data_1PKG # _model_server_result.job_id ORpoeHxffUxtvJvGp_n2Og _model_server_result.datetime_utc '2025-02-26 15:04:12' _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 1pkg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1480}' # _entry.id 1PKG # _exptl.entry_id 1PKG _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 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 1PKG _cell.length_a 92.667 _cell.length_b 116.458 _cell.length_c 60.066 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PKG _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # 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 monomeric 1 author_and_software_defined_assembly 1 PQS monomeric 1 author_and_software_defined_assembly 2 PISA tetrameric 4 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,C,D,G 1 1 B,E,F 2 1 A,B,C,D,E,F,G 3 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 92.667 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F 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 ASN 19 A ASN 567 1_555 A N PTR 20 A PTR 568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C PTR 20 A PTR 568 1_555 A N VAL 21 A VAL 569 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale3 A C VAL 21 A VAL 569 1_555 A N PTR 22 A PTR 570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 A C PTR 22 A PTR 570 1_555 A N ILE 23 A ILE 571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale5 B C ASN 19 B ASN 567 1_555 B N PTR 20 B PTR 568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale6 B C PTR 20 B PTR 568 1_555 B N VAL 21 B VAL 569 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale7 B C VAL 21 B VAL 569 1_555 B N PTR 22 B PTR 570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale8 B C PTR 22 B PTR 570 1_555 B N ILE 23 B ILE 571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 A O3P PTR 20 A PTR 568 2_655 E MG MG . B MG 1485 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc2 A OD1 ASN 191 A ASN 797 1_555 C MG MG . A MG 1481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc3 A OD1 ASP 204 A ASP 810 1_555 C MG MG . A MG 1481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.974 ? metalc ? metalc4 D O2A ADP . A ADP 1480 1_555 C MG MG . A MG 1481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc5 D O3B ADP . A ADP 1480 1_555 C MG MG . A MG 1481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc6 C MG MG . A MG 1481 1_555 B O2P PTR 20 B PTR 568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc7 B OD1 ASN 191 B ASN 797 1_555 E MG MG . B MG 1485 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc8 B OD1 ASP 204 B ASP 810 1_555 E MG MG . B MG 1485 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? metalc ? metalc9 E MG MG . B MG 1485 1_555 F O2A ADP . B ADP 1486 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.896 ? metalc ? metalc10 E MG MG . B MG 1485 1_555 F O3B ADP . B ADP 1486 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? # _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 1PKG _atom_sites.fract_transf_matrix[1][1] 0.010791 _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] 0.008587 _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] 0.016648 _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 C 2 MG A 1 1481 1481 MG MG . D 3 ADP A 1 1480 1480 ADP ADP . E 2 MG B 1 1485 1481 MG MG . F 3 ADP B 1 1486 1481 ADP ADP . G 4 HOH A 1 1482 1482 HOH HOH . G 4 HOH A 2 1483 1483 HOH HOH . G 4 HOH A 3 1484 1484 HOH HOH . # 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 . . . D 3 24.09 26.568 24.287 1 11.17 ? PB ADP 1480 A 1 HETATM 2 O O1B ADP . . . D 3 23.317 27.727 23.783 1 13.64 ? O1B ADP 1480 A 1 HETATM 3 O O2B ADP . . . D 3 24.147 25.484 23.176 1 13.19 ? O2B ADP 1480 A 1 HETATM 4 O O3B ADP . . . D 3 25.497 26.929 24.827 1 11.48 ? O3B ADP 1480 A 1 HETATM 5 P PA ADP . . . D 3 23.815 25.047 26.615 1 9.66 ? PA ADP 1480 A 1 HETATM 6 O O1A ADP . . . D 3 23.221 23.696 26.388 1 8.08 ? O1A ADP 1480 A 1 HETATM 7 O O2A ADP . . . D 3 25.369 25.052 26.554 1 10.62 ? O2A ADP 1480 A 1 HETATM 8 O O3A ADP . . . D 3 23.215 26.006 25.488 1 10.46 ? O3A ADP 1480 A 1 HETATM 9 O O5' ADP . . . D 3 23.223 25.79 27.913 1 5 ? O5' ADP 1480 A 1 HETATM 10 C C5' ADP . . . D 3 23.332 27.185 27.991 1 7.3 ? C5' ADP 1480 A 1 HETATM 11 C C4' ADP . . . D 3 23.421 27.474 29.467 1 10.26 ? C4' ADP 1480 A 1 HETATM 12 O O4' ADP . . . D 3 22.196 27.095 30.062 1 11.61 ? O4' ADP 1480 A 1 HETATM 13 C C3' ADP . . . D 3 24.462 26.608 30.166 1 11.25 ? C3' ADP 1480 A 1 HETATM 14 O O3' ADP . . . D 3 25.773 27.13 30.141 1 9.51 ? O3' ADP 1480 A 1 HETATM 15 C C2' ADP . . . D 3 23.89 26.491 31.558 1 12.04 ? C2' ADP 1480 A 1 HETATM 16 O O2' ADP . . . D 3 24.129 27.674 32.288 1 13.21 ? O2' ADP 1480 A 1 HETATM 17 C C1' ADP . . . D 3 22.403 26.426 31.29 1 11.82 ? C1' ADP 1480 A 1 HETATM 18 N N9 ADP . . . D 3 21.88 25.053 31.206 1 11.74 ? N9 ADP 1480 A 1 HETATM 19 C C8 ADP . . . D 3 21.793 24.264 30.089 1 11.95 ? C8 ADP 1480 A 1 HETATM 20 N N7 ADP . . . D 3 21.239 23.079 30.433 1 12.55 ? N7 ADP 1480 A 1 HETATM 21 C C5 ADP . . . D 3 20.954 23.116 31.756 1 12.33 ? C5 ADP 1480 A 1 HETATM 22 C C6 ADP . . . D 3 20.372 22.189 32.625 1 13 ? C6 ADP 1480 A 1 HETATM 23 N N6 ADP . . . D 3 20.16 20.937 32.234 1 11.65 ? N6 ADP 1480 A 1 HETATM 24 N N1 ADP . . . D 3 20.193 22.524 33.958 1 13.18 ? N1 ADP 1480 A 1 HETATM 25 C C2 ADP . . . D 3 20.613 23.76 34.411 1 12.14 ? C2 ADP 1480 A 1 HETATM 26 N N3 ADP . . . D 3 21.199 24.665 33.548 1 10.75 ? N3 ADP 1480 A 1 HETATM 27 C C4 ADP . . . D 3 21.355 24.352 32.247 1 11.35 ? C4 ADP 1480 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #