data_8XAY # _model_server_result.job_id TGyZszo2DFGpmYR929rXaA _model_server_result.datetime_utc '2025-03-07 00:30:32' _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 8xay # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"EA","auth_seq_id":601}' # _entry.id 8XAY # _exptl.entry_id 8XAY _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 8XAY _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XAY _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,DA,EA,FA _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 CA N N ? 7 EA 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 B NE2 GLN 466 B GLN 466 1_555 W O3G AGS . B AGS 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.304 ? covale ? covale2 W S1G AGS . B AGS 601 1_555 C NH1 ARG 455 C ARG 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.629 ? covale ? covale3 E CA GLY 156 E GLY 156 1_555 CA O1A ADP . E ADP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? metalc ? metalc1 A OG SER 158 A SER 158 1_555 V MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc2 A OE2 GLU 192 A GLU 192 1_555 V MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc3 U O2G AGS . A AGS 601 1_555 V MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc4 U O2B AGS . A AGS 601 1_555 V MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? metalc ? metalc5 B OG SER 158 B SER 158 1_555 X MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc6 W O2G AGS . B AGS 601 1_555 X MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc7 W O2B AGS . B AGS 601 1_555 X MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc8 C OG SER 158 C SER 158 1_555 Z MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc9 Y O2G AGS . C AGS 601 1_555 Z MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc10 Y O2B AGS . C AGS 601 1_555 Z MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc11 D OG SER 158 D SER 158 1_555 BA MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc12 AA O2G AGS . D AGS 601 1_555 BA MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc13 AA O2B AGS . D AGS 601 1_555 BA MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc14 E OG SER 158 E SER 158 1_555 DA MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc15 E OE2 GLU 192 E GLU 192 1_555 DA MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.978 ? metalc ? metalc16 CA O2B ADP . E ADP 601 1_555 DA MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc17 F OG SER 158 F SER 158 1_555 FA MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc18 EA O2B ADP . F ADP 601 1_555 FA MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? hydrog 'DG-DC PAIR' hydrog1 S N2 DG 1 S DG 1 1_555 T O2 DC 59 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 S N3 DC 2 S DC 2 1_555 T N1 DG 58 T DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 S N4 DC 2 S DC 2 1_555 T O6 DG 58 T DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 S O2 DC 2 S DC 2 1_555 T N2 DG 58 T DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 S N3 DT 3 S DT 3 1_555 T N1 DA 57 T DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 S O4 DT 3 S DT 3 1_555 T N6 DA 57 T DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 S N3 DT 4 S DT 4 1_555 T N1 DA 56 T DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 S O4 DT 4 S DT 4 1_555 T N6 DA 56 T DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 S N3 DT 5 S DT 5 1_555 T N1 DA 55 T DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 S O4 DT 5 S DT 5 1_555 T N6 DA 55 T DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 S N1 DA 6 S DA 6 1_555 T N3 DT 54 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 S N6 DA 6 S DA 6 1_555 T O4 DT 54 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 S N3 DT 7 S DT 7 1_555 T N1 DA 53 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 S O4 DT 7 S DT 7 1_555 T N6 DA 53 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog15 S N3 DC 8 S DC 8 1_555 T N2 DG 52 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog16 S O2 DC 8 S DC 8 1_555 T N1 DG 52 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DC MISPAIR' hydrog17 S N1 DA 9 S DA 9 1_555 T N4 DC 50 T DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog18 S N1 DG 10 S DG 10 1_555 T O2 DC 50 T DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog19 S N2 DG 10 S DG 10 1_555 T N3 DC 50 T DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 S N1 DA 11 S DA 11 1_555 T N3 DT 49 T DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 S N6 DA 11 S DA 11 1_555 T O4 DT 49 T DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 S N1 DA 12 S DA 12 1_555 T N3 DT 48 T DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 S N6 DA 12 S DA 12 1_555 T O4 DT 48 T DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog24 S N1 DG 13 S DG 13 1_555 T O2 DC 47 T DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog25 S N2 DG 13 S DG 13 1_555 T N3 DC 47 T DC 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 8XAY _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 AGS A 1 601 601 AGS AGS . V 6 MG A 1 602 701 MG MG . W 5 AGS B 1 601 601 AGS AGS . X 6 MG B 1 602 701 MG MG . Y 5 AGS C 1 601 601 AGS AGS . Z 6 MG C 1 602 701 MG MG . AA 5 AGS D 1 601 601 AGS AGS . BA 6 MG D 1 602 701 MG MG . CA 7 ADP E 1 601 601 ADP ADP . DA 6 MG E 1 602 701 MG MG . EA 7 ADP F 1 601 601 ADP ADP . FA 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 . . . EA 7 119.928 148.526 171.743 1 12.38 ? PB ADP 601 F 1 HETATM 2 O O1B ADP . . . EA 7 120.529 147.57 170.753 1 5.02 ? O1B ADP 601 F 1 HETATM 3 O O2B ADP . . . EA 7 119.438 147.878 173.006 1 13.47 ? O2B ADP 601 F 1 HETATM 4 O O3B ADP . . . EA 7 120.767 149.752 172.002 1 22.66 ? O3B ADP 601 F 1 HETATM 5 P PA ADP . . . EA 7 117.109 148.423 171.214 1 17.55 ? PA ADP 601 F 1 HETATM 6 O O1A ADP . . . EA 7 117.029 147.01 170.707 1 6.8 ? O1A ADP 601 F 1 HETATM 7 O O2A ADP . . . EA 7 116.664 148.723 172.62 1 22.87 ? O2A ADP 601 F 1 HETATM 8 O O3A ADP . . . EA 7 118.587 149.042 171.007 1 13.58 ? O3A ADP 601 F 1 HETATM 9 O O5' ADP . . . EA 7 116.202 149.313 170.227 1 15.72 ? O5' ADP 601 F 1 HETATM 10 C C5' ADP . . . EA 7 116.705 149.834 169 1 8.38 ? C5' ADP 601 F 1 HETATM 11 C C4' ADP . . . EA 7 115.561 150.129 168.041 1 9.79 ? C4' ADP 601 F 1 HETATM 12 O O4' ADP . . . EA 7 115.764 149.322 166.895 1 12.58 ? O4' ADP 601 F 1 HETATM 13 C C3' ADP . . . EA 7 114.183 149.765 168.578 1 14.62 ? C3' ADP 601 F 1 HETATM 14 O O3' ADP . . . EA 7 113.398 150.941 168.804 1 15.06 ? O3' ADP 601 F 1 HETATM 15 C C2' ADP . . . EA 7 113.539 148.883 167.524 1 15.37 ? C2' ADP 601 F 1 HETATM 16 O O2' ADP . . . EA 7 112.337 149.474 167.03 1 15.16 ? O2' ADP 601 F 1 HETATM 17 C C1' ADP . . . EA 7 114.549 148.78 166.404 1 15.33 ? C1' ADP 601 F 1 HETATM 18 N N9 ADP . . . EA 7 114.827 147.363 166.095 1 6.63 ? N9 ADP 601 F 1 HETATM 19 C C8 ADP . . . EA 7 115.553 146.528 166.856 1 2.5 ? C8 ADP 601 F 1 HETATM 20 N N7 ADP . . . EA 7 115.627 145.3 166.289 1 14.77 ? N7 ADP 601 F 1 HETATM 21 C C5 ADP . . . EA 7 114.937 145.348 165.139 1 15.14 ? C5 ADP 601 F 1 HETATM 22 C C6 ADP . . . EA 7 114.616 144.393 164.053 1 9.41 ? C6 ADP 601 F 1 HETATM 23 N N6 ADP . . . EA 7 115.054 143.112 164.08 1 12.64 ? N6 ADP 601 F 1 HETATM 24 N N1 ADP . . . EA 7 113.87 144.839 163.028 1 4.08 ? N1 ADP 601 F 1 HETATM 25 C C2 ADP . . . EA 7 113.425 146.109 162.981 1 13.11 ? C2 ADP 601 F 1 HETATM 26 N N3 ADP . . . EA 7 113.674 147.03 163.926 1 13.69 ? N3 ADP 601 F 1 HETATM 27 C C4 ADP . . . EA 7 114.412 146.714 165.013 1 11.55 ? C4 ADP 601 F 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 50 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #