data_8V5R # _model_server_result.job_id P15MmglgVjVfvTlOeAC7EQ _model_server_result.datetime_utc '2025-03-05 22:28:22' _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 8v5r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1302}' # _entry.id 8V5R # _exptl.entry_id 8V5R _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 466.169 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE" _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 8V5R _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8V5R _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 6 _struct_asym.id G _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 covale ? covale1 D O3' DA 50 P DA 23 1_555 D P 2DT 51 P 2DT 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.607 ? metalc ? metalc1 A O VAL 881 A VAL 891 1_555 F MG MG . A MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc2 A OD2 ASP 1125 A ASP 1135 1_555 F MG MG . A MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc3 F MG MG . A MG 1301 1_555 G O1A D3T . A D3T 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? metalc ? metalc4 F MG MG . A MG 1301 1_555 G O1G D3T . A D3T 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc5 F MG MG . A MG 1301 1_555 G O1B D3T . A D3T 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? hydrog WATSON-CRICK hydrog1 D N3 DT 32 P DT 5 1_555 E N1 DA 49 T DA 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 D O4 DT 32 P DT 5 1_555 E N6 DA 49 T DA 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 D N3 DT 33 P DT 6 1_555 E N1 DA 48 T DA 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 D O4 DT 33 P DT 6 1_555 E N6 DA 48 T DA 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 D N3 DT 34 P DT 7 1_555 E N1 DA 47 T DA 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 D O4 DT 34 P DT 7 1_555 E N6 DA 47 T DA 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 D N1 DA 35 P DA 8 1_555 E N3 DT 46 T DT 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 D N6 DA 35 P DA 8 1_555 E O4 DT 46 T DT 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 D N3 DT 36 P DT 9 1_555 E N1 DA 45 T DA 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 D O4 DT 36 P DT 9 1_555 E N6 DA 45 T DA 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 D N1 DG 37 P DG 10 1_555 E N3 DC 44 T DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 D N2 DG 37 P DG 10 1_555 E O2 DC 44 T DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 D O6 DG 37 P DG 10 1_555 E N4 DC 44 T DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 D N1 DG 38 P DG 11 1_555 E N3 DC 43 T DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 D N2 DG 38 P DG 11 1_555 E O2 DC 43 T DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 D O6 DG 38 P DG 11 1_555 E N4 DC 43 T DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 D N3 DT 39 P DT 12 1_555 E N1 DA 42 T DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 D O4 DT 39 P DT 12 1_555 E N6 DA 42 T DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 D N1 DA 40 P DA 13 1_555 E N3 DT 41 T DT 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 D N6 DA 40 P DA 13 1_555 E O4 DT 41 T DT 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 D N3 DC 41 P DC 14 1_555 E N1 DG 40 T DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 D N4 DC 41 P DC 14 1_555 E O6 DG 40 T DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 D O2 DC 41 P DC 14 1_555 E N2 DG 40 T DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 D N3 DC 42 P DC 15 1_555 E N1 DG 39 T DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 D N4 DC 42 P DC 15 1_555 E O6 DG 39 T DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 D O2 DC 42 P DC 15 1_555 E N2 DG 39 T DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 D N1 DG 43 P DG 16 1_555 E N3 DC 38 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 D N2 DG 43 P DG 16 1_555 E O2 DC 38 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 D O6 DG 43 P DG 16 1_555 E N4 DC 38 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 D N3 DT 44 P DT 17 1_555 E N1 DA 37 T DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 D O4 DT 44 P DT 17 1_555 E N6 DA 37 T DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 D N1 DA 45 P DA 18 1_555 E N3 DT 36 T DT 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 D N6 DA 45 P DA 18 1_555 E O4 DT 36 T DT 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 D N3 DC 46 P DC 19 1_555 E N1 DG 35 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 D N4 DC 46 P DC 19 1_555 E O6 DG 35 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 D O2 DC 46 P DC 19 1_555 E N2 DG 35 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 D N1 DA 47 P DA 20 1_555 E N3 DT 34 T DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 D N6 DA 47 P DA 20 1_555 E O4 DT 34 T DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 D N1 DA 48 P DA 21 1_555 E N3 DT 33 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 D N6 DA 48 P DA 21 1_555 E O4 DT 33 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 D N3 DT 49 P DT 22 1_555 E N1 DA 32 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 D O4 DT 49 P DT 22 1_555 E N6 DA 32 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 D N1 DA 50 P DA 23 1_555 E N3 DT 31 T DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 D N6 DA 50 P DA 23 1_555 E O4 DT 31 T DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 D N3 2DT 51 P 2DT 24 1_555 E N1 DA 30 T DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 D O4 2DT 51 P 2DT 24 1_555 E N6 DA 30 T DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H17 N2 O13 P3' _chem_comp.formula_weight 466.169 _chem_comp.id D3T _chem_comp.mon_nstd_flag n _chem_comp.name "2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE" _chem_comp.type 'dna oh 3 prime terminus' _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 PA O1A D3T doub 119 n n PA O2A D3T sing 120 n n PA O5' D3T sing 121 n n PA O3A D3T sing 122 n n O2A HOA2 D3T sing 123 n n O5' C5' D3T sing 124 n n C5' C4' D3T sing 125 n n C5' "H5'1" D3T sing 126 n n C5' "H5'2" D3T sing 127 n n C4' O4' D3T sing 128 n n C4' C3' D3T sing 129 n n C4' H4' D3T sing 130 n n O4' C1' D3T sing 131 n n C1' N1 D3T sing 132 n n C1' C2' D3T sing 133 n n C1' H1' D3T sing 134 n n N1 C6 D3T sing 135 n n N1 C2 D3T sing 136 n n C6 C5 D3T doub 137 n n C6 H6 D3T sing 138 n n C2 O2 D3T doub 139 n n C2 N3 D3T sing 140 n n N3 C4 D3T sing 141 n n N3 HN3 D3T sing 142 n n C4 O4 D3T doub 143 n n C4 C5 D3T sing 144 n n C5 C5M D3T sing 145 n n C5M H5M1 D3T sing 146 n n C5M H5M2 D3T sing 147 n n C5M H5M3 D3T sing 148 n n C2' C3' D3T sing 149 n n C2' "H2'1" D3T sing 150 n n C2' "H2'2" D3T sing 151 n n C3' "H3'1" D3T sing 152 n n C3' "H3'2" D3T sing 153 n n O3A PB D3T sing 154 n n PB O1B D3T doub 155 n n PB O2B D3T sing 156 n n PB O3B D3T sing 157 n n O2B HOB2 D3T sing 158 n n O3B PG D3T sing 159 n n PG O1G D3T doub 160 n n PG O2G D3T sing 161 n n PG O3G D3T sing 162 n n O3G HOG3 D3T sing 163 n n HO1 O2G D3T sing 164 n n # _atom_sites.entry_id 8V5R _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 F 5 MG A 1 1301 1 MG MG . G 6 D3T A 1 1302 2 D3T 23T . # 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 D3T . . . G 6 139.419 125.166 159.673 1 46.59 ? PA D3T 1302 A 1 HETATM 2 O O1A D3T . . . G 6 139.317 126.54 159.059 1 46.59 ? O1A D3T 1302 A 1 HETATM 3 O O2A D3T . . . G 6 138.514 124.215 158.926 1 46.59 ? O2A D3T 1302 A 1 HETATM 4 O O5' D3T . . . G 6 138.976 125.228 161.22 1 46.59 ? O5' D3T 1302 A 1 HETATM 5 C C5' D3T . . . G 6 137.642 125.74 161.253 1 46.59 ? C5' D3T 1302 A 1 HETATM 6 C C4' D3T . . . G 6 136.719 124.71 161.903 1 46.59 ? C4' D3T 1302 A 1 HETATM 7 O O4' D3T . . . G 6 136.249 123.76 160.921 1 46.59 ? O4' D3T 1302 A 1 HETATM 8 C C1' D3T . . . G 6 135.84 122.581 161.628 1 46.59 ? C1' D3T 1302 A 1 HETATM 9 N N1 D3T . . . G 6 136.101 121.408 160.791 1 46.59 ? N1 D3T 1302 A 1 HETATM 10 C C6 D3T . . . G 6 136.826 121.558 159.679 1 46.59 ? C6 D3T 1302 A 1 HETATM 11 C C2 D3T . . . G 6 135.587 120.144 161.16 1 46.59 ? C2 D3T 1302 A 1 HETATM 12 O O2 D3T . . . G 6 134.909 120.028 162.203 1 46.59 ? O2 D3T 1302 A 1 HETATM 13 N N3 D3T . . . G 6 135.814 119.059 160.408 1 46.59 ? N3 D3T 1302 A 1 HETATM 14 C C4 D3T . . . G 6 136.533 119.142 159.286 1 46.59 ? C4 D3T 1302 A 1 HETATM 15 O O4 D3T . . . G 6 136.739 118.125 158.591 1 46.59 ? O4 D3T 1302 A 1 HETATM 16 C C5 D3T . . . G 6 137.081 120.457 158.878 1 46.59 ? C5 D3T 1302 A 1 HETATM 17 C C5M D3T . . . G 6 137.897 120.593 157.621 1 46.59 ? C5M D3T 1302 A 1 HETATM 18 C C2' D3T . . . G 6 136.687 122.522 162.912 1 46.59 ? C2' D3T 1302 A 1 HETATM 19 C C3' D3T . . . G 6 137.505 123.834 162.911 1 46.59 ? C3' D3T 1302 A 1 HETATM 20 O O3A D3T . . . G 6 140.939 124.646 159.574 1 46.59 ? O3A D3T 1302 A 1 HETATM 21 P PB D3T . . . G 6 142.061 125.189 160.593 1 46.59 ? PB D3T 1302 A 1 HETATM 22 O O1B D3T . . . G 6 141.609 126.47 161.253 1 46.59 ? O1B D3T 1302 A 1 HETATM 23 O O2B D3T . . . G 6 142.39 124.139 161.627 1 46.59 ? O2B D3T 1302 A 1 HETATM 24 O O3B D3T . . . G 6 143.328 125.456 159.636 1 46.59 ? O3B D3T 1302 A 1 HETATM 25 P PG D3T . . . G 6 144.016 126.908 159.557 1 46.59 ? PG D3T 1302 A 1 HETATM 26 O O1G D3T . . . G 6 142.976 127.945 159.208 1 46.59 ? O1G D3T 1302 A 1 HETATM 27 O O2G D3T . . . G 6 145.089 126.899 158.494 1 46.59 ? O2G D3T 1302 A 1 HETATM 28 O O3G D3T . . . G 6 144.638 127.24 160.892 1 46.59 ? O3G D3T 1302 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #