data_8UB4 # _model_server_result.job_id P273rEkBUNey8uECPxPkYw _model_server_result.datetime_utc '2024-11-28 07:54:38' _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 8ub4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":903}' # _entry.id 8UB4 # _exptl.entry_id 8UB4 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 492.201 _entity.id 4 _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 ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 8UB4 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8UB4 _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,T,U,V,W,X,Y,Z,AA,BA _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 ? 4 K N N ? 4 M N N ? 4 O N N ? 4 Q N N ? 4 S N N ? 4 U N N ? 4 W N N ? 4 Y 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 L MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.804 ? metalc ? metalc2 A OG1 THR 535 A THR 535 1_555 N MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.839 ? metalc ? metalc3 K O2B 08T . A 08T 901 1_555 L MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.603 ? metalc ? metalc4 B OG1 THR 262 B THR 262 1_555 P MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.775 ? metalc ? metalc5 B OG1 THR 535 B THR 535 1_555 R MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? metalc ? metalc6 O O2B 08T . B 08T 901 1_555 P MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.774 ? metalc ? metalc7 Q O2B 08T . B 08T 903 1_555 R MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.87 ? metalc ? metalc8 C OG1 THR 262 C THR 262 1_555 T MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.785 ? metalc ? metalc9 C OG1 THR 535 C THR 535 1_555 V MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.847 ? metalc ? metalc10 S O2B 08T . C 08T 901 1_555 T MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc11 U O2B 08T . C 08T 903 1_555 V MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.873 ? metalc ? metalc12 D OG1 THR 262 D THR 262 1_555 X MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.778 ? metalc ? metalc13 D OG1 THR 535 D THR 535 1_555 Z MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? metalc ? metalc14 W O2B 08T . D 08T 901 1_555 X MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc15 Y O2B 08T . D 08T 903 1_555 Z MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? # _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 8UB4 _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 4 08T A 1 901 901 08T ADP . L 5 MG A 1 902 903 MG MG . M 4 08T A 1 903 904 08T ADP . N 5 MG A 1 904 906 MG MG . O 4 08T B 1 901 901 08T ADP . P 5 MG B 1 902 903 MG MG . Q 4 08T B 1 903 904 08T ADP . R 5 MG B 1 904 906 MG MG . S 4 08T C 1 901 901 08T ADP . T 5 MG C 1 902 903 MG MG . U 4 08T C 1 903 904 08T ADP . V 5 MG C 1 904 906 MG MG . W 4 08T D 1 901 901 08T ADP . X 5 MG D 1 902 903 MG MG . Y 4 08T D 1 903 904 08T ADP . Z 5 MG D 1 904 906 MG MG . AA 6 ADP E 1 901 901 ADP ADP . BA 6 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 . . . Y 4 178.044 147.665 113.304 1 107.16 ? PA 08T 903 D 1 HETATM 2 P PB 08T . . . Y 4 180.081 146.723 115.227 1 102.07 ? PB 08T 903 D 1 HETATM 3 BE BE 08T . . . Y 4 181.123 148.404 117.092 1 111.32 ? BE 08T 903 D 1 HETATM 4 C C5' 08T . . . Y 4 178.123 149.617 111.543 1 107.31 ? C5' 08T 903 D 1 HETATM 5 O O5' 08T . . . Y 4 178.366 148.233 111.867 1 111.55 ? O5' 08T 903 D 1 HETATM 6 C C4' 08T . . . Y 4 177.528 149.683 110.161 1 104.19 ? C4' 08T 903 D 1 HETATM 7 O O4' 08T . . . Y 4 178.527 149.336 109.182 1 103.08 ? O4' 08T 903 D 1 HETATM 8 C C3' 08T . . . Y 4 176.414 148.676 109.932 1 105.01 ? C3' 08T 903 D 1 HETATM 9 O O3' 08T . . . Y 4 175.185 149.231 110.385 1 109.95 ? O3' 08T 903 D 1 HETATM 10 C C2' 08T . . . Y 4 176.434 148.539 108.412 1 106.33 ? C2' 08T 903 D 1 HETATM 11 O O2' 08T . . . Y 4 175.765 149.636 107.8 1 112.66 ? O2' 08T 903 D 1 HETATM 12 C C1' 08T . . . Y 4 177.943 148.577 108.136 1 104.4 ? C1' 08T 903 D 1 HETATM 13 N N1 08T . . . Y 4 178 143.814 106.173 1 103.18 ? N1 08T 903 D 1 HETATM 14 O O1A 08T . . . Y 4 177.197 146.467 113.193 1 106.38 ? O1A 08T 903 D 1 HETATM 15 O O1B 08T . . . Y 4 180.859 145.47 114.828 1 106.94 ? O1B 08T 903 D 1 HETATM 16 F F1 08T . . . Y 4 179.88 147.95 117.866 1 111.67 ? F1 08T 903 D 1 HETATM 17 C C2 08T . . . Y 4 177.25 144.883 105.893 1 102.5 ? C2 08T 903 D 1 HETATM 18 O O2A 08T . . . Y 4 177.47 148.723 114.235 1 108.12 ? O2A 08T 903 D 1 HETATM 19 O O2B 08T . . . Y 4 179.029 146.509 116.248 1 105.61 ? O2B 08T 903 D 1 HETATM 20 F F2 08T . . . Y 4 182.432 147.961 117.815 1 109.48 ? F2 08T 903 D 1 HETATM 21 N N3 08T . . . Y 4 177.287 146.097 106.445 1 99.14 ? N3 08T 903 D 1 HETATM 22 O O3A 08T . . . Y 4 179.442 147.242 113.877 1 100.76 ? O3A 08T 903 D 1 HETATM 23 O O3B 08T . . . Y 4 181.071 147.795 115.619 1 108.28 ? O3B 08T 903 D 1 HETATM 24 F F3 08T . . . Y 4 181.155 149.948 117.043 1 114.74 ? F3 08T 903 D 1 HETATM 25 C C4 08T . . . Y 4 178.223 146.168 107.396 1 98.39 ? C4 08T 903 D 1 HETATM 26 C C5 08T . . . Y 4 179.075 145.151 107.795 1 99.55 ? C5 08T 903 D 1 HETATM 27 C C6 08T . . . Y 4 178.94 143.914 107.136 1 104.19 ? C6 08T 903 D 1 HETATM 28 N N6 08T . . . Y 4 179.687 142.84 107.411 1 108.9 ? N6 08T 903 D 1 HETATM 29 N N7 08T . . . Y 4 179.918 145.586 108.805 1 100.42 ? N7 08T 903 D 1 HETATM 30 C C8 08T . . . Y 4 179.561 146.833 108.991 1 99.4 ? C8 08T 903 D 1 HETATM 31 N N9 08T . . . Y 4 178.547 147.253 108.171 1 97.48 ? N9 08T 903 D 1 HETATM 32 H H1 08T . . . Y 4 179.07 150.193 111.649 1 106.69 ? H1 08T 903 D 1 HETATM 33 H H2 08T . . . Y 4 177.504 150.107 112.331 1 106.6 ? H2 08T 903 D 1 HETATM 34 H H3 08T . . . Y 4 177.149 150.716 109.979 1 106.35 ? H3 08T 903 D 1 HETATM 35 H H4 08T . . . Y 4 176.617 147.692 110.416 1 104.18 ? H4 08T 903 D 1 HETATM 36 H H6 08T . . . Y 4 176.011 147.563 108.081 1 103.9 ? H6 08T 903 D 1 HETATM 37 H H7 08T . . . Y 4 175.133 149.516 107.101 1 110.57 ? H7 08T 903 D 1 HETATM 38 H H8 08T . . . Y 4 178.142 149.051 107.146 1 108.04 ? H8 08T 903 D 1 HETATM 39 H H10 08T . . . Y 4 176.499 144.743 105.097 1 107.92 ? H10 08T 903 D 1 HETATM 40 H H12 08T . . . Y 4 179.566 142.155 108.155 1 107.6 ? H12 08T 903 D 1 HETATM 41 H H13 08T . . . Y 4 180.484 142.687 106.793 1 108.3 ? H13 08T 903 D 1 HETATM 42 H H14 08T . . . Y 4 180.041 147.49 109.736 1 102.69 ? H14 08T 903 D 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 54 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 42 #