data_9C88 # _model_server_result.job_id PeamMKyF35qDmL4oqVCLXg _model_server_result.datetime_utc '2024-10-18 05:19:22' _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 9c88 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":500}' # _entry.id 9C88 # _exptl.entry_id 9C88 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 507.181 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 9C88 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9C88 _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 21-meric _pdbx_struct_assembly.oligomeric_count 21 _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,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA _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 ? 4 V N N ? 4 X N N ? 4 Z 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 90 A THR 126 1_555 W MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc2 B OD2 ASP 148 A ASP 184 1_555 W MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.909 ? metalc ? metalc3 V O2G ATP . A ATP 500 1_555 W MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc4 V O2B ATP . A ATP 500 1_555 W MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc5 C OG1 THR 90 B THR 126 1_555 Y MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc6 C OD2 ASP 148 B ASP 184 1_555 Y MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc7 X O3G ATP . B ATP 500 1_555 Y MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc8 X O3B ATP . B ATP 500 1_555 Y MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.854 ? metalc ? metalc9 D OG1 THR 90 C THR 126 1_555 AA MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc10 D OD2 ASP 148 C ASP 184 1_555 AA MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc11 Z O2G ATP . C ATP 500 1_555 AA MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.827 ? metalc ? metalc12 Z O2B ATP . C ATP 500 1_555 AA MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc13 Z O3B ATP . C ATP 500 1_555 AA MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? metalc ? metalc14 E OG1 THR 90 D THR 126 1_555 CA MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc15 BA O3B ADP . D ADP 500 1_555 CA MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? # _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 114 n n PG O2G ATP sing 115 n n PG O3G ATP sing 116 n n PG O3B ATP sing 117 n n O2G HOG2 ATP sing 118 n n O3G HOG3 ATP sing 119 n n PB O1B ATP doub 120 n n PB O2B ATP sing 121 n n PB O3B ATP sing 122 n n PB O3A ATP sing 123 n n O2B HOB2 ATP sing 124 n n PA O1A ATP doub 125 n n PA O2A ATP sing 126 n n PA O3A ATP sing 127 n n PA O5' ATP sing 128 n n O2A HOA2 ATP sing 129 n n O5' C5' ATP sing 130 n n C5' C4' ATP sing 131 n n C5' "H5'1" ATP sing 132 n n C5' "H5'2" ATP sing 133 n n C4' O4' ATP sing 134 n n C4' C3' ATP sing 135 n n C4' H4' ATP sing 136 n n O4' C1' ATP sing 137 n n C3' O3' ATP sing 138 n n C3' C2' ATP sing 139 n n C3' H3' ATP sing 140 n n O3' HO3' ATP sing 141 n n C2' O2' ATP sing 142 n n C2' C1' ATP sing 143 n n C2' H2' ATP sing 144 n n O2' HO2' ATP sing 145 n n C1' N9 ATP sing 146 n n C1' H1' ATP sing 147 n n N9 C8 ATP sing 148 n y N9 C4 ATP sing 149 n y C8 N7 ATP doub 150 n y C8 H8 ATP sing 151 n n N7 C5 ATP sing 152 n y C5 C6 ATP sing 153 n y C5 C4 ATP doub 154 n y C6 N6 ATP sing 155 n n C6 N1 ATP doub 156 n y N6 HN61 ATP sing 157 n n N6 HN62 ATP sing 158 n n N1 C2 ATP sing 159 n y C2 N3 ATP doub 160 n y C2 H2 ATP sing 161 n n N3 C4 ATP sing 162 n y # _atom_sites.entry_id 9C88 _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 V 4 ATP A 1 500 500 ATP ATP . W 5 MG A 1 501 501 MG MG . X 4 ATP B 1 500 500 ATP ATP . Y 5 MG B 1 501 501 MG MG . Z 4 ATP C 1 500 500 ATP ATP . AA 5 MG C 1 501 501 MG MG . BA 6 ADP D 1 500 500 ADP ADP . CA 5 MG D 1 501 501 MG MG . DA 6 ADP E 1 500 500 ADP ADP . EA 6 ADP F 1 500 500 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 PG ATP . . . V 4 119.496 162.04 175.861 1 158.59 ? PG ATP 500 A 1 HETATM 2 O O1G ATP . . . V 4 118.863 160.811 175.306 1 152.5 ? O1G ATP 500 A 1 HETATM 3 O O2G ATP . . . V 4 119.958 161.888 177.316 1 155.68 ? O2G ATP 500 A 1 HETATM 4 O O3G ATP . . . V 4 120.663 162.563 175.019 1 149.6 ? O3G ATP 500 A 1 HETATM 5 P PB ATP . . . V 4 116.904 163.54 176.231 1 157.03 ? PB ATP 500 A 1 HETATM 6 O O1B ATP . . . V 4 116.032 163.357 175.052 1 151.78 ? O1B ATP 500 A 1 HETATM 7 O O2B ATP . . . V 4 116.551 162.693 177.456 1 154.51 ? O2B ATP 500 A 1 HETATM 8 O O3B ATP . . . V 4 118.444 163.258 175.893 1 159.33 ? O3B ATP 500 A 1 HETATM 9 P PA ATP . . . V 4 116.187 165.971 177.779 1 155.95 ? PA ATP 500 A 1 HETATM 10 O O1A ATP . . . V 4 116.586 165.621 179.157 1 160.08 ? O1A ATP 500 A 1 HETATM 11 O O2A ATP . . . V 4 114.69 165.874 177.49 1 149.78 ? O2A ATP 500 A 1 HETATM 12 O O3A ATP . . . V 4 116.947 165.061 176.702 1 156.33 ? O3A ATP 500 A 1 HETATM 13 O O5' ATP . . . V 4 116.651 167.444 177.448 1 160.65 ? O5' ATP 500 A 1 HETATM 14 C C5' ATP . . . V 4 116.349 168.538 178.34 1 155.97 ? C5' ATP 500 A 1 HETATM 15 C C4' ATP . . . V 4 116.139 169.801 177.536 1 155.97 ? C4' ATP 500 A 1 HETATM 16 O O4' ATP . . . V 4 115.289 169.444 176.426 1 154.29 ? O4' ATP 500 A 1 HETATM 17 C C3' ATP . . . V 4 115.354 170.846 178.338 1 154.66 ? C3' ATP 500 A 1 HETATM 18 O O3' ATP . . . V 4 115.958 172.101 178.05 1 155.81 ? O3' ATP 500 A 1 HETATM 19 C C2' ATP . . . V 4 113.959 170.838 177.693 1 156.84 ? C2' ATP 500 A 1 HETATM 20 O O2' ATP . . . V 4 113.516 172.187 177.586 1 158.89 ? O2' ATP 500 A 1 HETATM 21 C C1' ATP . . . V 4 114.282 170.412 176.268 1 154.08 ? C1' ATP 500 A 1 HETATM 22 N N9 ATP . . . V 4 113.155 169.727 175.641 1 151.84 ? N9 ATP 500 A 1 HETATM 23 C C8 ATP . . . V 4 113.2 168.537 174.962 1 152.73 ? C8 ATP 500 A 1 HETATM 24 N N7 ATP . . . V 4 112.04 168.141 174.496 1 151.04 ? N7 ATP 500 A 1 HETATM 25 C C5 ATP . . . V 4 111.165 169.138 174.899 1 151.52 ? C5 ATP 500 A 1 HETATM 26 C C6 ATP . . . V 4 109.778 169.315 174.723 1 153.83 ? C6 ATP 500 A 1 HETATM 27 N N6 ATP . . . V 4 108.993 168.454 174.065 1 152.89 ? N6 ATP 500 A 1 HETATM 28 N N1 ATP . . . V 4 109.215 170.423 175.254 1 158.44 ? N1 ATP 500 A 1 HETATM 29 C C2 ATP . . . V 4 109.991 171.286 175.915 1 158 ? C2 ATP 500 A 1 HETATM 30 N N3 ATP . . . V 4 111.306 171.225 176.142 1 157.22 ? N3 ATP 500 A 1 HETATM 31 C C4 ATP . . . V 4 111.838 170.123 175.606 1 153.65 ? C4 ATP 500 A 1 HETATM 32 H "H5'1" ATP . . . V 4 117.085 168.66 178.961 1 155.56 ? "H5'1" ATP 500 A 1 HETATM 33 H "H5'2" ATP . . . V 4 115.55 168.307 178.841 1 155.51 ? "H5'2" ATP 500 A 1 HETATM 34 H H4' ATP . . . V 4 116.989 170.158 177.235 1 154.67 ? H4' ATP 500 A 1 HETATM 35 H H3' ATP . . . V 4 115.318 170.66 179.289 1 154.28 ? H3' ATP 500 A 1 HETATM 36 H HO3' ATP . . . V 4 115.906 172.223 177.21 1 156.11 ? HO3' ATP 500 A 1 HETATM 37 H H2' ATP . . . V 4 113.321 170.269 178.149 1 155.62 ? H2' ATP 500 A 1 HETATM 38 H HO2' ATP . . . V 4 114.122 172.645 177.204 1 157.07 ? HO2' ATP 500 A 1 HETATM 39 H H1' ATP . . . V 4 114.577 171.166 175.731 1 153.91 ? H1' ATP 500 A 1 HETATM 40 H H8 ATP . . . V 4 113.988 168.057 174.84 1 153.26 ? H8 ATP 500 A 1 HETATM 41 H HN61 ATP . . . V 4 109.335 167.752 173.706 1 153.24 ? HN61 ATP 500 A 1 HETATM 42 H HN62 ATP . . . V 4 108.148 168.597 173.997 1 155.42 ? HN62 ATP 500 A 1 HETATM 43 H H2 ATP . . . V 4 109.561 172.036 176.261 1 158.06 ? H2 ATP 500 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 93 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #