data_8UMY # _model_server_result.job_id qs019jGleTN3vNoR80v8Zw _model_server_result.datetime_utc '2025-01-03 14:55:06' _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 8umy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":2000}' # _entry.id 8UMY # _exptl.entry_id 8UMY _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 11 _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 8UMY _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8UMY _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 decameric _pdbx_struct_assembly.oligomeric_count 10 _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,R,S _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 # _struct_asym.details ? _struct_asym.entity_id 11 _struct_asym.id S _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 metalc ? metalc1 A OG1 THR 381 A THR 381 1_555 K MG MG . A MG 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc2 K MG MG . A MG 1201 1_555 L O3G AGS . A AGS 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc3 B OG1 THR 83 B THR 83 1_555 M MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc4 M MG MG . B MG 401 1_555 N O1B AGS . B AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc5 M MG MG . B MG 401 1_555 N O2G AGS . B AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc6 C OG1 THR 67 C THR 67 1_555 O MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc7 O MG MG . C MG 401 1_555 P O1B AGS . C AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? metalc ? metalc8 O MG MG . C MG 401 1_555 P O3G AGS . C AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc9 D OG1 THR 85 D THR 85 1_555 Q MG MG . D MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc10 Q MG MG . D MG 401 1_555 R O2G AGS . D AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc11 Q MG MG . D MG 401 1_555 R O2B AGS . D AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? hydrog WATSON-CRICK hydrog1 I N3 DT 13 I DT 13 1_555 J N1 DA 18 J DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 I O4 DT 13 I DT 13 1_555 J N6 DA 18 J DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 I N1 DG 14 I DG 14 1_555 J N3 DC 17 J DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 I N2 DG 14 I DG 14 1_555 J O2 DC 17 J DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 I O6 DG 14 I DG 14 1_555 J N4 DC 17 J DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 I N3 DT 15 I DT 15 1_555 J N1 DA 16 J DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 I O4 DT 15 I DT 15 1_555 J N6 DA 16 J DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 I N1 DA 16 I DA 16 1_555 J N3 DT 15 J DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 I N6 DA 16 I DA 16 1_555 J O4 DT 15 J DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 I N3 DC 17 I DC 17 1_555 J N1 DG 14 J DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 I N4 DC 17 I DC 17 1_555 J O6 DG 14 J DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 I O2 DC 17 I DC 17 1_555 J N2 DG 14 J DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 I N3 DT 18 I DT 18 1_555 J N1 DA 13 J DA 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 I O4 DT 18 I DT 18 1_555 J N6 DA 13 J DA 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 I N3 DC 19 I DC 19 1_555 J N1 DG 12 J DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 I N4 DC 19 I DC 19 1_555 J O6 DG 12 J DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 I O2 DC 19 I DC 19 1_555 J N2 DG 12 J DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 I N1 DG 20 I DG 20 1_555 J N3 DC 11 J DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 I N2 DG 20 I DG 20 1_555 J O2 DC 11 J DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 I O6 DG 20 I DG 20 1_555 J N4 DC 11 J DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 I N3 DT 21 I DT 21 1_555 J N1 DA 10 J DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 I O4 DT 21 I DT 21 1_555 J N6 DA 10 J DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 I N1 DA 22 I DA 22 1_555 J N3 DT 9 J DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 I N6 DA 22 I DA 22 1_555 J O4 DT 9 J DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 I N1 DG 23 I DG 23 1_555 J N3 DC 8 J DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 I N2 DG 23 I DG 23 1_555 J O2 DC 8 J DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 I O6 DG 23 I DG 23 1_555 J N4 DC 8 J DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 I N3 DT 24 I DT 24 1_555 J N1 DA 7 J DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 I O4 DT 24 I DT 24 1_555 J N6 DA 7 J DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 I N1 DG 25 I DG 25 1_555 J N3 DC 6 J DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 I N2 DG 25 I DG 25 1_555 J O2 DC 6 J DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 I O6 DG 25 I DG 25 1_555 J N4 DC 6 J DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 I N3 DT 26 I DT 26 1_555 J N1 DA 5 J DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 I O4 DT 26 I DT 26 1_555 J N6 DA 5 J DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 I N3 DC 27 I DC 27 1_555 J N1 DG 4 J DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 I N4 DC 27 I DC 27 1_555 J O6 DG 4 J DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 I O2 DC 27 I DC 27 1_555 J N2 DG 4 J DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 I N3 DT 28 I DT 28 1_555 J N1 DA 3 J DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 I O4 DT 28 I DT 28 1_555 J N6 DA 3 J DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 I N1 DG 29 I DG 29 1_555 J N3 DC 2 J DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 I N2 DG 29 I DG 29 1_555 J O2 DC 2 J DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 I O6 DG 29 I DG 29 1_555 J N4 DC 2 J DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 8UMY _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 K 9 MG A 1 1201 1201 MG MG . L 10 AGS A 1 1202 1202 AGS AGS . M 9 MG B 1 401 401 MG MG . N 10 AGS B 1 402 402 AGS AGS . O 9 MG C 1 401 401 MG MG . P 10 AGS C 1 402 402 AGS AGS . Q 9 MG D 1 401 401 MG MG . R 10 AGS D 1 402 402 AGS AGS . S 11 ADP E 1 2000 2000 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 . . . S 11 133.585 149.962 167.792 1 51.76 ? PB ADP 2000 E 1 HETATM 2 O O1B ADP . . . S 11 134.524 149.613 166.665 1 57.49 ? O1B ADP 2000 E 1 HETATM 3 O O2B ADP . . . S 11 133.329 148.831 168.756 1 57.84 -1 O2B ADP 2000 E 1 HETATM 4 O O3B ADP . . . S 11 132.344 150.703 167.365 1 70.05 ? O3B ADP 2000 E 1 HETATM 5 P PA ADP . . . S 11 134.73 152.516 168.135 1 59.41 ? PA ADP 2000 E 1 HETATM 6 O O1A ADP . . . S 11 134.735 152.521 166.626 1 68.1 -1 O1A ADP 2000 E 1 HETATM 7 O O2A ADP . . . S 11 135.93 153.021 168.897 1 54.59 ? O2A ADP 2000 E 1 HETATM 8 O O3A ADP . . . S 11 134.404 151.033 168.67 1 57.46 ? O3A ADP 2000 E 1 HETATM 9 O O5' ADP . . . S 11 133.474 153.386 168.636 1 54.51 ? O5' ADP 2000 E 1 HETATM 10 C C5' ADP . . . S 11 133.217 153.518 170.03 1 54.24 ? C5' ADP 2000 E 1 HETATM 11 C C4' ADP . . . S 11 133.01 154.987 170.371 1 59.39 ? C4' ADP 2000 E 1 HETATM 12 O O4' ADP . . . S 11 133.133 155.157 171.782 1 61.64 ? O4' ADP 2000 E 1 HETATM 13 C C3' ADP . . . S 11 134.068 155.857 169.716 1 64.36 ? C3' ADP 2000 E 1 HETATM 14 O O3' ADP . . . S 11 133.44 156.853 168.905 1 68.01 ? O3' ADP 2000 E 1 HETATM 15 C C2' ADP . . . S 11 134.83 156.528 170.837 1 53.8 ? C2' ADP 2000 E 1 HETATM 16 O O2' ADP . . . S 11 134.806 157.945 170.661 1 62.38 ? O2' ADP 2000 E 1 HETATM 17 C C1' ADP . . . S 11 134.106 156.148 172.114 1 56.64 ? C1' ADP 2000 E 1 HETATM 18 N N9 ADP . . . S 11 135.069 155.555 173.071 1 57.51 ? N9 ADP 2000 E 1 HETATM 19 C C8 ADP . . . S 11 135.574 154.31 172.996 1 59.83 ? C8 ADP 2000 E 1 HETATM 20 N N7 ADP . . . S 11 136.426 154.061 174.02 1 59.27 ? N7 ADP 2000 E 1 HETATM 21 C C5 ADP . . . S 11 136.474 155.171 174.775 1 57.01 ? C5 ADP 2000 E 1 HETATM 22 C C6 ADP . . . S 11 137.177 155.589 176.007 1 59.01 ? C6 ADP 2000 E 1 HETATM 23 N N6 ADP . . . S 11 138.019 154.746 176.647 1 61.63 ? N6 ADP 2000 E 1 HETATM 24 N N1 ADP . . . S 11 136.951 156.837 176.469 1 56.18 ? N1 ADP 2000 E 1 HETATM 25 C C2 ADP . . . S 11 136.116 157.683 175.841 1 58.59 ? C2 ADP 2000 E 1 HETATM 26 N N3 ADP . . . S 11 135.446 157.37 174.72 1 59.6 ? N3 ADP 2000 E 1 HETATM 27 C C4 ADP . . . S 11 135.581 156.153 174.146 1 57.94 ? C4 ADP 2000 E 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #