data_8U9P # _model_server_result.job_id UUsDWSz7_gkY3NrdbkPnNw _model_server_result.datetime_utc '2024-11-28 07:54:06' _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 8u9p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":903}' # _entry.id 8U9P # _exptl.entry_id 8U9P _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 8 _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,V,W,X,Y _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 ? 3 T N N ? 3 V 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc2 A OG1 THR 535 A THR 535 1_555 K MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.79 ? metalc ? metalc3 H O2B 08T . A 08T 901 1_555 I MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc4 J O2B 08T . A 08T 903 1_555 K MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? metalc ? metalc5 B OG1 THR 262 B THR 262 1_555 M MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? metalc ? metalc6 B OG1 THR 535 B THR 535 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc7 L O1B 08T . B 08T 901 1_555 M MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc8 N O1B 08T . B 08T 903 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc9 C OG1 THR 262 C THR 262 1_555 Q MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc10 C OG1 THR 535 C THR 535 1_555 S MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc11 P O2B 08T . C 08T 901 1_555 Q MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc12 R O2B 08T . C 08T 903 1_555 S MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.836 ? metalc ? metalc13 R O3A 08T . C 08T 903 1_555 S MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc14 R O3B 08T . C 08T 903 1_555 S MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? metalc ? metalc15 D OG1 THR 262 D THR 262 1_555 U MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.732 ? metalc ? metalc16 D OG1 THR 535 D THR 535 1_555 W MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.811 ? metalc ? metalc17 T O2B 08T . D 08T 901 1_555 U MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? metalc ? metalc18 V O2B 08T . D 08T 903 1_555 W MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? # _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 8U9P _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 3 08T D 1 901 901 08T ADP . U 4 MG D 1 902 903 MG MG . V 3 08T D 1 903 904 08T ADP . W 4 MG D 1 904 906 MG MG . X 5 ADP E 1 901 901 ADP ADP . Y 5 ADP E 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 . . . V 3 177.804 147.561 113.607 1 112.78 ? PA 08T 903 D 1 HETATM 2 P PB 08T . . . V 3 180.12 146.914 115.301 1 103.71 ? PB 08T 903 D 1 HETATM 3 BE BE 08T . . . V 3 181.077 148.393 117.359 1 102.53 ? BE 08T 903 D 1 HETATM 4 C C5' 08T . . . V 3 178.267 149.422 111.805 1 104.4 ? C5' 08T 903 D 1 HETATM 5 O O5' 08T . . . V 3 177.996 148.041 112.117 1 106.87 ? O5' 08T 903 D 1 HETATM 6 C C4' 08T . . . V 3 177.698 149.728 110.446 1 100.8 ? C4' 08T 903 D 1 HETATM 7 O O4' 08T . . . V 3 178.694 149.468 109.433 1 97.31 ? O4' 08T 903 D 1 HETATM 8 C C3' 08T . . . V 3 176.485 148.898 110.045 1 101.44 ? C3' 08T 903 D 1 HETATM 9 O O3' 08T . . . V 3 175.284 149.515 110.494 1 104.99 ? O3' 08T 903 D 1 HETATM 10 C C2' 08T . . . V 3 176.59 148.904 108.523 1 100.65 ? C2' 08T 903 D 1 HETATM 11 O O2' 08T . . . V 3 176.038 150.094 107.972 1 101.32 ? O2' 08T 903 D 1 HETATM 12 C C1' 08T . . . V 3 178.104 148.804 108.329 1 98.95 ? C1' 08T 903 D 1 HETATM 13 N N1 08T . . . V 3 177.738 144.077 106.302 1 104.5 ? N1 08T 903 D 1 HETATM 14 O O1A 08T . . . V 3 176.934 148.435 114.409 1 110.97 ? O1A 08T 903 D 1 HETATM 15 O O1B 08T . . . V 3 180.965 145.888 114.548 1 99.39 ? O1B 08T 903 D 1 HETATM 16 F F1 08T . . . V 3 179.813 147.871 118.052 1 108.31 ? F1 08T 903 D 1 HETATM 17 C C2 08T . . . V 3 177.053 145.199 106.069 1 109.28 ? C2 08T 903 D 1 HETATM 18 O O2A 08T . . . V 3 177.383 146.099 113.623 1 104.67 ? O2A 08T 903 D 1 HETATM 19 O O2B 08T . . . V 3 179.239 146.358 116.35 1 107.32 ? O2B 08T 903 D 1 HETATM 20 F F2 08T . . . V 3 182.365 147.814 118.019 1 97.8 ? F2 08T 903 D 1 HETATM 21 N N3 08T . . . V 3 177.199 146.399 106.635 1 102.89 ? N3 08T 903 D 1 HETATM 22 O O3A 08T . . . V 3 179.259 147.606 114.184 1 104.19 ? O3A 08T 903 D 1 HETATM 23 O O3B 08T . . . V 3 181.028 148 115.815 1 98.86 ? O3B 08T 903 D 1 HETATM 24 F F3 08T . . . V 3 181.154 149.926 117.534 1 107.15 ? F3 08T 903 D 1 HETATM 25 C C4 08T . . . V 3 178.181 146.392 107.54 1 97.91 ? C4 08T 903 D 1 HETATM 26 C C5 08T . . . V 3 178.976 145.312 107.888 1 98.95 ? C5 08T 903 D 1 HETATM 27 C C6 08T . . . V 3 178.726 144.098 107.222 1 102.91 ? C6 08T 903 D 1 HETATM 28 N N6 08T . . . V 3 179.409 142.972 107.447 1 107.89 ? N6 08T 903 D 1 HETATM 29 N N7 08T . . . V 3 179.894 145.674 108.861 1 100.21 ? N7 08T 903 D 1 HETATM 30 C C8 08T . . . V 3 179.634 146.939 109.077 1 95.32 ? C8 08T 903 D 1 HETATM 31 N N9 08T . . . V 3 178.614 147.439 108.315 1 94.9 ? N9 08T 903 D 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 135 _model_server_stats.query_time_ms 486 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #