data_8U9Q # _model_server_result.job_id Xu4RYp1UY72No-E9S35LxQ _model_server_result.datetime_utc '2024-11-30 23:57:06' _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 8u9q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":901}' # _entry.id 8U9Q # _exptl.entry_id 8U9Q _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,V _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.873 ? metalc ? metalc2 H O2A 08T . A 08T 901 1_555 I MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.768 ? metalc ? metalc3 H O2B 08T . A 08T 901 1_555 I MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? metalc ? metalc4 I MG MG . A MG 902 1_555 B OD1 ASP 343 B ASP 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc5 I MG MG . A MG 902 1_555 B OD2 ASP 343 B ASP 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc6 J O1A 08T . A 08T 903 1_555 K MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? metalc ? metalc7 J O2B 08T . A 08T 903 1_555 K MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.895 ? metalc ? metalc8 B OG1 THR 262 B THR 262 1_555 M MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.87 ? metalc ? metalc9 B OG1 THR 535 B THR 535 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc10 L O2B 08T . B 08T 901 1_555 M MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc11 N O1A 08T . B 08T 903 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? metalc ? metalc12 N O2A 08T . B 08T 903 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.956 ? metalc ? metalc13 N O2B 08T . B 08T 903 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc14 N O3A 08T . B 08T 903 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc15 C OG1 THR 262 C THR 262 1_555 Q MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc16 C OG1 THR 535 C THR 535 1_555 S MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.789 ? metalc ? metalc17 P O1A 08T . C 08T 901 1_555 Q MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc18 P O2B 08T . C 08T 901 1_555 Q MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc19 Q MG MG . C MG 902 1_555 D OD2 ASP 343 D ASP 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc20 R O2B 08T . C 08T 903 1_555 S MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? # _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 8U9Q _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 . V 5 ADP E 1 901 904 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 . . . H 3 143.895 179.294 189.083 1 197.28 ? PA 08T 901 A 1 HETATM 2 P PB 08T . . . H 3 144.792 179.364 186.236 1 197.28 ? PB 08T 901 A 1 HETATM 3 BE BE 08T . . . H 3 145.432 177.58 184.314 1 196.03 ? BE 08T 901 A 1 HETATM 4 C C5' 08T . . . H 3 145.076 178.116 191.12 1 197.28 ? C5' 08T 901 A 1 HETATM 5 O O5' 08T . . . H 3 144.86 179.306 190.333 1 197.28 ? O5' 08T 901 A 1 HETATM 6 C C4' 08T . . . H 3 145.977 178.462 192.277 1 197.28 ? C4' 08T 901 A 1 HETATM 7 O O4' 08T . . . H 3 147.121 179.197 191.784 1 197.28 ? O4' 08T 901 A 1 HETATM 8 C C3' 08T . . . H 3 145.325 179.332 193.355 1 197.28 ? C3' 08T 901 A 1 HETATM 9 O O3' 08T . . . H 3 145.575 178.8 194.651 1 197.28 ? O3' 08T 901 A 1 HETATM 10 C C2' 08T . . . H 3 145.991 180.697 193.161 1 197.28 ? C2' 08T 901 A 1 HETATM 11 O O2' 08T . . . H 3 146.062 181.429 194.381 1 197.28 ? O2' 08T 901 A 1 HETATM 12 C C1' 08T . . . H 3 147.365 180.295 192.635 1 197.28 ? C1' 08T 901 A 1 HETATM 13 N N1 08T . . . H 3 148.951 185.207 192.396 1 197.28 ? N1 08T 901 A 1 HETATM 14 O O1A 08T . . . H 3 143.053 180.504 189.073 1 197.28 ? O1A 08T 901 A 1 HETATM 15 O O1B 08T . . . H 3 145.814 180.408 185.785 1 197.28 ? O1B 08T 901 A 1 HETATM 16 F F1 08T . . . H 3 144.039 177.651 183.674 1 196.03 ? F1 08T 901 A 1 HETATM 17 C C2 08T . . . H 3 148.331 184.519 193.36 1 197.28 ? C2 08T 901 A 1 HETATM 18 O O2A 08T . . . H 3 143.137 177.982 188.958 1 197.28 ? O2A 08T 901 A 1 HETATM 19 O O2B 08T . . . H 3 143.404 179.576 185.758 1 197.28 ? O2B 08T 901 A 1 HETATM 20 F F2 08T . . . H 3 146.427 178.54 183.594 1 196.03 ? F2 08T 901 A 1 HETATM 21 N N3 08T . . . H 3 147.948 183.24 193.36 1 197.28 ? N3 08T 901 A 1 HETATM 22 O O3A 08T . . . H 3 144.864 179.38 187.831 1 197.28 ? O3A 08T 901 A 1 HETATM 23 O O3B 08T . . . H 3 145.348 178.014 185.844 1 197.28 ? O3B 08T 901 A 1 HETATM 24 F F3 08T . . . H 3 145.984 176.144 184.179 1 196.03 ? F3 08T 901 A 1 HETATM 25 C C4 08T . . . H 3 148.259 182.64 192.206 1 197.28 ? C4 08T 901 A 1 HETATM 26 C C5 08T . . . H 3 148.899 183.218 191.12 1 197.28 ? C5 08T 901 A 1 HETATM 27 C C6 08T . . . H 3 149.256 184.576 191.241 1 197.28 ? C6 08T 901 A 1 HETATM 28 N N6 08T . . . H 3 149.876 185.27 190.281 1 197.28 ? N6 08T 901 A 1 HETATM 29 N N7 08T . . . H 3 149.058 182.297 190.096 1 197.28 ? N7 08T 901 A 1 HETATM 30 C C8 08T . . . H 3 148.524 181.202 190.579 1 197.28 ? C8 08T 901 A 1 HETATM 31 N N9 08T . . . H 3 148.021 181.335 191.847 1 197.28 ? N9 08T 901 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 505 _model_server_stats.encode_time_ms 30 _model_server_stats.element_count 31 #