data_8H9E # _model_server_result.job_id 1QdJAEOknRcw7RyIFGrmtQ _model_server_result.datetime_utc '2025-07-03 16:50:00' _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 8h9e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":501}' # _entry.id 8H9E # _exptl.entry_id 8H9E _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 8 _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 8H9E _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8H9E _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 nonameric _pdbx_struct_assembly.oligomeric_count 9 _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 _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 ? 8 P N N ? 8 R 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 176 A THR 176 1_555 K MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc2 J O3G ATP . A ATP 601 1_555 K MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc3 J O1B ATP . A ATP 601 1_555 K MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc4 B OG1 THR 176 B THR 176 1_555 M MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc5 L O3G ATP . B ATP 601 1_555 M MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc6 L O1B ATP . B ATP 601 1_555 M MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc7 C OG1 THR 176 C THR 176 1_555 O MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc8 N O1G ATP . C ATP 601 1_555 O MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc9 N O1B ATP . C ATP 601 1_555 O MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc10 E OG1 THR 166 F THR 166 1_555 Q MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc11 P O1B ADP . F ADP 501 1_555 Q MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc12 F OG1 THR 166 D THR 166 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc13 R O1B ADP . D ADP 501 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? # _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 8H9E _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 J 6 ATP A 1 601 551 ATP ATP . K 7 MG A 1 602 552 MG MG . L 6 ATP B 1 601 551 ATP ATP . M 7 MG B 1 602 552 MG MG . N 6 ATP C 1 601 551 ATP ATP . O 7 MG C 1 602 552 MG MG . P 8 ADP F 1 501 551 ADP ADP . Q 7 MG F 1 502 552 MG MG . R 8 ADP D 1 501 551 ADP ADP . S 7 MG D 1 502 552 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 . . . P 8 187.636 212.735 142.677 1 21.67 ? PB ADP 501 F 1 HETATM 2 O O1B ADP . . . P 8 188.361 213.59 141.682 1 21.67 ? O1B ADP 501 F 1 HETATM 3 O O2B ADP . . . P 8 186.255 212.466 142.191 1 21.67 ? O2B ADP 501 F 1 HETATM 4 O O3B ADP . . . P 8 188.354 211.403 142.856 1 21.67 ? O3B ADP 501 F 1 HETATM 5 P PA ADP . . . P 8 186.88 214.918 144.473 1 21.67 ? PA ADP 501 F 1 HETATM 6 O O1A ADP . . . P 8 185.997 215.359 143.295 1 21.67 ? O1A ADP 501 F 1 HETATM 7 O O2A ADP . . . P 8 187.945 216.008 144.726 1 21.67 ? O2A ADP 501 F 1 HETATM 8 O O3A ADP . . . P 8 187.609 213.475 144.129 1 21.67 ? O3A ADP 501 F 1 HETATM 9 O O5' ADP . . . P 8 185.936 214.737 145.842 1 21.67 ? O5' ADP 501 F 1 HETATM 10 C C5' ADP . . . P 8 184.569 215.07 145.719 1 21.67 ? C5' ADP 501 F 1 HETATM 11 C C4' ADP . . . P 8 183.961 215.168 147.047 1 21.67 ? C4' ADP 501 F 1 HETATM 12 O O4' ADP . . . P 8 184.676 214.256 148.03 1 21.67 ? O4' ADP 501 F 1 HETATM 13 C C3' ADP . . . P 8 184.121 216.509 147.589 1 21.67 ? C3' ADP 501 F 1 HETATM 14 O O3' ADP . . . P 8 183.108 217.411 147.061 1 21.67 ? O3' ADP 501 F 1 HETATM 15 C C2' ADP . . . P 8 183.916 216.296 149.007 1 21.67 ? C2' ADP 501 F 1 HETATM 16 O O2' ADP . . . P 8 182.497 216.097 149.248 1 21.67 ? O2' ADP 501 F 1 HETATM 17 C C1' ADP . . . P 8 184.608 215.039 149.306 1 21.67 ? C1' ADP 501 F 1 HETATM 18 N N9 ADP . . . P 8 185.941 215.338 149.752 1 21.67 ? N9 ADP 501 F 1 HETATM 19 C C8 ADP . . . P 8 186.968 215.035 149.057 1 21.67 ? C8 ADP 501 F 1 HETATM 20 N N7 ADP . . . P 8 188.052 215.44 149.729 1 21.67 ? N7 ADP 501 F 1 HETATM 21 C C5 ADP . . . P 8 187.629 216.015 150.882 1 21.67 ? C5 ADP 501 F 1 HETATM 22 C C6 ADP . . . P 8 188.212 216.599 151.952 1 21.67 ? C6 ADP 501 F 1 HETATM 23 N N6 ADP . . . P 8 189.705 216.717 152.027 1 21.67 ? N6 ADP 501 F 1 HETATM 24 N N1 ADP . . . P 8 187.446 217.062 152.937 1 21.67 ? N1 ADP 501 F 1 HETATM 25 C C2 ADP . . . P 8 186.105 216.964 152.884 1 21.67 ? C2 ADP 501 F 1 HETATM 26 N N3 ADP . . . P 8 185.494 216.413 151.879 1 21.67 ? N3 ADP 501 F 1 HETATM 27 C C4 ADP . . . P 8 186.185 215.924 150.856 1 21.67 ? C4 ADP 501 F 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 384 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #