data_2JKI # _model_server_result.job_id HBXdcNvVusIJezx1fHL15g _model_server_result.datetime_utc '2025-01-02 16:30:36' _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 2jki # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1218}' # _entry.id 2JKI # _exptl.entry_id 2JKI _exptl.method 'X-RAY DIFFRACTION' # _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 3 _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 2JKI _cell.length_a 100.268 _cell.length_b 129.654 _cell.length_c 135.998 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2JKI _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS dimeric 2 author_and_software_defined_assembly 1 PQS dimeric 2 author_and_software_defined_assembly 2 PQS dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G 1 1 B,E,H 2 1 C,F,I 3 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 ? 3 G N N ? 3 H N N ? 3 I N N # _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 2JKI _atom_sites.fract_transf_matrix[1][1] 0.009973 _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] 0.007713 _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] 0.007353 _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 G 3 ADP A 1 1218 1218 ADP ADP . H 3 ADP B 1 1218 1218 ADP ADP . I 3 ADP C 1 1218 1218 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 . . . G 3 68.696 -42.386 11.08 1 41.68 ? PB ADP 1218 A 1 HETATM 2 O O1B ADP . . . G 3 68.523 -42.178 12.56 1 29.99 ? O1B ADP 1218 A 1 HETATM 3 O O2B ADP . . . G 3 67.964 -43.652 10.656 1 22.99 ? O2B ADP 1218 A 1 HETATM 4 O O3B ADP . . . G 3 70.134 -42.075 10.571 1 17.08 ? O3B ADP 1218 A 1 HETATM 5 P PA ADP . . . G 3 68.056 -40.694 8.956 1 38 ? PA ADP 1218 A 1 HETATM 6 O O1A ADP . . . G 3 67.175 -39.512 8.654 1 22.08 ? O1A ADP 1218 A 1 HETATM 7 O O2A ADP . . . G 3 69.566 -40.534 9.014 1 45.86 ? O2A ADP 1218 A 1 HETATM 8 O O3A ADP . . . G 3 67.74 -41.254 10.439 1 55.18 ? O3A ADP 1218 A 1 HETATM 9 O O5' ADP . . . G 3 67.555 -41.902 7.985 1 30.42 ? O5' ADP 1218 A 1 HETATM 10 C C5' ADP . . . G 3 66.352 -42.631 8.288 1 42.97 ? C5' ADP 1218 A 1 HETATM 11 C C4' ADP . . . G 3 66.105 -43.856 7.404 1 37.38 ? C4' ADP 1218 A 1 HETATM 12 O O4' ADP . . . G 3 66.428 -43.58 6.042 1 29.4 ? O4' ADP 1218 A 1 HETATM 13 C C3' ADP . . . G 3 66.954 -45.052 7.807 1 48.26 ? C3' ADP 1218 A 1 HETATM 14 O O3' ADP . . . G 3 66.291 -45.905 8.757 1 57.77 ? O3' ADP 1218 A 1 HETATM 15 C C2' ADP . . . G 3 67.297 -45.737 6.488 1 54.6 ? C2' ADP 1218 A 1 HETATM 16 O O2' ADP . . . G 3 66.514 -46.901 6.22 1 53.39 ? O2' ADP 1218 A 1 HETATM 17 C C1' ADP . . . G 3 66.959 -44.74 5.405 1 35.5 ? C1' ADP 1218 A 1 HETATM 18 N N9 ADP . . . G 3 68.185 -44.397 4.644 1 35.7 ? N9 ADP 1218 A 1 HETATM 19 C C8 ADP . . . G 3 68.747 -43.174 4.571 1 49.15 ? C8 ADP 1218 A 1 HETATM 20 N N7 ADP . . . G 3 69.855 -43.156 3.784 1 49.68 ? N7 ADP 1218 A 1 HETATM 21 C C5 ADP . . . G 3 70.007 -44.416 3.336 1 40.2 ? C5 ADP 1218 A 1 HETATM 22 C C6 ADP . . . G 3 70.986 -45.095 2.461 1 41.77 ? C6 ADP 1218 A 1 HETATM 23 N N6 ADP . . . G 3 72.018 -44.392 1.913 1 56.24 ? N6 ADP 1218 A 1 HETATM 24 N N1 ADP . . . G 3 70.809 -46.416 2.239 1 37.54 ? N1 ADP 1218 A 1 HETATM 25 C C2 ADP . . . G 3 69.778 -47.072 2.801 1 46.64 ? C2 ADP 1218 A 1 HETATM 26 N N3 ADP . . . G 3 68.855 -46.524 3.61 1 33.7 ? N3 ADP 1218 A 1 HETATM 27 C C4 ADP . . . G 3 68.918 -45.221 3.91 1 29.04 ? C4 ADP 1218 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 33 _model_server_stats.create_model_time_ms 79 _model_server_stats.query_time_ms 406 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #