data_6VFX # _model_server_result.job_id tHIv4uSioY3WrqytxhFbrg _model_server_result.datetime_utc '2025-07-06 14:45:52' _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 6vfx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":501}' # _entry.id 6VFX # _exptl.entry_id 6VFX _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 5 _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,FA _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 X N N ? 4 Z N N ? 4 CA N N ? 4 EA 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 C THR 126 1_555 W MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc2 A OD2 ASP 184 C ASP 184 1_555 W MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc3 V O3G ATP . C ATP 501 1_555 W MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc4 V O1B ATP . C ATP 501 1_555 W MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.974 ? metalc ? metalc5 B OG1 THR 126 B THR 126 1_555 Y MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc6 B OD2 ASP 184 B ASP 184 1_555 Y MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? metalc ? metalc7 X O3G ATP . B ATP 501 1_555 Y MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc8 X O1B ATP . B ATP 501 1_555 Y MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc9 C OG1 THR 126 E THR 126 1_555 AA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc10 Z O3G ATP . E ATP 501 1_555 AA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc11 Z O1B ATP . E ATP 501 1_555 AA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc12 E OG1 THR 126 D THR 126 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc13 E OD2 ASP 184 D ASP 184 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc14 CA O3G ATP . D ATP 501 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc15 CA O1B ATP . D ATP 501 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? metalc ? metalc16 F OG1 THR 126 A THR 126 1_555 FA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc17 F OD2 ASP 184 A ASP 184 1_555 FA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? metalc ? metalc18 EA O3G ATP . A ATP 501 1_555 FA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc19 EA O1B ATP . A ATP 501 1_555 FA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? # _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 6VFX _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 C 1 501 1 ATP ATP . W 5 MG C 1 502 2 MG MG . X 4 ATP B 1 501 1 ATP ATP . Y 5 MG B 1 502 1 MG MG . Z 4 ATP E 1 501 1 ATP ATP . AA 5 MG E 1 502 4 MG MG . BA 6 ADP F 1 501 1 ADP ADP . CA 4 ATP D 1 501 1 ATP ATP . DA 5 MG D 1 502 3 MG MG . EA 4 ATP A 1 501 1 ATP ATP . FA 5 MG A 1 502 5 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 . . . V 4 184.826 157.633 94.077 1 48.52 ? PG ATP 501 C 1 HETATM 2 O O1G ATP . . . V 4 184.805 156.36 94.885 1 48.52 ? O1G ATP 501 C 1 HETATM 3 O O2G ATP . . . V 4 184.328 158.845 94.826 1 48.52 ? O2G ATP 501 C 1 HETATM 4 O O3G ATP . . . V 4 184.257 157.498 92.685 1 48.52 ? O3G ATP 501 C 1 HETATM 5 P PB ATP . . . V 4 187.327 156.995 92.941 1 48.52 ? PB ATP 501 C 1 HETATM 6 O O1B ATP . . . V 4 186.605 156.707 91.65 1 48.52 ? O1B ATP 501 C 1 HETATM 7 O O2B ATP . . . V 4 187.833 155.848 93.783 1 48.52 ? O2B ATP 501 C 1 HETATM 8 O O3B ATP . . . V 4 186.393 157.935 93.857 1 48.52 ? O3B ATP 501 C 1 HETATM 9 P PA ATP . . . V 4 189.095 158.185 91.121 1 48.52 ? PA ATP 501 C 1 HETATM 10 O O1A ATP . . . V 4 187.94 158.663 90.273 1 48.52 ? O1A ATP 501 C 1 HETATM 11 O O2A ATP . . . V 4 189.869 156.965 90.685 1 48.52 ? O2A ATP 501 C 1 HETATM 12 O O3A ATP . . . V 4 188.562 157.979 92.627 1 48.52 ? O3A ATP 501 C 1 HETATM 13 O O5' ATP . . . V 4 190.112 159.424 91.264 1 48.52 ? O5' ATP 501 C 1 HETATM 14 C C5' ATP . . . V 4 189.929 160.579 90.448 1 48.52 ? C5' ATP 501 C 1 HETATM 15 C C4' ATP . . . V 4 191.236 161.352 90.332 1 48.52 ? C4' ATP 501 C 1 HETATM 16 O O4' ATP . . . V 4 192.029 161.158 91.505 1 48.52 ? O4' ATP 501 C 1 HETATM 17 C C3' ATP . . . V 4 192.049 160.865 89.145 1 48.52 ? C3' ATP 501 C 1 HETATM 18 O O3' ATP . . . V 4 192.059 161.856 88.114 1 48.52 ? O3' ATP 501 C 1 HETATM 19 C C2' ATP . . . V 4 193.45 160.638 89.671 1 48.52 ? C2' ATP 501 C 1 HETATM 20 O O2' ATP . . . V 4 194.348 161.581 89.078 1 48.52 ? O2' ATP 501 C 1 HETATM 21 C C1' ATP . . . V 4 193.389 160.866 91.173 1 48.52 ? C1' ATP 501 C 1 HETATM 22 N N9 ATP . . . V 4 193.789 159.629 91.889 1 48.52 ? N9 ATP 501 C 1 HETATM 23 C C8 ATP . . . V 4 193.066 159.028 92.852 1 48.52 ? C8 ATP 501 C 1 HETATM 24 N N7 ATP . . . V 4 193.694 157.92 93.321 1 48.52 ? N7 ATP 501 C 1 HETATM 25 C C5 ATP . . . V 4 194.853 157.801 92.65 1 48.52 ? C5 ATP 501 C 1 HETATM 26 C C6 ATP . . . V 4 195.991 156.853 92.653 1 48.52 ? C6 ATP 501 C 1 HETATM 27 N N6 ATP . . . V 4 196.011 155.788 93.49 1 48.52 ? N6 ATP 501 C 1 HETATM 28 N N1 ATP . . . V 4 197.008 157.087 91.795 1 48.52 ? N1 ATP 501 C 1 HETATM 29 C C2 ATP . . . V 4 196.999 158.142 90.96 1 48.52 ? C2 ATP 501 C 1 HETATM 30 N N3 ATP . . . V 4 196 159.041 90.904 1 48.52 ? N3 ATP 501 C 1 HETATM 31 C C4 ATP . . . V 4 194.916 158.932 91.711 1 48.52 ? C4 ATP 501 C 1 HETATM 32 H "H5'1" ATP . . . V 4 189.582 160.283 89.456 1 48.52 ? "H5'1" ATP 501 C 1 HETATM 33 H "H5'2" ATP . . . V 4 189.169 161.222 90.892 1 48.52 ? "H5'2" ATP 501 C 1 HETATM 34 H H4' ATP . . . V 4 191.011 162.419 90.199 1 48.52 ? H4' ATP 501 C 1 HETATM 35 H H3' ATP . . . V 4 191.64 159.916 88.773 1 48.52 ? H3' ATP 501 C 1 HETATM 36 H HO3' ATP . . . V 4 192.448 161.484 87.311 1 48.52 ? HO3' ATP 501 C 1 HETATM 37 H H2' ATP . . . V 4 193.759 159.61 89.445 1 48.52 ? H2' ATP 501 C 1 HETATM 38 H HO2' ATP . . . V 4 194.492 161.354 88.149 1 48.52 ? HO2' ATP 501 C 1 HETATM 39 H H1' ATP . . . V 4 194.045 161.704 91.446 1 48.52 ? H1' ATP 501 C 1 HETATM 40 H H8 ATP . . . V 4 192.105 159.38 93.206 1 48.52 ? H8 ATP 501 C 1 HETATM 41 H HN61 ATP . . . V 4 196.792 155.154 93.474 1 48.52 ? HN61 ATP 501 C 1 HETATM 42 H HN62 ATP . . . V 4 195.245 155.63 94.124 1 48.52 ? HN62 ATP 501 C 1 HETATM 43 H H2 ATP . . . V 4 197.844 158.275 90.296 1 48.52 ? H2 ATP 501 C 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 130 _model_server_stats.query_time_ms 556 _model_server_stats.encode_time_ms 35 _model_server_stats.element_count 43 #