data_6QS7 # _model_server_result.job_id Ei-Oc1ywxnyPb8YBC6hp5g _model_server_result.datetime_utc '2025-01-10 20:07:09' _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 6qs7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":1001}' # _entry.id 6QS7 # _exptl.entry_id 6QS7 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details heptameric _pdbx_struct_assembly.oligomeric_count 7 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id Y _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 H O2G AGS . A AGS 1001 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc2 B OG1 THR 612 B THR 612 1_555 M MG MG . B MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc3 J O2G AGS . B AGS 1001 1_555 L MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc4 J O1B AGS . B AGS 1001 1_555 L MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc5 K O2G AGS . B AGS 1002 1_555 M MG MG . B MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? metalc ? metalc6 K O1B AGS . B AGS 1002 1_555 M MG MG . B MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc7 C OG1 THR 213 C THR 213 1_555 P MG MG . C MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc8 C OG1 THR 612 C THR 612 1_555 Q MG MG . C MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc9 C OD1 ASP 677 C ASP 677 1_555 Q MG MG . C MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc10 C OD2 ASP 677 C ASP 677 1_555 Q MG MG . C MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc11 N O2G AGS . C AGS 1001 1_555 P MG MG . C MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc12 N O1B AGS . C AGS 1001 1_555 P MG MG . C MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc13 O O2G AGS . C AGS 1002 1_555 Q MG MG . C MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc14 O O1B AGS . C AGS 1002 1_555 Q MG MG . C MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc15 D OG1 THR 213 D THR 213 1_555 T MG MG . D MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc16 D OG1 THR 612 D THR 612 1_555 U MG MG . D MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc17 R O2G AGS . D AGS 1001 1_555 T MG MG . D MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc18 R O1B AGS . D AGS 1001 1_555 T MG MG . D MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc19 S O1B AGS . D AGS 1002 1_555 U MG MG . D MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? metalc ? metalc20 E OG1 THR 612 E THR 612 1_555 X MG MG . E MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc21 E OD1 ASP 677 E ASP 677 1_555 X MG MG . E MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.863 ? metalc ? metalc22 W O2G AGS . E AGS 1002 1_555 X MG MG . E MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? # _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 6QS7 _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 H 3 AGS A 1 1001 1001 AGS AGS . I 4 MG A 1 1002 1 MG MG . J 3 AGS B 1 1001 1001 AGS AGS . K 3 AGS B 1 1002 1002 AGS AGS . L 4 MG B 1 1003 1 MG MG . M 4 MG B 1 1004 4 MG MG . N 3 AGS C 1 1001 1001 AGS AGS . O 3 AGS C 1 1002 1002 AGS AGS . P 4 MG C 1 1003 2 MG MG . Q 4 MG C 1 1004 5 MG MG . R 3 AGS D 1 1001 1001 AGS AGS . S 3 AGS D 1 1002 1002 AGS AGS . T 4 MG D 1 1003 3 MG MG . U 4 MG D 1 1004 6 MG MG . V 3 AGS E 1 1001 1001 AGS AGS . W 3 AGS E 1 1002 1002 AGS AGS . X 4 MG E 1 1003 7 MG MG . Y 5 ADP F 1 1001 1001 ADP ADP . Z 3 AGS F 1 1002 1001 AGS AGS . # 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 5 145.682 116.851 139.272 1 167.46 ? PB ADP 1001 F 1 HETATM 2 O O1B ADP . . . Y 5 145.707 117.668 138.009 1 167.46 ? O1B ADP 1001 F 1 HETATM 3 O O2B ADP . . . Y 5 146.942 116.922 140.094 1 167.46 ? O2B ADP 1001 F 1 HETATM 4 O O3B ADP . . . Y 5 144.412 117.002 140.069 1 167.46 ? O3B ADP 1001 F 1 HETATM 5 P PA ADP . . . Y 5 145.691 114.101 139.745 1 167.46 ? PA ADP 1001 F 1 HETATM 6 O O1A ADP . . . Y 5 147.021 114.088 140.449 1 167.46 ? O1A ADP 1001 F 1 HETATM 7 O O2A ADP . . . Y 5 144.429 114.106 140.567 1 167.46 ? O2A ADP 1001 F 1 HETATM 8 O O3A ADP . . . Y 5 145.638 115.34 138.728 1 167.46 ? O3A ADP 1001 F 1 HETATM 9 O O5' ADP . . . Y 5 145.592 112.83 138.774 1 167.46 ? O5' ADP 1001 F 1 HETATM 10 C C5' ADP . . . Y 5 146.614 112.492 137.842 1 167.46 ? C5' ADP 1001 F 1 HETATM 11 C C4' ADP . . . Y 5 146.044 111.548 136.788 1 167.46 ? C4' ADP 1001 F 1 HETATM 12 O O4' ADP . . . Y 5 146.865 110.388 136.631 1 167.46 ? O4' ADP 1001 F 1 HETATM 13 C C3' ADP . . . Y 5 144.663 111.05 137.167 1 167.46 ? C3' ADP 1001 F 1 HETATM 14 O O3' ADP . . . Y 5 143.652 111.809 136.506 1 167.46 ? O3' ADP 1001 F 1 HETATM 15 C C2' ADP . . . Y 5 144.629 109.609 136.726 1 167.46 ? C2' ADP 1001 F 1 HETATM 16 O O2' ADP . . . Y 5 143.904 109.505 135.502 1 167.46 ? O2' ADP 1001 F 1 HETATM 17 C C1' ADP . . . Y 5 146.073 109.206 136.498 1 167.46 ? C1' ADP 1001 F 1 HETATM 18 N N9 ADP . . . Y 5 146.48 108.252 137.557 1 167.46 ? N9 ADP 1001 F 1 HETATM 19 C C8 ADP . . . Y 5 147.474 108.471 138.429 1 167.46 ? C8 ADP 1001 F 1 HETATM 20 N N7 ADP . . . Y 5 147.629 107.431 139.282 1 167.46 ? N7 ADP 1001 F 1 HETATM 21 C C5 ADP . . . Y 5 146.709 106.51 138.957 1 167.46 ? C5 ADP 1001 F 1 HETATM 22 C C6 ADP . . . Y 5 146.321 105.174 139.458 1 167.46 ? C6 ADP 1001 F 1 HETATM 23 N N6 ADP . . . Y 5 146.963 104.598 140.499 1 167.46 ? N6 ADP 1001 F 1 HETATM 24 N N1 ADP . . . Y 5 145.309 104.539 138.84 1 167.46 ? N1 ADP 1001 F 1 HETATM 25 C C2 ADP . . . Y 5 144.661 105.092 137.805 1 167.46 ? C2 ADP 1001 F 1 HETATM 26 N N3 ADP . . . Y 5 144.957 106.299 137.301 1 167.46 ? N3 ADP 1001 F 1 HETATM 27 C C4 ADP . . . Y 5 145.955 107.05 137.819 1 167.46 ? C4 ADP 1001 F 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #