data_7S67 # _model_server_result.job_id oTkGUWIQEnvdpPgP5XUXdA _model_server_result.datetime_utc '2025-03-13 17:48:06' _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 7s67 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":902}' # _entry.id 7S67 # _exptl.entry_id 7S67 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 I N N ? 4 O N N ? 4 S N N ? 4 W N N ? 4 Z N N ? 4 CA 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 53 A THR 53 1_555 H MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.781 ? metalc ? metalc2 A OG1 THR 295 A THR 295 1_555 J MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc3 G O2G ATP . A ATP 601 1_555 H MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? metalc ? metalc4 G O1B ATP . A ATP 601 1_555 H MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.764 ? metalc ? metalc5 G O1A ATP . A ATP 601 1_555 H MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3 ? metalc ? metalc6 I O1B ADP . A ADP 603 1_555 J MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc7 K O2G ATP . A ATP 605 1_555 L MG MG . A MG 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc8 K O1B ATP . A ATP 605 1_555 L MG MG . A MG 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc9 L MG MG . A MG 606 1_555 F OG1 THR 53 F THR 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.781 ? metalc ? metalc10 B OG1 THR 53 B THR 53 1_555 N MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.781 ? metalc ? metalc11 B OG1 THR 295 B THR 295 1_555 P MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? metalc ? metalc12 M O2G ATP . B ATP 601 1_555 N MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc13 M O1B ATP . B ATP 601 1_555 N MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.764 ? metalc ? metalc14 M O1A ATP . B ATP 601 1_555 N MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.999 ? metalc ? metalc15 O O1B ADP . B ADP 603 1_555 P MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc16 C OG1 THR 53 C THR 53 1_555 R MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? metalc ? metalc17 C OG1 THR 295 C THR 295 1_555 T MG MG . C MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc18 Q O2G ATP . C ATP 601 1_555 R MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc19 Q O1B ATP . C ATP 601 1_555 R MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.764 ? metalc ? metalc20 Q O1A ATP . C ATP 601 1_555 R MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.999 ? metalc ? metalc21 S O1B ADP . C ADP 603 1_555 T MG MG . C MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc22 D OG1 THR 53 D THR 53 1_555 V MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.781 ? metalc ? metalc23 D OG1 THR 295 D THR 295 1_555 X MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc24 U O2G ATP . D ATP 601 1_555 V MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.919 ? metalc ? metalc25 U O1B ATP . D ATP 601 1_555 V MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc26 W O1B ADP . D ADP 603 1_555 X MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc27 E OG1 THR 53 E THR 53 1_555 Y MG MG . E MG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.782 ? metalc ? metalc28 E OG1 THR 295 E THR 295 1_555 AA MG MG . E MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? metalc ? metalc29 Y MG MG . E MG 901 1_555 BA O1A ATP . F ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.999 ? metalc ? metalc30 Y MG MG . E MG 901 1_555 BA O2G ATP . F ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc31 Y MG MG . E MG 901 1_555 BA O1B ATP . F ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.764 ? metalc ? metalc32 Z O1B ADP . E ADP 902 1_555 AA MG MG . E MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc33 F OG1 THR 295 F THR 295 1_555 DA MG MG . F MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc34 CA O1B ADP . F ADP 602 1_555 DA MG MG . F MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? # _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 7S67 _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 G 2 ATP A 1 601 900 ATP ATP . H 3 MG A 1 602 901 MG MG . I 4 ADP A 1 603 1000 ADP ADP . J 3 MG A 1 604 1001 MG MG . K 2 ATP A 1 605 900 ATP ATP . L 3 MG A 1 606 901 MG MG . M 2 ATP B 1 601 900 ATP ATP . N 3 MG B 1 602 901 MG MG . O 4 ADP B 1 603 1000 ADP ADP . P 3 MG B 1 604 1001 MG MG . Q 2 ATP C 1 601 900 ATP ATP . R 3 MG C 1 602 901 MG MG . S 4 ADP C 1 603 1000 ADP ADP . T 3 MG C 1 604 1001 MG MG . U 2 ATP D 1 601 900 ATP ATP . V 3 MG D 1 602 901 MG MG . W 4 ADP D 1 603 1000 ADP ADP . X 3 MG D 1 604 1001 MG MG . Y 3 MG E 1 901 901 MG MG . Z 4 ADP E 1 902 1000 ADP ADP . AA 3 MG E 1 903 1001 MG MG . BA 2 ATP F 1 601 900 ATP ATP . CA 4 ADP F 1 602 1000 ADP ADP . DA 3 MG F 1 603 1001 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 . . . Z 4 91.338 130.215 131.94 1 20 ? PB ADP 902 E 1 HETATM 2 O O1B ADP . . . Z 4 91.215 131.293 130.946 1 20 ? O1B ADP 902 E 1 HETATM 3 O O2B ADP . . . Z 4 92.733 130.127 132.411 1 20 ? O2B ADP 902 E 1 HETATM 4 O O3B ADP . . . Z 4 91.047 129.069 131.061 1 20 ? O3B ADP 902 E 1 HETATM 5 P PA ADP . . . Z 4 89.34 131.502 133.291 1 20 ? PA ADP 902 E 1 HETATM 6 O O1A ADP . . . Z 4 88.236 131.442 132.306 1 20 ? O1A ADP 902 E 1 HETATM 7 O O2A ADP . . . Z 4 90.032 132.812 133.318 1 20 ? O2A ADP 902 E 1 HETATM 8 O O3A ADP . . . Z 4 90.34 130.3 133.136 1 20 ? O3A ADP 902 E 1 HETATM 9 O O5' ADP . . . Z 4 88.808 131.169 134.759 1 20 ? O5' ADP 902 E 1 HETATM 10 C C5' ADP . . . Z 4 87.681 130.306 134.916 1 20 ? C5' ADP 902 E 1 HETATM 11 C C4' ADP . . . Z 4 87.499 130.009 136.427 1 20 ? C4' ADP 902 E 1 HETATM 12 O O4' ADP . . . Z 4 86.791 131.086 137.056 1 20 ? O4' ADP 902 E 1 HETATM 13 C C3' ADP . . . Z 4 86.579 128.824 136.728 1 20 ? C3' ADP 902 E 1 HETATM 14 O O3' ADP . . . Z 4 87.23 127.559 136.578 1 20 ? O3' ADP 902 E 1 HETATM 15 C C2' ADP . . . Z 4 86.153 129.081 138.174 1 20 ? C2' ADP 902 E 1 HETATM 16 O O2' ADP . . . Z 4 87.103 128.484 139.066 1 20 ? O2' ADP 902 E 1 HETATM 17 C C1' ADP . . . Z 4 86.219 130.627 138.296 1 20 ? C1' ADP 902 E 1 HETATM 18 N N9 ADP . . . Z 4 84.931 131.268 138.463 1 20 ? N9 ADP 902 E 1 HETATM 19 C C8 ADP . . . Z 4 84.102 131.821 137.485 1 20 ? C8 ADP 902 E 1 HETATM 20 N N7 ADP . . . Z 4 83.116 132.571 138.008 1 20 ? N7 ADP 902 E 1 HETATM 21 C C5 ADP . . . Z 4 83.33 132.418 139.342 1 20 ? C5 ADP 902 E 1 HETATM 22 C C6 ADP . . . Z 4 82.631 132.968 140.406 1 20 ? C6 ADP 902 E 1 HETATM 23 N N6 ADP . . . Z 4 81.589 133.795 140.258 1 20 ? N6 ADP 902 E 1 HETATM 24 N N1 ADP . . . Z 4 82.959 132.756 141.659 1 20 ? N1 ADP 902 E 1 HETATM 25 C C2 ADP . . . Z 4 84.013 131.95 141.846 1 20 ? C2 ADP 902 E 1 HETATM 26 N N3 ADP . . . Z 4 84.763 131.371 140.89 1 20 ? N3 ADP 902 E 1 HETATM 27 C C4 ADP . . . Z 4 84.383 131.632 139.64 1 20 ? C4 ADP 902 E 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #