data_8U9Z # _model_server_result.job_id 7Czvc_sYz0ZZ1gyRyC3dFA _model_server_result.datetime_utc '2024-12-01 01:11:43' _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 8u9z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":901}' # _entry.id 8U9Z # _exptl.entry_id 8U9Z _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 492.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium' _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details heptameric _pdbx_struct_assembly.oligomeric_count 7 _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,T,U _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 H N N ? 3 J N N ? 3 L N N ? 3 N N N ? 3 P N N ? 3 R 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 A OG1 THR 262 A THR 262 1_555 I MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.831 ? metalc ? metalc2 A OG1 THR 535 A THR 535 1_555 K MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc3 H O2B 08T . A 08T 901 1_555 I MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc4 J O1A 08T . A 08T 903 1_555 K MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? metalc ? metalc5 J O2B 08T . A 08T 903 1_555 K MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc6 J O3B 08T . A 08T 903 1_555 K MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.949 ? metalc ? metalc7 B OG1 THR 262 B THR 262 1_555 M MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc8 B OG1 THR 535 B THR 535 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? metalc ? metalc9 L O1A 08T . B 08T 901 1_555 M MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc10 L O2A 08T . B 08T 901 1_555 M MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc11 L O2B 08T . B 08T 901 1_555 M MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc12 L O3A 08T . B 08T 901 1_555 M MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.688 ? metalc ? metalc13 N O2B 08T . B 08T 903 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc14 C OG1 THR 262 C THR 262 1_555 Q MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? metalc ? metalc15 C OG1 THR 535 C THR 535 1_555 S MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.817 ? metalc ? metalc16 P O2B 08T . C 08T 901 1_555 Q MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc17 R O2B 08T . C 08T 903 1_555 S MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? # _chem_comp.formula 'C10 H14 Be F3 N5 O10 P2' _chem_comp.formula_weight 492.201 _chem_comp.id 08T _chem_comp.mon_nstd_flag . _chem_comp.name '[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium' _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 O3' C3' 08T sing 1 n n O2' C2' 08T sing 2 n n C3' C4' 08T sing 3 n n C3' C2' 08T sing 4 n n C4' C5' 08T sing 5 n n C4' O4' 08T sing 6 n n C2' C1' 08T sing 7 n n C5' O5' 08T sing 8 n n O4' C1' 08T sing 9 n n C1' N9 08T sing 10 n n N3 C2 08T doub 11 n y N3 C4 08T sing 12 n y O2A PA 08T doub 13 n n C2 N1 08T sing 14 n y O5' PA 08T sing 15 n n C4 N9 08T sing 16 n y C4 C5 08T doub 17 n y N9 C8 08T sing 18 n y PA O1A 08T sing 19 n n PA O3A 08T sing 20 n n N1 C6 08T doub 21 n y C5 C6 08T sing 22 n y C5 N7 08T sing 23 n y O3A PB 08T sing 24 n n C8 N7 08T doub 25 n y C6 N6 08T sing 26 n n O1B PB 08T doub 27 n n PB O3B 08T sing 28 n n PB O2B 08T sing 29 n n F1 BE 08T sing 30 n n BE F3 08T sing 31 n n O3B BE 08T sing 32 n n BE F2 08T sing 33 n n C5' H1 08T sing 34 n n C5' H2 08T sing 35 n n C4' H3 08T sing 36 n n C3' H4 08T sing 37 n n O3' H5 08T sing 38 n n C2' H6 08T sing 39 n n O2' H7 08T sing 40 n n C1' H8 08T sing 41 n n O1A H9 08T sing 42 n n C2 H10 08T sing 43 n n O2B H11 08T sing 44 n n N6 H12 08T sing 45 n n N6 H13 08T sing 46 n n C8 H14 08T sing 47 n n # _atom_sites.entry_id 8U9Z _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 H 3 08T A 1 901 901 08T ADP . I 4 MG A 1 902 903 MG MG . J 3 08T A 1 903 904 08T ADP . K 4 MG A 1 904 906 MG MG . L 3 08T B 1 901 901 08T ADP . M 4 MG B 1 902 903 MG MG . N 3 08T B 1 903 904 08T ADP . O 4 MG B 1 904 906 MG MG . P 3 08T C 1 901 901 08T ADP . Q 4 MG C 1 902 903 MG MG . R 3 08T C 1 903 904 08T ADP . S 4 MG C 1 904 906 MG MG . T 5 ADP D 1 901 901 ADP ADP . U 5 ADP D 1 902 904 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 PA 08T . . . L 3 147.555 145.636 190.51 1 145.46 ? PA 08T 901 B 1 HETATM 2 P PB 08T . . . L 3 149.264 147.609 189.094 1 145.46 ? PB 08T 901 B 1 HETATM 3 BE BE 08T . . . L 3 148.223 147.654 186.555 1 128.4 ? BE 08T 901 B 1 HETATM 4 C C5' 08T . . . L 3 147.638 143.01 190.672 1 145.46 ? C5' 08T 901 B 1 HETATM 5 O O5' 08T . . . L 3 148.078 144.296 191.158 1 145.46 ? O5' 08T 901 B 1 HETATM 6 C C4' 08T . . . L 3 148.051 141.939 191.649 1 145.46 ? C4' 08T 901 B 1 HETATM 7 O O4' 08T . . . L 3 149.48 141.964 191.823 1 145.46 ? O4' 08T 901 B 1 HETATM 8 C C3' 08T . . . L 3 147.477 142.088 193.051 1 145.46 ? C3' 08T 901 B 1 HETATM 9 O O3' 08T . . . L 3 146.204 141.455 193.121 1 145.46 ? O3' 08T 901 B 1 HETATM 10 C C2' 08T . . . L 3 148.512 141.365 193.916 1 145.46 ? C2' 08T 901 B 1 HETATM 11 O O2' 08T . . . L 3 148.169 139.991 194.059 1 145.46 ? O2' 08T 901 B 1 HETATM 12 C C1' 08T . . . L 3 149.822 141.565 193.139 1 145.46 ? C1' 08T 901 B 1 HETATM 13 N N1 08T . . . L 3 151.905 143.725 197.353 1 145.46 ? N1 08T 901 B 1 HETATM 14 O O1A 08T . . . L 3 146.625 145.335 189.407 1 145.46 ? O1A 08T 901 B 1 HETATM 15 O O1B 08T . . . L 3 150.679 147.891 189.599 1 145.46 ? O1B 08T 901 B 1 HETATM 16 F F1 08T . . . L 3 146.867 147.813 187.255 1 128.4 ? F1 08T 901 B 1 HETATM 17 C C2 08T . . . L 3 151.072 142.691 197.207 1 145.46 ? C2 08T 901 B 1 HETATM 18 O O2A 08T . . . L 3 147.046 146.639 191.539 1 145.46 ? O2A 08T 901 B 1 HETATM 19 O O2B 08T . . . L 3 148.265 148.678 189.337 1 145.46 ? O2B 08T 901 B 1 HETATM 20 F F2 08T . . . L 3 148.645 148.978 185.843 1 128.4 ? F2 08T 901 B 1 HETATM 21 N N3 08T . . . L 3 150.566 142.177 196.083 1 145.46 ? N3 08T 901 B 1 HETATM 22 O O3A 08T . . . L 3 148.829 146.27 189.83 1 145.46 ? O3A 08T 901 B 1 HETATM 23 O O3B 08T . . . L 3 149.331 147.225 187.623 1 145.46 ? O3B 08T 901 B 1 HETATM 24 F F3 08T . . . L 3 148.101 146.584 185.448 1 128.4 ? F3 08T 901 B 1 HETATM 25 C C4 08T . . . L 3 150.997 142.844 195.007 1 145.46 ? C4 08T 901 B 1 HETATM 26 C C5 08T . . . L 3 151.861 143.928 195 1 145.46 ? C5 08T 901 B 1 HETATM 27 C C6 08T . . . L 3 152.328 144.379 196.249 1 145.46 ? C6 08T 901 B 1 HETATM 28 N N6 08T . . . L 3 153.162 145.412 196.402 1 145.46 ? N6 08T 901 B 1 HETATM 29 N N7 08T . . . L 3 152.093 144.361 193.704 1 145.46 ? N7 08T 901 B 1 HETATM 30 C C8 08T . . . L 3 151.379 143.544 192.971 1 145.46 ? C8 08T 901 B 1 HETATM 31 N N9 08T . . . L 3 150.69 142.602 193.688 1 145.46 ? N9 08T 901 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 428 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #