G ATP 801 A 1 HETATM 5 P PB ATP . . . E 3 106.136 140.112 81.04 1 68.42 ? PB ATP 801 A 1 HETATM 6 O O1B ATP . . . E 3 105.943 140.546 79.641 1 59.48 -1 O1B ATP 801 A 1 HETATM 7 O O2B ATP . . . E 3 107.46 140.526 81.682 1 59.06 ? O2B ATP 801 A 1 HETATM 8 O O3B ATP . . . E 3 104.97 140.629 81.99 1 62.04 ? O3B ATP 801 A 1 HETATM 9 P PA ATP . . . E 3 106.232 137.458 82.347 1 63.87 ? PA ATP 801 A 1 HETATM 10 O O1A ATP . . . E 3 107.434 136.637 82.095 1 60.02 -1 O1A ATP 801 A 1 HETATM 11 O O2A ATP . . . E 3 104.931 136.668 82.485 1 58.33 ? O2A ATP 801 A 1 HETATM 12 O O3A ATP . . . E 3 106.008 138.533 81.195 1 62.45 ? O3A ATP 801 A 1 HETATM 13 O O5' ATP . . . E 3 106.409 138.35 83.637 1 59.78 ? O5' ATP 801 A 1 HETATM 14 C C5' ATP . . . E 3 105.352 138.479 84.61 1 58.13 ? C5' ATP 801 A 1 HETATM 15 C C4' ATP . . . E 3 105.859 139.288 85.776 1 59.51 ? C4' ATP 801 A 1 HETATM 16 O O4' ATP . . . E 3 106.424 138.402 86.769 1 62.13 ? O4' ATP 801 A 1 HETATM 17 C C3' ATP . . . E 3 106.965 140.285 85.444 1 57.82 ? C3' ATP 801 A 1 HETATM 18 O O3' ATP . . . E 3 106.423 141.546 85.069 1 58.51 ? O3' ATP 801 A 1 HETATM 19 C C2' ATP . . . E 3 107.732 140.374 86.763 1 58.31 ? C2' ATP 801 A 1 HETATM 20 O O2' ATP . . . E 3 107.102 141.26 87.68 1 58.66 ? O2' ATP 801 A 1 HETATM 21 C C1' ATP . . . E 3 107.644 138.929 87.26 1 58.5 ? C1' ATP 801 A 1 HETATM 22 N N9 ATP . . . E 3 108.733 138.075 86.8 1 58.48 ? N9 ATP 801 A 1 HETATM 23 C C8 ATP . . . E 3 108.64 136.986 85.973 1 58.26 ? C8 ATP 801 A 1 HETATM 24 N N7 ATP . . . E 3 109.786 136.403 85.725 1 56.05 ? N7 ATP 801 A 1 HETATM 25 C C5 ATP . . . E 3 110.702 137.16 86.441 1 58.55 ? C5 ATP 801 A 1 HETATM 26 C C6 ATP . . . E 3 112.098 137.065 86.599 1 56.46 ? C6 ATP 801 A 1 HETATM 27 N N6 ATP . . . E 3 112.851 136.125 86.02 1 55.74 ? N6 ATP 801 A 1 HETATM 28 N N1 ATP . . . E 3 112.704 137.982 87.385 1 57.23 ? N1 ATP 801 A 1 HETATM 29 C C2 ATP . . . E 3 111.96 138.927 87.963 1 55.67 ? C2 ATP 801 A 1 HETATM 30 N N3 ATP . . . E 3 110.641 139.115 87.888 1 57.17 ? N3 ATP 801 A 1 HETATM 31 C C4 ATP . . . E 3 110.066 138.195 87.108 1 59.07 ? C4 ATP 801 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #