data_6VFS # _model_server_result.job_id qPidCZQU7RMjbhVneW1lgw _model_server_result.datetime_utc '2025-07-04 18:45:17' _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 6vfs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"DA","auth_seq_id":501}' # _entry.id 6VFS # _exptl.entry_id 6VFS _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 21-meric _pdbx_struct_assembly.oligomeric_count 21 _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,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 ? _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 Z N N ? 4 BA N N ? 4 DA 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 OG1 THR 126 E THR 126 1_555 W MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc2 A OD2 ASP 184 E ASP 184 1_555 W MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc3 V O3G ATP . E ATP 501 1_555 W MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.953 ? metalc ? metalc4 V O1B ATP . E ATP 501 1_555 W MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc5 D OG1 THR 126 C THR 126 1_555 AA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc6 D OD2 ASP 184 C ASP 184 1_555 AA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? metalc ? metalc7 Z O1G ATP . C ATP 501 1_555 AA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.901 ? metalc ? metalc8 Z O1B ATP . C ATP 501 1_555 AA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc9 E OG1 THR 126 B THR 126 1_555 CA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc10 BA O3G ATP . B ATP 501 1_555 CA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc11 BA O1B ATP . B ATP 501 1_555 CA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc12 F OG1 THR 126 D THR 126 1_555 EA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc13 DA O1G ATP . D ATP 501 1_555 EA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc14 DA O3G ATP . D ATP 501 1_555 EA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.815 ? metalc ? metalc15 DA O1B ATP . D ATP 501 1_555 EA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? # _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 6VFS _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 E 1 501 1 ATP ATP . W 5 MG E 1 502 1 MG MG . X 6 ADP A 1 501 1 ADP ADP . Y 6 ADP F 1 501 1 ADP ADP . Z 4 ATP C 1 501 1 ATP ATP . AA 5 MG C 1 502 3 MG MG . BA 4 ATP B 1 501 1 ATP ATP . CA 5 MG B 1 502 2 MG MG . DA 4 ATP D 1 501 1 ATP ATP . EA 5 MG D 1 502 4 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 . . . DA 4 170.147 183.191 94.806 1 45.02 ? PG ATP 501 D 1 HETATM 2 O O1G ATP . . . DA 4 171.259 182.367 94.203 1 45.02 ? O1G ATP 501 D 1 HETATM 3 O O2G ATP . . . DA 4 170.088 183.138 96.313 1 45.02 ? O2G ATP 501 D 1 HETATM 4 O O3G ATP . . . DA 4 168.81 183.013 94.127 1 45.02 ? O3G ATP 501 D 1 HETATM 5 P PB ATP . . . DA 4 170.909 185.017 92.903 1 45.02 ? PB ATP 501 D 1 HETATM 6 O O1B ATP . . . DA 4 169.779 184.463 92.07 1 45.02 ? O1B ATP 501 D 1 HETATM 7 O O2B ATP . . . DA 4 172.318 184.544 92.641 1 45.02 ? O2B ATP 501 D 1 HETATM 8 O O3B ATP . . . DA 4 170.561 184.706 94.443 1 45.02 ? O3B ATP 501 D 1 HETATM 9 P PA ATP . . . DA 4 171.175 187.23 91.289 1 45.02 ? PA ATP 501 D 1 HETATM 10 O O1A ATP . . . DA 4 170.231 186.562 90.319 1 45.02 ? O1A ATP 501 D 1 HETATM 11 O O2A ATP . . . DA 4 172.658 187.155 91.018 1 45.02 ? O2A ATP 501 D 1 HETATM 12 O O3A ATP . . . DA 4 170.886 186.62 92.753 1 45.02 ? O3A ATP 501 D 1 HETATM 13 O O5' ATP . . . DA 4 170.78 188.786 91.413 1 45.02 ? O5' ATP 501 D 1 HETATM 14 C C5' ATP . . . DA 4 169.43 189.245 91.423 1 45.02 ? C5' ATP 501 D 1 HETATM 15 C C4' ATP . . . DA 4 169.452 190.765 91.532 1 45.02 ? C4' ATP 501 D 1 HETATM 16 O O4' ATP . . . DA 4 170.454 191.128 92.488 1 45.02 ? O4' ATP 501 D 1 HETATM 17 C C3' ATP . . . DA 4 169.819 191.461 90.228 1 45.02 ? C3' ATP 501 D 1 HETATM 18 O O3' ATP . . . DA 4 169.009 192.628 90.049 1 45.02 ? O3' ATP 501 D 1 HETATM 19 C C2' ATP . . . DA 4 171.269 191.858 90.402 1 45.02 ? C2' ATP 501 D 1 HETATM 20 O O2' ATP . . . DA 4 171.601 193.061 89.702 1 45.02 ? O2' ATP 501 D 1 HETATM 21 C C1' ATP . . . DA 4 171.375 192.054 91.903 1 45.02 ? C1' ATP 501 D 1 HETATM 22 N N9 ATP . . . DA 4 172.745 191.849 92.432 1 45.02 ? N9 ATP 501 D 1 HETATM 23 C C8 ATP . . . DA 4 173.086 190.975 93.401 1 45.02 ? C8 ATP 501 D 1 HETATM 24 N N7 ATP . . . DA 4 174.408 191.06 93.677 1 45.02 ? N7 ATP 501 D 1 HETATM 25 C C5 ATP . . . DA 4 174.92 192.008 92.88 1 45.02 ? C5 ATP 501 D 1 HETATM 26 C C6 ATP . . . DA 4 176.254 192.584 92.671 1 45.02 ? C6 ATP 501 D 1 HETATM 27 N N6 ATP . . . DA 4 177.282 192.119 93.406 1 45.02 ? N6 ATP 501 D 1 HETATM 28 N N1 ATP . . . DA 4 176.397 193.56 91.747 1 45.02 ? N1 ATP 501 D 1 HETATM 29 C C2 ATP . . . DA 4 175.352 194.007 91.023 1 45.02 ? C2 ATP 501 D 1 HETATM 30 N N3 ATP . . . DA 4 174.103 193.52 91.167 1 45.02 ? N3 ATP 501 D 1 HETATM 31 C C4 ATP . . . DA 4 173.827 192.539 92.064 1 45.02 ? C4 ATP 501 D 1 HETATM 32 H "H5'1" ATP . . . DA 4 168.915 188.821 92.288 1 45.02 ? "H5'1" ATP 501 D 1 HETATM 33 H "H5'2" ATP . . . DA 4 168.9 188.932 90.521 1 45.02 ? "H5'2" ATP 501 D 1 HETATM 34 H H4' ATP . . . DA 4 168.464 191.117 91.863 1 45.02 ? H4' ATP 501 D 1 HETATM 35 H H3' ATP . . . DA 4 169.702 190.774 89.379 1 45.02 ? H3' ATP 501 D 1 HETATM 36 H HO3' ATP . . . DA 4 169.263 193.086 89.236 1 45.02 ? HO3' ATP 501 D 1 HETATM 37 H H2' ATP . . . DA 4 171.916 191.028 90.084 1 45.02 ? H2' ATP 501 D 1 HETATM 38 H HO2' ATP . . . DA 4 171.511 192.918 88.75 1 45.02 ? HO2' ATP 501 D 1 HETATM 39 H H1' ATP . . . DA 4 171.059 193.079 92.14 1 45.02 ? H1' ATP 501 D 1 HETATM 40 H H8 ATP . . . DA 4 172.403 190.294 93.892 1 45.02 ? H8 ATP 501 D 1 HETATM 41 H HN61 ATP . . . DA 4 178.194 192.5 93.266 1 45.02 ? HN61 ATP 501 D 1 HETATM 42 H HN62 ATP . . . DA 4 177.132 191.388 94.087 1 45.02 ? HN62 ATP 501 D 1 HETATM 43 H H2 ATP . . . DA 4 175.525 194.792 90.295 1 45.02 ? H2 ATP 501 D 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 95 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #