data_9DLP # _model_server_result.job_id AM7yZndxu2u5eDG5HZYvGQ _model_server_result.datetime_utc '2025-07-06 19:13:30' _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 9dlp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 9DLP # _exptl.entry_id 9DLP _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 9DLP _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DLP _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_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 B CD ARG 93 B ARG 93 1_555 D CN1 A1AMM 113 D A1AMM 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.577 ? covale ? covale2 D C LEU 112 D LEU 107 1_555 D N A1AMM 113 D A1AMM 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 D C A1AMM 113 D A1AMM 108 1_555 D N PRO 114 D PRO 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? metalc ? metalc1 D OG1 THR 101 D THR 96 1_555 F MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc2 E O1B ADP . D ADP 501 1_555 F MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc3 E O2B ADP . D ADP 501 1_555 F MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.782 ? metalc ? metalc4 E O1A ADP . D ADP 501 1_555 F MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? # _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 38 n n PB O2B ADP sing 39 n n PB O3B ADP sing 40 n n PB O3A ADP sing 41 n n O2B HOB2 ADP sing 42 n n O3B HOB3 ADP sing 43 n n PA O1A ADP doub 44 n n PA O2A ADP sing 45 n n PA O3A ADP sing 46 n n PA O5' ADP sing 47 n n O2A HOA2 ADP sing 48 n n O5' C5' ADP sing 49 n n C5' C4' ADP sing 50 n n C5' "H5'1" ADP sing 51 n n C5' "H5'2" ADP sing 52 n n C4' O4' ADP sing 53 n n C4' C3' ADP sing 54 n n C4' H4' ADP sing 55 n n O4' C1' ADP sing 56 n n C3' O3' ADP sing 57 n n C3' C2' ADP sing 58 n n C3' H3' ADP sing 59 n n O3' HO3' ADP sing 60 n n C2' O2' ADP sing 61 n n C2' C1' ADP sing 62 n n C2' H2' ADP sing 63 n n O2' HO2' ADP sing 64 n n C1' N9 ADP sing 65 n n C1' H1' ADP sing 66 n n N9 C8 ADP sing 67 n y N9 C4 ADP sing 68 n y C8 N7 ADP doub 69 n y C8 H8 ADP sing 70 n n N7 C5 ADP sing 71 n y C5 C6 ADP sing 72 n y C5 C4 ADP doub 73 n y C6 N6 ADP sing 74 n n C6 N1 ADP doub 75 n y N6 HN61 ADP sing 76 n n N6 HN62 ADP sing 77 n n N1 C2 ADP sing 78 n y C2 N3 ADP doub 79 n y C2 H2 ADP sing 80 n n N3 C4 ADP sing 81 n y # _atom_sites.entry_id 9DLP _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 5 ADP D 1 501 301 ADP ADP . F 6 MG D 1 502 1 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 . . . E 5 111.853 100.655 134.921 1 106.03 ? PB ADP 501 D 1 HETATM 2 O O1B ADP . . . E 5 111.803 101.478 136.185 1 103.31 ? O1B ADP 501 D 1 HETATM 3 O O2B ADP . . . E 5 111.409 99.223 135.094 1 103.5 ? O2B ADP 501 D 1 HETATM 4 O O3B ADP . . . E 5 111.279 101.347 133.709 1 100.36 ? O3B ADP 501 D 1 HETATM 5 P PA ADP . . . E 5 114.477 100.145 135.737 1 110.36 ? PA ADP 501 D 1 HETATM 6 O O1A ADP . . . E 5 113.732 99.491 136.876 1 110.35 ? O1A ADP 501 D 1 HETATM 7 O O2A ADP . . . E 5 115.35 101.349 135.994 1 96.11 ? O2A ADP 501 D 1 HETATM 8 O O3A ADP . . . E 5 113.423 100.537 134.587 1 102.03 ? O3A ADP 501 D 1 HETATM 9 O O5' ADP . . . E 5 115.387 99.027 135.026 1 107.56 ? O5' ADP 501 D 1 HETATM 10 C C5' ADP . . . E 5 115.882 99.251 133.71 1 103.09 ? C5' ADP 501 D 1 HETATM 11 C C4' ADP . . . E 5 117.299 98.707 133.609 1 99.72 ? C4' ADP 501 D 1 HETATM 12 O O4' ADP . . . E 5 117.899 99.223 132.423 1 100.87 ? O4' ADP 501 D 1 HETATM 13 C C3' ADP . . . E 5 118.137 99.162 134.789 1 98.11 ? C3' ADP 501 D 1 HETATM 14 O O3' ADP . . . E 5 118.667 98.024 135.47 1 98.34 ? O3' ADP 501 D 1 HETATM 15 C C2' ADP . . . E 5 119.27 99.984 134.216 1 96.13 ? C2' ADP 501 D 1 HETATM 16 O O2' ADP . . . E 5 120.524 99.414 134.6 1 101.42 ? O2' ADP 501 D 1 HETATM 17 C C1' ADP . . . E 5 119.108 99.925 132.709 1 97.23 ? C1' ADP 501 D 1 HETATM 18 N N9 ADP . . . E 5 118.995 101.3 132.172 1 94.12 ? N9 ADP 501 D 1 HETATM 19 C C8 ADP . . . E 5 118.098 102.218 132.57 1 93.54 ? C8 ADP 501 D 1 HETATM 20 N N7 ADP . . . E 5 118.251 103.38 131.887 1 91.38 ? N7 ADP 501 D 1 HETATM 21 C C5 ADP . . . E 5 119.272 103.21 131.028 1 89.33 ? C5 ADP 501 D 1 HETATM 22 C C6 ADP . . . E 5 119.959 104.035 130.01 1 88.89 ? C6 ADP 501 D 1 HETATM 23 N N6 ADP . . . E 5 119.578 105.311 129.764 1 88.71 ? N6 ADP 501 D 1 HETATM 24 N N1 ADP . . . E 5 120.982 103.473 129.332 1 92.37 ? N1 ADP 501 D 1 HETATM 25 C C2 ADP . . . E 5 121.373 102.208 129.564 1 91.13 ? C2 ADP 501 D 1 HETATM 26 N N3 ADP . . . E 5 120.797 101.402 130.47 1 88.06 ? N3 ADP 501 D 1 HETATM 27 C C4 ADP . . . E 5 119.761 101.838 131.223 1 90.5 ? C4 ADP 501 D 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 27 #