data_8VB8 # _model_server_result.job_id WWK9enwdIlOAdZqeojGiDA _model_server_result.datetime_utc '2025-04-08 07:39:53' _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 8vb8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":701}' # _entry.id 8VB8 # _exptl.entry_id 8VB8 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 491.182 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE 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 8VB8 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VB8 _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 4 _struct_asym.id D _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 C O3' DC 6 F DC 1 1_555 C P OMC 7 F OMC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.601 ? covale ? covale2 C O3' OMC 7 F OMC 2 1_555 C P DC 8 F DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.603 ? covale ? covale3 C O3' DC 8 F DC 3 1_555 C P OMC 9 F OMC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? covale ? covale4 C O3' OMC 9 F OMC 4 1_555 C P DC 10 F DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? metalc ? metalc1 A OD1 ASP 112 A ASP 110 1_555 E MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc2 A OD2 ASP 112 A ASP 110 1_555 F MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc3 A O VAL 113 A VAL 111 1_555 E MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc4 A OD2 ASP 187 A ASP 185 1_555 E MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc5 D O2G DTP . A DTP 701 1_555 E MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? metalc ? metalc6 D O2B DTP . A DTP 701 1_555 E MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc7 D O2A DTP . A DTP 701 1_555 E MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? hydrog WATSON-CRICK hydrog1 C N3 DC 6 F DC 1 1_555 C N1 DG 38 F DG 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 C N4 DC 6 F DC 1 1_555 C O6 DG 38 F DG 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 C O2 DC 6 F DC 1 1_555 C N2 DG 38 F DG 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C N3 OMC 7 F OMC 2 1_555 C N1 DG 37 F DG 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 C N4 OMC 7 F OMC 2 1_555 C O6 DG 37 F DG 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 C O2 OMC 7 F OMC 2 1_555 C N2 DG 37 F DG 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 C N3 DC 8 F DC 3 1_555 C N1 DG 36 F DG 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 C N4 DC 8 F DC 3 1_555 C O6 DG 36 F DG 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C O2 DC 8 F DC 3 1_555 C N2 DG 36 F DG 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C N3 OMC 9 F OMC 4 1_555 C N1 DG 35 F DG 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C N4 OMC 9 F OMC 4 1_555 C O6 DG 35 F DG 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C O2 OMC 9 F OMC 4 1_555 C N2 DG 35 F DG 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 C N3 DC 10 F DC 5 1_555 C N1 DG 34 F DG 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 C N4 DC 10 F DC 5 1_555 C O6 DG 34 F DG 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C O2 DC 10 F DC 5 1_555 C N2 DG 34 F DG 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 C N3 DC 11 F DC 6 1_555 C N1 DG 33 F DG 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 C N4 DC 11 F DC 6 1_555 C O6 DG 33 F DG 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 C O2 DC 11 F DC 6 1_555 C N2 DG 33 F DG 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 C N3 DC 12 F DC 7 1_555 C N1 DG 32 F DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 C N4 DC 12 F DC 7 1_555 C O6 DG 32 F DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 C O2 DC 12 F DC 7 1_555 C N2 DG 32 F DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 C N3 DT 13 F DT 8 1_555 C N1 DA 31 F DA 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 C O4 DT 13 F DT 8 1_555 C N6 DA 31 F DA 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 C N3 DT 14 F DT 9 1_555 C N1 DA 30 F DA 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 C O4 DT 14 F DT 9 1_555 C N6 DA 30 F DA 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 C N3 DC 15 F DC 10 1_555 C N1 DG 29 F DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 C N4 DC 15 F DC 10 1_555 C O6 DG 29 F DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 C O2 DC 15 F DC 10 1_555 C N2 DG 29 F DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 C N1 DG 16 F DG 11 1_555 C N3 DC 28 F DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 C N2 DG 16 F DG 11 1_555 C O2 DC 28 F DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 C O6 DG 16 F DG 11 1_555 C N4 DC 28 F DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 C N1 DG 17 F DG 12 1_555 C N3 DC 27 F DC 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 C N2 DG 17 F DG 12 1_555 C O2 DC 27 F DC 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 C O6 DG 17 F DG 12 1_555 C N4 DC 27 F DC 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 C N3 DT 18 F DT 13 1_555 C N1 DA 26 F DA 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 C O4 DT 18 F DT 13 1_555 C N6 DA 26 F DA 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 C N1 DG 19 F DG 14 1_555 C N3 DC 25 F DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 C N2 DG 19 F DG 14 1_555 C O2 DC 25 F DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 C O6 DG 19 F DG 14 1_555 C N4 DC 25 F DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 C N3 DC 20 F DC 15 1_555 C N1 DG 24 F DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 C N4 DC 20 F DC 15 1_555 C O6 DG 24 F DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 C O2 DC 20 F DC 15 1_555 C N2 DG 24 F DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H16 N5 O12 P3' _chem_comp.formula_weight 491.182 _chem_comp.id DTP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE 5'-TRIPHOSPHATE" _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 PG O1G DTP doub 232 n n PG O2G DTP sing 233 n n PG O3G DTP sing 234 n n PG O3B DTP sing 235 n n O2G HOG2 DTP sing 236 n n O3G HOG3 DTP sing 237 n n PB O1B DTP doub 238 n n PB O2B DTP sing 239 n n PB O3B DTP sing 240 n n PB O3A DTP sing 241 n n O2B HOB2 DTP sing 242 n n PA O1A DTP doub 243 n n PA O2A DTP sing 244 n n PA O3A DTP sing 245 n n PA O5' DTP sing 246 n n O2A HOA2 DTP sing 247 n n O5' C5' DTP sing 248 n n C5' C4' DTP sing 249 n n C5' "H5'1" DTP sing 250 n n C5' "H5'2" DTP sing 251 n n C4' O4' DTP sing 252 n n C4' C3' DTP sing 253 n n C4' H4' DTP sing 254 n n O4' C1' DTP sing 255 n n C3' O3' DTP sing 256 n n C3' C2' DTP sing 257 n n C3' H3' DTP sing 258 n n O3' HO3' DTP sing 259 n n C2' C1' DTP sing 260 n n C2' "H2'1" DTP sing 261 n n C2' "H2'2" DTP sing 262 n n C1' N9 DTP sing 263 n n C1' H1' DTP sing 264 n n N9 C8 DTP sing 265 n y N9 C4 DTP sing 266 n y C8 N7 DTP doub 267 n y C8 H8 DTP sing 268 n n N7 C5 DTP sing 269 n y C5 C6 DTP sing 270 n y C5 C4 DTP doub 271 n y C6 N6 DTP sing 272 n n C6 N1 DTP doub 273 n y N6 HN61 DTP sing 274 n n N6 HN62 DTP sing 275 n n N1 C2 DTP sing 276 n y C2 N3 DTP doub 277 n y C2 H2 DTP sing 278 n n N3 C4 DTP sing 279 n y # _atom_sites.entry_id 8VB8 _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 D 4 DTP A 1 701 701 DTP DTP . E 5 MG A 1 702 1 MG MG . F 5 MG A 1 703 2 MG MG . # 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 PG DTP . . . D 4 159.451 157.323 122.649 1 87.17 ? PG DTP 701 A 1 HETATM 2 O O1G DTP . . . D 4 159.483 156.657 121.333 1 76.87 ? O1G DTP 701 A 1 HETATM 3 O O2G DTP . . . D 4 160.603 156.966 123.482 1 81.16 ? O2G DTP 701 A 1 HETATM 4 O O3G DTP . . . D 4 159.286 158.778 122.531 1 78.14 ? O3G DTP 701 A 1 HETATM 5 P PB DTP . . . D 4 157.947 155.953 124.74 1 77.62 ? PB DTP 701 A 1 HETATM 6 O O1B DTP . . . D 4 156.716 155.162 124.585 1 83.2 ? O1B DTP 701 A 1 HETATM 7 O O2B DTP . . . D 4 159.211 155.28 125.022 1 80.8 ? O2B DTP 701 A 1 HETATM 8 O O3B DTP . . . D 4 158.171 156.822 123.431 1 71.07 ? O3B DTP 701 A 1 HETATM 9 P PA DTP . . . D 4 158.551 157.708 127.032 1 81.46 ? PA DTP 701 A 1 HETATM 10 O O1A DTP . . . D 4 158.316 159.167 127.042 1 84.31 ? O1A DTP 701 A 1 HETATM 11 O O2A DTP . . . D 4 159.956 157.299 126.874 1 71.6 ? O2A DTP 701 A 1 HETATM 12 O O3A DTP . . . D 4 157.681 157.022 125.889 1 66.52 ? O3A DTP 701 A 1 HETATM 13 O O5' DTP . . . D 4 157.979 157.053 128.36 1 77.62 ? O5' DTP 701 A 1 HETATM 14 C C5' DTP . . . D 4 158.217 155.66 128.629 1 73.41 ? C5' DTP 701 A 1 HETATM 15 C C4' DTP . . . D 4 156.924 155.027 129.052 1 67.89 ? C4' DTP 701 A 1 HETATM 16 O O4' DTP . . . D 4 156.39 155.812 130.124 1 71.92 ? O4' DTP 701 A 1 HETATM 17 C C3' DTP . . . D 4 155.851 155.105 127.992 1 69.51 ? C3' DTP 701 A 1 HETATM 18 O O3' DTP . . . D 4 155.936 154.005 127.103 1 77.34 ? O3' DTP 701 A 1 HETATM 19 C C2' DTP . . . D 4 154.587 155.039 128.827 1 72.69 ? C2' DTP 701 A 1 HETATM 20 C C1' DTP . . . D 4 154.974 155.758 130.098 1 70.44 ? C1' DTP 701 A 1 HETATM 21 N N9 DTP . . . D 4 154.505 157.086 130.088 1 67.34 ? N9 DTP 701 A 1 HETATM 22 C C8 DTP . . . D 4 155.234 158.203 129.914 1 73.04 ? C8 DTP 701 A 1 HETATM 23 N N7 DTP . . . D 4 154.507 159.289 129.935 1 71.09 ? N7 DTP 701 A 1 HETATM 24 C C5 DTP . . . D 4 153.214 158.833 130.127 1 70.55 ? C5 DTP 701 A 1 HETATM 25 C C6 DTP . . . D 4 151.984 159.486 130.234 1 73.24 ? C6 DTP 701 A 1 HETATM 26 N N6 DTP . . . D 4 151.835 160.8 130.153 1 77.89 ? N6 DTP 701 A 1 HETATM 27 N N1 DTP . . . D 4 150.895 158.717 130.407 1 68.75 ? N1 DTP 701 A 1 HETATM 28 C C2 DTP . . . D 4 151.048 157.395 130.479 1 67.84 ? C2 DTP 701 A 1 HETATM 29 N N3 DTP . . . D 4 152.151 156.675 130.401 1 66.8 ? N3 DTP 701 A 1 HETATM 30 C C4 DTP . . . D 4 153.208 157.469 130.22 1 67.97 ? C4 DTP 701 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 30 #