data_5JLF # _model_server_result.job_id bqljBWuQzqdoyzBVoAIDcw _model_server_result.datetime_utc '2025-02-20 01:52:27' _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 5jlf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":401}' # _entry.id 5JLF # _exptl.entry_id 5JLF _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 5 _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 5JLF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JLF _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 heptameric _pdbx_struct_assembly.oligomeric_count 7 _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 _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 H N N ? 3 J N N ? 3 L N N ? 3 N N N ? 3 P 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 GLU 72 A GLU 72 1_555 A N HIC 73 A HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C HIC 73 A HIC 73 1_555 A N GLY 74 A GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 B C GLU 72 B GLU 72 1_555 B N HIC 73 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 B C HIC 73 B HIC 73 1_555 B N GLY 74 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale5 C C GLU 72 C GLU 72 1_555 C N HIC 73 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale6 C C HIC 73 C HIC 73 1_555 C N GLY 74 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale7 D C GLU 72 D GLU 72 1_555 D N HIC 73 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 D C HIC 73 D HIC 73 1_555 D N GLY 74 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale9 E C GLU 72 E GLU 72 1_555 E N HIC 73 E HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale10 E C HIC 73 E HIC 73 1_555 E N GLY 74 E GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? metalc ? metalc1 H O1B ADP . A ADP 401 1_555 I MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc2 J O1B ADP . B ADP 401 1_555 K MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc3 L O1B ADP . C ADP 401 1_555 M MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc4 N O1B ADP . D ADP 401 1_555 O MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc5 P O1B ADP . E ADP 401 1_555 Q MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? # _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 5JLF _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 H 3 ADP A 1 401 377 ADP ADP . I 4 MG A 1 402 376 MG MG . J 3 ADP B 1 401 377 ADP ADP . K 4 MG B 1 402 376 MG MG . L 3 ADP C 1 401 377 ADP ADP . M 4 MG C 1 402 376 MG MG . N 3 ADP D 1 401 377 ADP ADP . O 4 MG D 1 402 376 MG MG . P 3 ADP E 1 401 377 ADP ADP . Q 4 MG E 1 402 376 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 . . . J 3 15.115 7.949 55.794 1 75.69 ? PB ADP 401 B 1 HETATM 2 O O1B ADP . . . J 3 16.227 8.272 54.819 1 73.8 ? O1B ADP 401 B 1 HETATM 3 O O2B ADP . . . J 3 15.205 8.675 57.119 1 70.68 ? O2B ADP 401 B 1 HETATM 4 O O3B ADP . . . J 3 13.741 7.86 55.137 1 76.03 ? O3B ADP 401 B 1 HETATM 5 P PA ADP . . . J 3 16.865 5.894 56.414 1 68.86 ? PA ADP 401 B 1 HETATM 6 O O1A ADP . . . J 3 17.38 5.618 55.023 1 66.31 ? O1A ADP 401 B 1 HETATM 7 O O2A ADP . . . J 3 17.641 6.812 57.309 1 71.68 ? O2A ADP 401 B 1 HETATM 8 O O3A ADP . . . J 3 15.372 6.444 56.273 1 72.61 ? O3A ADP 401 B 1 HETATM 9 O O5' ADP . . . J 3 16.539 4.513 57.177 1 71.55 ? O5' ADP 401 B 1 HETATM 10 C C5' ADP . . . J 3 16.418 4.444 58.595 1 76.67 ? C5' ADP 401 B 1 HETATM 11 C C4' ADP . . . J 3 15.459 3.324 58.986 1 78.87 ? C4' ADP 401 B 1 HETATM 12 O O4' ADP . . . J 3 15.966 2.06 58.553 1 84.39 ? O4' ADP 401 B 1 HETATM 13 C C3' ADP . . . J 3 15.258 3.235 60.495 1 82.47 ? C3' ADP 401 B 1 HETATM 14 O O3' ADP . . . J 3 13.95 3.681 60.875 1 76.85 ? O3' ADP 401 B 1 HETATM 15 C C2' ADP . . . J 3 15.467 1.777 60.856 1 87.25 ? C2' ADP 401 B 1 HETATM 16 O O2' ADP . . . J 3 14.219 1.165 61.181 1 94.45 ? O2' ADP 401 B 1 HETATM 17 C C1' ADP . . . J 3 16.085 1.121 59.63 1 85.83 ? C1' ADP 401 B 1 HETATM 18 N N9 ADP . . . J 3 17.515 0.806 59.866 1 80.74 ? N9 ADP 401 B 1 HETATM 19 C C8 ADP . . . J 3 18.493 1.689 60.147 1 78.32 ? C8 ADP 401 B 1 HETATM 20 N N7 ADP . . . J 3 19.683 1.058 60.299 1 78.19 ? N7 ADP 401 B 1 HETATM 21 C C5 ADP . . . J 3 19.472 -0.25 60.106 1 78.42 ? C5 ADP 401 B 1 HETATM 22 C C6 ADP . . . J 3 20.302 -1.474 60.129 1 78.68 ? C6 ADP 401 B 1 HETATM 23 N N6 ADP . . . J 3 21.627 -1.421 60.381 1 78.95 ? N6 ADP 401 B 1 HETATM 24 N N1 ADP . . . J 3 19.684 -2.648 59.872 1 81.07 ? N1 ADP 401 B 1 HETATM 25 C C2 ADP . . . J 3 18.357 -2.722 59.615 1 81.95 ? C2 ADP 401 B 1 HETATM 26 N N3 ADP . . . J 3 17.533 -1.654 59.581 1 78.36 ? N3 ADP 401 B 1 HETATM 27 C C4 ADP . . . J 3 18.032 -0.415 59.817 1 79.16 ? C4 ADP 401 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #