data_9EMA # _model_server_result.job_id S8X0SOCYAVvoVWqgEBjMdw _model_server_result.datetime_utc '2025-07-03 14:47:53' _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 9ema # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":801}' # _entry.id 9EMA # _exptl.entry_id 9EMA _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 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 x,y,z _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 G N N ? 3 I N N ? 3 K N N ? 3 M N N ? 3 O N N ? 3 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 G O3G ATP . A ATP 501 1_555 Q MG MG . F MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc2 G O3B ATP . A ATP 501 1_555 Q MG MG . F MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc3 G O1A ATP . A ATP 501 1_555 Q MG MG . F MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc4 D OG1 THR 102 D THR 84 1_555 N MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc5 M O1G ATP . D ATP 801 1_555 N MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc6 M O2B ATP . D ATP 801 1_555 N MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc7 E OG1 THR 102 E THR 84 1_555 P MG MG . E MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc8 O O1G ATP . E ATP 801 1_555 P MG MG . E MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc9 O O2B ATP . E ATP 801 1_555 P MG MG . E MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc10 O O1A ATP . E ATP 801 1_555 P MG MG . E MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? metalc ? metalc11 F OG1 THR 102 F THR 84 1_555 S MG MG . F MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc12 F OE2 GLU 335 F GLU 317 1_555 Q MG MG . F MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc13 R O1G ATP . F ATP 802 1_555 S MG MG . F MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc14 R O2B ATP . F ATP 802 1_555 S MG MG . F MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc15 R O1A ATP . F ATP 802 1_555 S MG MG . F MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? # _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 147 n n PG O2G ATP sing 148 n n PG O3G ATP sing 149 n n PG O3B ATP sing 150 n n O2G HOG2 ATP sing 151 n n O3G HOG3 ATP sing 152 n n PB O1B ATP doub 153 n n PB O2B ATP sing 154 n n PB O3B ATP sing 155 n n PB O3A ATP sing 156 n n O2B HOB2 ATP sing 157 n n PA O1A ATP doub 158 n n PA O2A ATP sing 159 n n PA O3A ATP sing 160 n n PA O5' ATP sing 161 n n O2A HOA2 ATP sing 162 n n O5' C5' ATP sing 163 n n C5' C4' ATP sing 164 n n C5' "H5'1" ATP sing 165 n n C5' "H5'2" ATP sing 166 n n C4' O4' ATP sing 167 n n C4' C3' ATP sing 168 n n C4' H4' ATP sing 169 n n O4' C1' ATP sing 170 n n C3' O3' ATP sing 171 n n C3' C2' ATP sing 172 n n C3' H3' ATP sing 173 n n O3' HO3' ATP sing 174 n n C2' O2' ATP sing 175 n n C2' C1' ATP sing 176 n n C2' H2' ATP sing 177 n n O2' HO2' ATP sing 178 n n C1' N9 ATP sing 179 n n C1' H1' ATP sing 180 n n N9 C8 ATP sing 181 n y N9 C4 ATP sing 182 n y C8 N7 ATP doub 183 n y C8 H8 ATP sing 184 n n N7 C5 ATP sing 185 n y C5 C6 ATP sing 186 n y C5 C4 ATP doub 187 n y C6 N6 ATP sing 188 n n C6 N1 ATP doub 189 n y N6 HN61 ATP sing 190 n n N6 HN62 ATP sing 191 n n N1 C2 ATP sing 192 n y C2 N3 ATP doub 193 n y C2 H2 ATP sing 194 n n N3 C4 ATP sing 195 n y # _atom_sites.entry_id 9EMA _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 G 3 ATP A 1 501 500 ATP ATP . H 4 A1H5V A 1 502 503 A1H5V CB6 . I 3 ATP B 1 500 500 ATP ATP . J 4 A1H5V B 1 501 501 A1H5V CB6 . K 3 ATP C 1 501 500 ATP ATP . L 4 A1H5V C 1 502 502 A1H5V CB6 . M 3 ATP D 1 801 500 ATP ATP . N 5 MG D 1 802 501 MG MG . O 3 ATP E 1 801 500 ATP ATP . P 5 MG E 1 802 501 MG MG . Q 5 MG F 1 801 501 MG MG . R 3 ATP F 1 802 500 ATP ATP . S 5 MG F 1 803 501 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 . . . O 3 103.988 144.895 101.79 1 33.95 ? PG ATP 801 E 1 HETATM 2 O O1G ATP . . . O 3 104.123 144.352 103.17 1 23.14 ? O1G ATP 801 E 1 HETATM 3 O O2G ATP . . . O 3 105.18 145.741 101.341 1 25.92 -1 O2G ATP 801 E 1 HETATM 4 O O3G ATP . . . O 3 103.707 143.827 100.734 1 18.83 ? O3G ATP 801 E 1 HETATM 5 P PB ATP . . . O 3 101.337 146.12 102.391 1 8.29 ? PB ATP 801 E 1 HETATM 6 O O1B ATP . . . O 3 100.228 145.881 101.457 1 16.42 -1 O1B ATP 801 E 1 HETATM 7 O O2B ATP . . . O 3 101.328 145.275 103.656 1 19.2 ? O2B ATP 801 E 1 HETATM 8 O O3B ATP . . . O 3 102.74 145.888 101.706 1 11.24 ? O3B ATP 801 E 1 HETATM 9 P PA ATP . . . O 3 101.433 148.42 104.23 1 28.92 ? PA ATP 801 E 1 HETATM 10 O O1A ATP . . . O 3 102.272 147.746 105.242 1 27.38 -1 O1A ATP 801 E 1 HETATM 11 O O2A ATP . . . O 3 99.974 148.598 104.607 1 0 ? O2A ATP 801 E 1 HETATM 12 O O3A ATP . . . O 3 101.443 147.636 102.856 1 9.95 ? O3A ATP 801 E 1 HETATM 13 O O5' ATP . . . O 3 102.1 149.813 103.894 1 28.7 ? O5' ATP 801 E 1 HETATM 14 C C5' ATP . . . O 3 101.415 150.805 103.105 1 13.22 ? C5' ATP 801 E 1 HETATM 15 C C4' ATP . . . O 3 101.367 152.166 103.77 1 19.46 ? C4' ATP 801 E 1 HETATM 16 O O4' ATP . . . O 3 100.143 152.797 103.325 1 22.31 ? O4' ATP 801 E 1 HETATM 17 C C3' ATP . . . O 3 101.206 152.106 105.287 1 14.28 ? C3' ATP 801 E 1 HETATM 18 O O3' ATP . . . O 3 101.438 153.429 105.748 1 19.75 ? O3' ATP 801 E 1 HETATM 19 C C2' ATP . . . O 3 99.705 151.882 105.43 1 12.07 ? C2' ATP 801 E 1 HETATM 20 O O2' ATP . . . O 3 99.323 152.452 106.672 1 17.07 ? O2' ATP 801 E 1 HETATM 21 C C1' ATP . . . O 3 99.184 152.845 104.367 1 8.75 ? C1' ATP 801 E 1 HETATM 22 N N9 ATP . . . O 3 97.922 152.369 103.808 1 12.02 ? N9 ATP 801 E 1 HETATM 23 C C8 ATP . . . O 3 97.735 151.303 102.969 1 11.83 ? C8 ATP 801 E 1 HETATM 24 N N7 ATP . . . O 3 96.489 151.09 102.64 1 15.81 ? N7 ATP 801 E 1 HETATM 25 C C5 ATP . . . O 3 95.799 152.089 103.302 1 12.05 ? C5 ATP 801 E 1 HETATM 26 C C6 ATP . . . O 3 94.432 152.424 103.366 1 13.65 ? C6 ATP 801 E 1 HETATM 27 N N6 ATP . . . O 3 93.473 151.756 102.721 1 13 ? N6 ATP 801 E 1 HETATM 28 N N1 ATP . . . O 3 94.076 153.485 104.13 1 13.47 ? N1 ATP 801 E 1 HETATM 29 C C2 ATP . . . O 3 95.027 154.158 104.781 1 10.66 ? C2 ATP 801 E 1 HETATM 30 N N3 ATP . . . O 3 96.344 153.939 104.779 1 16.56 ? N3 ATP 801 E 1 HETATM 31 C C4 ATP . . . O 3 96.668 152.88 104.033 1 10.86 ? C4 ATP 801 E 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 73 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #