data_8DNF # _model_server_result.job_id Jdt6elab9IohOi7jHB2M2w _model_server_result.datetime_utc '2025-04-25 14:14:20' _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 8dnf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":401}' # _entry.id 8DNF # _exptl.entry_id 8DNF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 8DNF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DNF _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 ? 3 F N N ? 3 H N N ? 3 J N N ? 3 L 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 A C ACE 1 A ACE 0 1_555 A N GLU 2 A GLU 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C GLU 72 A GLU 71 1_555 A N HIC 73 A HIC 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 A C HIC 73 A HIC 72 1_555 A N GLY 74 A GLY 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 B C ACE 1 B ACE 0 1_555 B N GLU 2 B GLU 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? covale ? covale5 B C GLU 72 B GLU 71 1_555 B N HIC 73 B HIC 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 B C HIC 73 B HIC 72 1_555 B N GLY 74 B GLY 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 C C ACE 1 C ACE 0 1_555 C N GLU 2 C GLU 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? covale ? covale8 C C GLU 72 C GLU 71 1_555 C N HIC 73 C HIC 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale9 C C HIC 73 C HIC 72 1_555 C N GLY 74 C GLY 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale10 D C ACE 1 D ACE 0 1_555 D N GLU 2 D GLU 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? covale ? covale11 D C GLU 72 D GLU 71 1_555 D N HIC 73 D HIC 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale12 D C HIC 73 D HIC 72 1_555 D N GLY 74 D GLY 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 E MG MG . A MG 400 1_555 F O1B ADP . A ADP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc2 G MG MG . B MG 400 1_555 H O1B ADP . B ADP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc3 I MG MG . C MG 400 1_555 J O1B ADP . C ADP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.803 ? metalc ? metalc4 K MG MG . D MG 400 1_555 L O1B ADP . D ADP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? # _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 ? # _atom_sites.entry_id 8DNF _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 E 2 MG A 1 400 400 MG MG . F 3 ADP A 1 401 401 ADP ADP . G 2 MG B 1 400 400 MG MG . H 3 ADP B 1 401 401 ADP ADP . I 2 MG C 1 400 400 MG MG . J 3 ADP C 1 401 401 ADP ADP . K 2 MG D 1 400 400 MG MG . L 3 ADP D 1 401 401 ADP ADP . # 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 . . . L 3 103.217 98.406 70.657 1 164.43 ? PB ADP 401 D 1 HETATM 2 O O1B ADP . . . L 3 103.792 98.689 69.289 1 152.76 ? O1B ADP 401 D 1 HETATM 3 O O2B ADP . . . L 3 102.393 97.144 70.731 1 149.54 ? O2B ADP 401 D 1 HETATM 4 O O3B ADP . . . L 3 104.196 98.586 71.792 1 150.51 ? O3B ADP 401 D 1 HETATM 5 P PA ADP . . . L 3 101.061 99.463 72.066 1 138.44 ? PA ADP 401 D 1 HETATM 6 O O1A ADP . . . L 3 99.757 98.992 71.474 1 147.67 ? O1A ADP 401 D 1 HETATM 7 O O2A ADP . . . L 3 101.707 98.707 73.201 1 140.68 ? O2A ADP 401 D 1 HETATM 8 O O3A ADP . . . L 3 102.146 99.584 70.883 1 152.26 ? O3A ADP 401 D 1 HETATM 9 O O5' ADP . . . L 3 100.887 100.99 72.539 1 138.3 ? O5' ADP 401 D 1 HETATM 10 C C5' ADP . . . L 3 100.495 101.278 73.879 1 148.49 ? C5' ADP 401 D 1 HETATM 11 C C4' ADP . . . L 3 100.445 102.785 74.082 1 149.53 ? C4' ADP 401 D 1 HETATM 12 O O4' ADP . . . L 3 99.188 103.302 73.644 1 151.62 ? O4' ADP 401 D 1 HETATM 13 C C3' ADP . . . L 3 100.594 103.159 75.546 1 147.51 ? C3' ADP 401 D 1 HETATM 14 O O3' ADP . . . L 3 101.888 103.718 75.778 1 145.94 ? O3' ADP 401 D 1 HETATM 15 C C2' ADP . . . L 3 99.521 104.193 75.82 1 142.78 ? C2' ADP 401 D 1 HETATM 16 O O2' ADP . . . L 3 100.128 105.445 76.157 1 144.46 ? O2' ADP 401 D 1 HETATM 17 C C1' ADP . . . L 3 98.733 104.327 74.529 1 145.26 ? C1' ADP 401 D 1 HETATM 18 N N9 ADP . . . L 3 97.287 104.149 74.808 1 142.87 ? N9 ADP 401 D 1 HETATM 19 C C8 ADP . . . L 3 96.665 102.967 74.98 1 145.42 ? C8 ADP 401 D 1 HETATM 20 N N7 ADP . . . L 3 95.343 103.14 75.222 1 144.32 ? N7 ADP 401 D 1 HETATM 21 C C5 ADP . . . L 3 95.101 104.465 75.206 1 144.42 ? C5 ADP 401 D 1 HETATM 22 C C6 ADP . . . L 3 93.915 105.331 75.389 1 145.94 ? C6 ADP 401 D 1 HETATM 23 N N6 ADP . . . L 3 92.695 104.803 75.643 1 146.84 ? N6 ADP 401 D 1 HETATM 24 N N1 ADP . . . L 3 94.095 106.668 75.293 1 145.97 ? N1 ADP 401 D 1 HETATM 25 C C2 ADP . . . L 3 95.303 107.203 75.039 1 149.12 ? C2 ADP 401 D 1 HETATM 26 N N3 ADP . . . L 3 96.419 106.475 74.863 1 150.31 ? N3 ADP 401 D 1 HETATM 27 C C4 ADP . . . L 3 96.387 105.124 74.933 1 144.98 ? C4 ADP 401 D 1 # _model_server_stats.io_time_ms 35 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #