data_6VFS # _model_server_result.job_id Gpu64ewnbIMP1Uq-nlvx0w _model_server_result.datetime_utc '2025-07-04 17:00:26' _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":"Y","auth_seq_id":501}' # _entry.id 6VFS # _exptl.entry_id 6VFS _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 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 ? 6 X N N ? 6 Y 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 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 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 PB ADP . . . Y 6 124.755 157.694 105.291 1 20 ? PB ADP 501 F 1 HETATM 2 O O1B ADP . . . Y 6 125.866 157.037 104.508 1 20 ? O1B ADP 501 F 1 HETATM 3 O O2B ADP . . . Y 6 124.948 157.679 106.786 1 20 ? O2B ADP 501 F 1 HETATM 4 O O3B ADP . . . Y 6 124.297 159.021 104.735 1 20 ? O3B ADP 501 F 1 HETATM 5 P PA ADP . . . Y 6 122.835 156.833 103.562 1 20 ? PA ADP 501 F 1 HETATM 6 O O1A ADP . . . Y 6 123.948 156.536 102.59 1 20 ? O1A ADP 501 F 1 HETATM 7 O O2A ADP . . . Y 6 122.089 158.14 103.493 1 20 ? O2A ADP 501 F 1 HETATM 8 O O3A ADP . . . Y 6 123.488 156.742 105.026 1 20 ? O3A ADP 501 F 1 HETATM 9 O O5' ADP . . . Y 6 121.753 155.645 103.522 1 20 ? O5' ADP 501 F 1 HETATM 10 C C5' ADP . . . Y 6 122.091 154.291 103.8 1 20 ? C5' ADP 501 F 1 HETATM 11 C C4' ADP . . . Y 6 120.81 153.47 103.749 1 20 ? C4' ADP 501 F 1 HETATM 12 O O4' ADP . . . Y 6 119.858 154.005 104.671 1 20 ? O4' ADP 501 F 1 HETATM 13 C C3' ADP . . . Y 6 120.153 153.491 102.376 1 20 ? C3' ADP 501 F 1 HETATM 14 O O3' ADP . . . Y 6 120.354 152.249 101.697 1 20 ? O3' ADP 501 F 1 HETATM 15 C C2' ADP . . . Y 6 118.678 153.741 102.629 1 20 ? C2' ADP 501 F 1 HETATM 16 O O2' ADP . . . Y 6 117.867 152.649 102.185 1 20 ? O2' ADP 501 F 1 HETATM 17 C C1' ADP . . . Y 6 118.538 153.888 104.134 1 20 ? C1' ADP 501 F 1 HETATM 18 N N9 ADP . . . Y 6 117.725 155.079 104.473 1 20 ? N9 ADP 501 F 1 HETATM 19 C C8 ADP . . . Y 6 118.088 156.061 105.319 1 20 ? C8 ADP 501 F 1 HETATM 20 N N7 ADP . . . Y 6 117.109 156.993 105.417 1 20 ? N7 ADP 501 F 1 HETATM 21 C C5 ADP . . . Y 6 116.097 156.6 104.627 1 20 ? C5 ADP 501 F 1 HETATM 22 C C6 ADP . . . Y 6 114.766 157.126 104.274 1 20 ? C6 ADP 501 F 1 HETATM 23 N N6 ADP . . . Y 6 114.342 158.287 104.818 1 20 ? N6 ADP 501 F 1 HETATM 24 N N1 ADP . . . Y 6 114.01 156.416 103.409 1 20 ? N1 ADP 501 F 1 HETATM 25 C C2 ADP . . . Y 6 114.441 155.257 102.873 1 20 ? C2 ADP 501 F 1 HETATM 26 N N3 ADP . . . Y 6 115.645 154.724 103.155 1 20 ? N3 ADP 501 F 1 HETATM 27 C C4 ADP . . . Y 6 116.5 155.334 104.01 1 20 ? C4 ADP 501 F 1 HETATM 28 H "H5'1" ADP . . . Y 6 122.815 153.91 103.076 1 20 ? "H5'1" ADP 501 F 1 HETATM 29 H "H5'2" ADP . . . Y 6 122.531 154.227 104.797 1 20 ? "H5'2" ADP 501 F 1 HETATM 30 H H4' ADP . . . Y 6 121.045 152.431 104.015 1 20 ? H4' ADP 501 F 1 HETATM 31 H H3' ADP . . . Y 6 120.564 154.322 101.785 1 20 ? H3' ADP 501 F 1 HETATM 32 H HO3' ADP . . . Y 6 120.007 152.316 100.797 1 20 ? HO3' ADP 501 F 1 HETATM 33 H H2' ADP . . . Y 6 118.377 154.672 102.129 1 20 ? H2' ADP 501 F 1 HETATM 34 H HO2' ADP . . . Y 6 117.85 152.622 101.22 1 20 ? HO2' ADP 501 F 1 HETATM 35 H H1' ADP . . . Y 6 118.055 152.987 104.534 1 20 ? H1' ADP 501 F 1 HETATM 36 H H8 ADP . . . Y 6 119.033 156.105 105.844 1 20 ? H8 ADP 501 F 1 HETATM 37 H HN61 ADP . . . Y 6 114.939 158.789 105.46 1 20 ? HN61 ADP 501 F 1 HETATM 38 H HN62 ADP . . . Y 6 113.437 158.655 104.583 1 20 ? HN62 ADP 501 F 1 HETATM 39 H H2 ADP . . . Y 6 113.791 154.731 102.185 1 20 ? H2 ADP 501 F 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 78 _model_server_stats.query_time_ms 222 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #