data_8XAX # _model_server_result.job_id DFK_htk3WLi0e7zxgsZvbw _model_server_result.datetime_utc '2025-03-07 00:34:16' _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":"Z","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 . . . Z 7 152.576 114.866 134.752 1 37.27 ? PB ADP 601 E 1 HETATM 2 O O1B ADP . . . Z 7 152.241 114.04 133.532 1 27.63 ? O1B ADP 601 E 1 HETATM 3 O O2B ADP . . . Z 7 151.394 115.453 135.487 1 24.57 ? O2B ADP 601 E 1 HETATM 4 O O3B ADP . . . Z 7 153.661 115.887 134.506 1 38.64 ? O3B ADP 601 E 1 HETATM 5 P PA ADP . . . Z 7 152.343 112.758 136.631 1 43.38 ? PA ADP 601 E 1 HETATM 6 O O1A ADP . . . Z 7 151.565 111.872 135.686 1 26.8 ? O1A ADP 601 E 1 HETATM 7 O O2A ADP . . . Z 7 151.602 113.545 137.681 1 35.56 ? O2A ADP 601 E 1 HETATM 8 O O3A ADP . . . Z 7 153.235 113.793 135.771 1 37.8 ? O3A ADP 601 E 1 HETATM 9 O O5' ADP . . . Z 7 153.479 111.9 137.393 1 31.54 ? O5' ADP 601 E 1 HETATM 10 C C5' ADP . . . Z 7 154.215 112.495 138.469 1 32.21 ? C5' ADP 601 E 1 HETATM 11 C C4' ADP . . . Z 7 154.3 111.611 139.714 1 36.61 ? C4' ADP 601 E 1 HETATM 12 O O4' ADP . . . Z 7 153.15 111.725 140.552 1 34.44 ? O4' ADP 601 E 1 HETATM 13 C C3' ADP . . . Z 7 154.418 110.135 139.371 1 30.16 ? C3' ADP 601 E 1 HETATM 14 O O3' ADP . . . Z 7 155.782 109.695 139.41 1 33.5 ? O3' ADP 601 E 1 HETATM 15 C C2' ADP . . . Z 7 153.594 109.401 140.418 1 33.22 ? C2' ADP 601 E 1 HETATM 16 O O2' ADP . . . Z 7 154.413 108.562 141.244 1 36.97 ? O2' ADP 601 E 1 HETATM 17 C C1' ADP . . . Z 7 152.982 110.503 141.273 1 32.76 ? C1' ADP 601 E 1 HETATM 18 N N9 ADP . . . Z 7 151.534 110.27 141.536 1 29.66 ? N9 ADP 601 E 1 HETATM 19 C C8 ADP . . . Z 7 150.507 110.461 140.682 1 31.28 ? C8 ADP 601 E 1 HETATM 20 N N7 ADP . . . Z 7 149.333 110.144 141.283 1 31.58 ? N7 ADP 601 E 1 HETATM 21 C C5 ADP . . . Z 7 149.584 109.759 142.539 1 30 ? C5 ADP 601 E 1 HETATM 22 C C6 ADP . . . Z 7 148.789 109.305 143.703 1 34.83 ? C6 ADP 601 E 1 HETATM 23 N N6 ADP . . . Z 7 147.431 109.194 143.658 1 37.96 ? N6 ADP 601 E 1 HETATM 24 N N1 ADP . . . Z 7 149.483 109.014 144.82 1 33.22 ? N1 ADP 601 E 1 HETATM 25 C C2 ADP . . . Z 7 150.823 109.127 144.891 1 32.11 ? C2 ADP 601 E 1 HETATM 26 N N3 ADP . . . Z 7 151.615 109.534 143.887 1 27.58 ? N3 ADP 601 E 1 HETATM 27 C C4 ADP . . . Z 7 151.046 109.859 142.707 1 29.13 ? C4 ADP 601 E 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 64 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #