data_8XAX # _model_server_result.job_id n8lVy9mv5qF6wqWehBax3Q _model_server_result.datetime_utc '2025-03-07 00:30:54' _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 8xax # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"BA","auth_seq_id":601}' # _entry.id 8XAX # _exptl.entry_id 8XAX _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 7 _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 ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 8XAX _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XAX _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 20-meric _pdbx_struct_assembly.oligomeric_count 20 _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,AA,BA,CA _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 x,y,z _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 ? 7 Z N N ? 7 BA 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 covale ? covale1 E CA GLY 156 E GLY 156 1_555 Z O2A ADP . E ADP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.373 ? covale ? covale2 E O ILE 534 E ILE 534 1_555 Z N6 ADP . E ADP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.302 ? covale ? covale3 F CA GLY 156 F GLY 156 1_555 BA O2A ADP . F ADP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? metalc ? metalc1 B OG SER 158 B SER 158 1_555 W MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc2 V O1G ANP . B ANP 601 1_555 W MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc3 V O1B ANP . B ANP 601 1_555 W MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc4 C OG SER 158 C SER 158 1_555 Y MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc5 X O3G ANP . C ANP 601 1_555 Y MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc6 X O2B ANP . C ANP 601 1_555 Y MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.705 ? metalc ? metalc7 E OG SER 158 E SER 158 1_555 AA MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.904 ? metalc ? metalc8 Z O1B ADP . E ADP 601 1_555 AA MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc9 F OG SER 158 F SER 158 1_555 CA MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc10 F OE2 GLU 192 F GLU 192 1_555 CA MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc11 BA O1B ADP . F ADP 601 1_555 CA MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? hydrog 'DG-DC PAIR' hydrog1 S N2 DG 1 S DG 1 1_555 T N3 DC 59 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 S N1 DA 2 S DA 2 1_555 T N3 DT 58 T DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 S N6 DA 2 S DA 2 1_555 T O4 DT 58 T DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog4 S O2 DC 4 S DC 4 1_555 T N2 DG 56 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog5 S O2 DC 5 S DC 5 1_555 T N2 DG 55 T DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 S N1 DA 6 S DA 6 1_555 T N3 DT 54 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 S N6 DA 6 S DA 6 1_555 T O4 DT 54 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog8 S N3 DT 7 S DT 7 1_555 T N1 DA 53 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog9 S N1 DG 8 S DG 8 1_555 T O2 DC 52 T DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog10 S O2 DC 9 S DC 9 1_555 T N2 DG 51 T DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog11 S O6 DG 10 S DG 10 1_555 T N4 DC 50 T DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 S N3 DC 11 S DC 11 1_555 T N1 DG 49 T DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 S N4 DC 11 S DC 11 1_555 T O6 DG 49 T DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 S O2 DC 11 S DC 11 1_555 T N2 DG 49 T DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog15 S O4 DT 13 S DT 13 1_555 T N6 DA 47 T DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 8XAX _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 U 5 ANP A 1 601 601 ANP ANP . V 5 ANP B 1 601 601 ANP ANP . W 6 MG B 1 602 701 MG MG . X 5 ANP C 1 601 601 ANP ANP . Y 6 MG C 1 602 701 MG MG . Z 7 ADP E 1 601 601 ADP ADP . AA 6 MG E 1 602 701 MG MG . BA 7 ADP F 1 601 601 ADP ADP . CA 6 MG F 1 602 701 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 . . . BA 7 178.823 134.671 127.417 1 30.28 ? PB ADP 601 F 1 HETATM 2 O O1B ADP . . . BA 7 179.054 133.708 126.274 1 21.87 ? O1B ADP 601 F 1 HETATM 3 O O2B ADP . . . BA 7 177.814 134.225 128.453 1 17.76 ? O2B ADP 601 F 1 HETATM 4 O O3B ADP . . . BA 7 178.625 136.099 126.961 1 28.32 ? O3B ADP 601 F 1 HETATM 5 P PA ADP . . . BA 7 180.886 133.447 128.94 1 27.59 ? PA ADP 601 F 1 HETATM 6 O O1A ADP . . . BA 7 181.257 132.398 127.922 1 14.75 ? O1A ADP 601 F 1 HETATM 7 O O2A ADP . . . BA 7 180.002 133.054 130.097 1 30.59 ? O2A ADP 601 F 1 HETATM 8 O O3A ADP . . . BA 7 180.233 134.725 128.206 1 30.28 ? O3A ADP 601 F 1 HETATM 9 O O5' ADP . . . BA 7 182.24 134.092 129.534 1 25.99 ? O5' ADP 601 F 1 HETATM 10 C C5' ADP . . . BA 7 182.162 134.987 130.643 1 22.2 ? C5' ADP 601 F 1 HETATM 11 C C4' ADP . . . BA 7 183.235 134.701 131.691 1 22.34 ? C4' ADP 601 F 1 HETATM 12 O O4' ADP . . . BA 7 182.665 134.067 132.837 1 24.69 ? O4' ADP 601 F 1 HETATM 13 C C3' ADP . . . BA 7 184.351 133.796 131.192 1 25.46 ? C3' ADP 601 F 1 HETATM 14 O O3' ADP . . . BA 7 185.529 134.559 130.913 1 22.97 ? O3' ADP 601 F 1 HETATM 15 C C2' ADP . . . BA 7 184.607 132.812 132.315 1 26.95 ? C2' ADP 601 F 1 HETATM 16 O O2' ADP . . . BA 7 185.935 132.953 132.818 1 24.59 ? O2' ADP 601 F 1 HETATM 17 C C1' ADP . . . BA 7 183.617 133.169 133.408 1 27.27 ? C1' ADP 601 F 1 HETATM 18 N N9 ADP . . . BA 7 182.918 131.937 133.844 1 24.94 ? N9 ADP 601 F 1 HETATM 19 C C8 ADP . . . BA 7 181.983 131.275 133.141 1 19.48 ? C8 ADP 601 F 1 HETATM 20 N N7 ADP . . . BA 7 181.531 130.184 133.808 1 26.98 ? N7 ADP 601 F 1 HETATM 21 C C5 ADP . . . BA 7 182.196 130.139 134.973 1 26.4 ? C5 ADP 601 F 1 HETATM 22 C C6 ADP . . . BA 7 182.209 129.246 136.154 1 25.32 ? C6 ADP 601 F 1 HETATM 23 N N6 ADP . . . BA 7 181.399 128.16 136.218 1 22.58 ? N6 ADP 601 F 1 HETATM 24 N N1 ADP . . . BA 7 183.054 129.551 137.167 1 26.43 ? N1 ADP 601 F 1 HETATM 25 C C2 ADP . . . BA 7 183.862 130.627 137.115 1 26.51 ? C2 ADP 601 F 1 HETATM 26 N N3 ADP . . . BA 7 183.902 131.48 136.073 1 27.16 ? N3 ADP 601 F 1 HETATM 27 C C4 ADP . . . BA 7 183.111 131.296 134.993 1 25.95 ? C4 ADP 601 F 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 67 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #