data_8ENK # _model_server_result.job_id x-rSLPZAz9S0z92xK5-4ag _model_server_result.datetime_utc '2025-02-16 22:26:32' _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 8enk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1000}' # _entry.id 8ENK # _exptl.entry_id 8ENK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 8ENK _cell.length_a 88.534 _cell.length_b 96.786 _cell.length_c 126.18 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8ENK _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 I 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 metalc ? metalc1 F O1B ADP . A ADP 1000 1_555 G BE BEF . A BEF 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? metalc ? metalc2 F O2B ADP . A ADP 1000 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc3 H MG MG . A MG 1002 1_555 L O HOH . A HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc4 H MG MG . A MG 1002 1_555 L O HOH . A HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc5 H MG MG . A MG 1002 1_555 L O HOH . A HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc6 H MG MG . A MG 1002 1_555 L O HOH . A HOH 1108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc7 I O2B ADP . B ADP 1000 1_555 J BE BEF . B BEF 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? metalc ? metalc8 I O1B ADP . B ADP 1000 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc9 K MG MG . B MG 1002 1_555 M O HOH . B HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc10 K MG MG . B MG 1002 1_555 M O HOH . B HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc11 K MG MG . B MG 1002 1_555 M O HOH . B HOH 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc12 K MG MG . B MG 1002 1_555 M O HOH . B HOH 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? # _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 8ENK _atom_sites.fract_transf_matrix[1][1] 0.011295 _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] 0.010332 _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] 0.007925 _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 F 4 ADP A 1 1000 1000 ADP ADP . G 5 BEF A 1 1001 1001 BEF BEF . H 6 MG A 1 1002 1002 MG MG . I 4 ADP B 1 1000 1000 ADP ADP . J 5 BEF B 1 1001 1001 BEF BEF . K 6 MG B 1 1002 1002 MG MG . L 7 HOH A 1 1101 10 HOH HOH . L 7 HOH A 2 1102 12 HOH HOH . L 7 HOH A 3 1103 11 HOH HOH . L 7 HOH A 4 1104 17 HOH HOH . L 7 HOH A 5 1105 15 HOH HOH . L 7 HOH A 6 1106 16 HOH HOH . L 7 HOH A 7 1107 14 HOH HOH . L 7 HOH A 8 1108 13 HOH HOH . M 7 HOH B 1 1101 3 HOH HOH . M 7 HOH B 2 1102 8 HOH HOH . M 7 HOH B 3 1103 2 HOH HOH . M 7 HOH B 4 1104 1 HOH HOH . M 7 HOH B 5 1105 5 HOH HOH . M 7 HOH B 6 1106 4 HOH HOH . M 7 HOH B 7 1107 9 HOH HOH . M 7 HOH B 8 1108 7 HOH HOH . M 7 HOH B 9 1109 6 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 . . . F 4 -4.292 -41.454 62.446 1 47.96 ? PB ADP 1000 A 1 HETATM 2 O O1B ADP . . . F 4 -4.662 -40.361 61.466 1 51.4 ? O1B ADP 1000 A 1 HETATM 3 O O2B ADP . . . F 4 -5.324 -42.546 62.588 1 47.51 ? O2B ADP 1000 A 1 HETATM 4 O O3B ADP . . . F 4 -3.808 -40.909 63.771 1 53.17 ? O3B ADP 1000 A 1 HETATM 5 P PA ADP . . . F 4 -2.994 -43.757 61.395 1 49.92 ? PA ADP 1000 A 1 HETATM 6 O O1A ADP . . . F 4 -3.796 -43.907 60.123 1 52.42 ? O1A ADP 1000 A 1 HETATM 7 O O2A ADP . . . F 4 -3.324 -44.586 62.606 1 50.65 ? O2A ADP 1000 A 1 HETATM 8 O O3A ADP . . . F 4 -2.999 -42.199 61.824 1 50.85 ? O3A ADP 1000 A 1 HETATM 9 O O5' ADP . . . F 4 -1.451 -43.991 61.017 1 51.36 ? O5' ADP 1000 A 1 HETATM 10 C C5' ADP . . . F 4 -0.988 -43.692 59.705 1 54.15 ? C5' ADP 1000 A 1 HETATM 11 C C4' ADP . . . F 4 0.246 -44.534 59.462 1 55.39 ? C4' ADP 1000 A 1 HETATM 12 O O4' ADP . . . F 4 1.157 -44.377 60.548 1 60.51 ? O4' ADP 1000 A 1 HETATM 13 C C3' ADP . . . F 4 -0.131 -46.004 59.402 1 55.37 ? C3' ADP 1000 A 1 HETATM 14 O O3' ADP . . . F 4 0.313 -46.494 58.137 1 50 ? O3' ADP 1000 A 1 HETATM 15 C C2' ADP . . . F 4 0.638 -46.667 60.53 1 59.43 ? C2' ADP 1000 A 1 HETATM 16 O O2' ADP . . . F 4 1.22 -47.913 60.139 1 63.4 ? O2' ADP 1000 A 1 HETATM 17 C C1' ADP . . . F 4 1.732 -45.658 60.813 1 61.07 ? C1' ADP 1000 A 1 HETATM 18 N N9 ADP . . . F 4 2.266 -45.758 62.187 1 65.79 ? N9 ADP 1000 A 1 HETATM 19 C C8 ADP . . . F 4 1.563 -45.82 63.336 1 64.39 ? C8 ADP 1000 A 1 HETATM 20 N N7 ADP . . . F 4 2.398 -45.91 64.402 1 60.63 ? N7 ADP 1000 A 1 HETATM 21 C C5 ADP . . . F 4 3.663 -45.911 63.934 1 65.88 ? C5 ADP 1000 A 1 HETATM 22 C C6 ADP . . . F 4 5.029 -45.985 64.515 1 67.36 ? C6 ADP 1000 A 1 HETATM 23 N N6 ADP . . . F 4 5.224 -46.074 65.851 1 66.24 ? N6 ADP 1000 A 1 HETATM 24 N N1 ADP . . . F 4 6.078 -45.955 63.663 1 68.6 ? N1 ADP 1000 A 1 HETATM 25 C C2 ADP . . . F 4 5.908 -45.866 62.331 1 65.29 ? C2 ADP 1000 A 1 HETATM 26 N N3 ADP . . . F 4 4.705 -45.796 61.739 1 66.2 ? N3 ADP 1000 A 1 HETATM 27 C C4 ADP . . . F 4 3.567 -45.814 62.474 1 65.84 ? C4 ADP 1000 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 355 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #