data_8D96 # _model_server_result.job_id cyFmSH2MK073sM5uY1HXBA _model_server_result.datetime_utc '2024-10-26 14:22:50' _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 8d96 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1501}' # _entry.id 8D96 # _exptl.entry_id 8D96 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 491.182 _entity.id 7 _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 8D96 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8D96 _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 7 _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 C O3' GTP 1 E GTP 1 1_555 C P G 2 E G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? metalc ? metalc1 A SG CYS 287 B CYS 287 1_555 E FE4 SF4 . B SF4 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc2 A OH TYR 345 B TYR 345 1_555 F MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.916 ? metalc ? metalc3 A SG CYS 367 B CYS 367 1_555 E FE1 SF4 . B SF4 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc4 A SG CYS 384 B CYS 384 1_555 E FE2 SF4 . B SF4 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc5 A SG CYS 424 B CYS 424 1_555 E FE3 SF4 . B SF4 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc6 F MG MG . B MG 602 1_555 C O1G GTP 1 E GTP 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.767 ? metalc ? metalc7 F MG MG . B MG 602 1_555 C O1A GTP 1 E GTP 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.838 ? hydrog 'GTP-DC MISPAIR' hydrog1 C O6 GTP 1 E GTP 1 1_555 D N4 DC 17 F DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 C N1 G 2 E G 2 1_555 D N3 DC 16 F DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 C N2 G 2 E G 2 1_555 D O2 DC 16 F DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C O6 G 2 E G 2 1_555 D N4 DC 16 F DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-DG PAIR' hydrog5 C N4 C 3 E C 3 1_555 D O6 DG 15 F DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-DC PAIR' hydrog6 C N1 G 4 E G 4 1_555 D O2 DC 14 F DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 C N1 G 5 E G 5 1_555 D N3 DC 13 F DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 C N2 G 5 E G 5 1_555 D O2 DC 13 F DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C O6 G 5 E G 5 1_555 D N4 DC 13 F DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C N3 C 6 E C 6 1_555 D N1 DG 12 F DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C N4 C 6 E C 6 1_555 D O6 DG 12 F DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C O2 C 6 E C 6 1_555 D N2 DG 12 F DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-DT PAIR' hydrog13 C N1 A 7 E A 7 1_555 D N3 DT 11 F DT 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 C N3 C 8 E C 8 1_555 D N1 DG 10 F DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C N4 C 8 E C 8 1_555 D O6 DG 10 F DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 C O2 C 8 E C 8 1_555 D N2 DG 10 F DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-DC PAIR' hydrog17 C N2 G 9 E G 9 1_555 D O2 DC 9 F DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 C N1 DA 10 E DA 10 1_555 D N3 DT 8 F DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 C N6 DA 10 E DA 10 1_555 D O4 DT 8 F DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 C N3 DC 11 E DC 11 1_555 D N1 DG 7 F DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 C N4 DC 11 E DC 11 1_555 D O6 DG 7 F DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 C O2 DC 11 E DC 11 1_555 D N2 DG 7 F DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 C N3 DC 12 E DC 12 1_555 D N1 DG 6 F DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 C N4 DC 12 E DC 12 1_555 D O6 DG 6 F DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 C O2 DC 12 E DC 12 1_555 D N2 DG 6 F DG 6 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 307 n n PG O2G DTP sing 308 n n PG O3G DTP sing 309 n n PG O3B DTP sing 310 n n O2G HOG2 DTP sing 311 n n O3G HOG3 DTP sing 312 n n PB O1B DTP doub 313 n n PB O2B DTP sing 314 n n PB O3B DTP sing 315 n n PB O3A DTP sing 316 n n O2B HOB2 DTP sing 317 n n PA O1A DTP doub 318 n n PA O2A DTP sing 319 n n PA O3A DTP sing 320 n n PA O5' DTP sing 321 n n O2A HOA2 DTP sing 322 n n O5' C5' DTP sing 323 n n C5' C4' DTP sing 324 n n C5' "H5'1" DTP sing 325 n n C5' "H5'2" DTP sing 326 n n C4' O4' DTP sing 327 n n C4' C3' DTP sing 328 n n C4' H4' DTP sing 329 n n O4' C1' DTP sing 330 n n C3' O3' DTP sing 331 n n C3' C2' DTP sing 332 n n C3' H3' DTP sing 333 n n O3' HO3' DTP sing 334 n n C2' C1' DTP sing 335 n n C2' "H2'1" DTP sing 336 n n C2' "H2'2" DTP sing 337 n n C1' N9 DTP sing 338 n n C1' H1' DTP sing 339 n n N9 C8 DTP sing 340 n y N9 C4 DTP sing 341 n y C8 N7 DTP doub 342 n y C8 H8 DTP sing 343 n n N7 C5 DTP sing 344 n y C5 C6 DTP sing 345 n y C5 C4 DTP doub 346 n y C6 N6 DTP sing 347 n n C6 N1 DTP doub 348 n y N6 HN61 DTP sing 349 n n N6 HN62 DTP sing 350 n n N1 C2 DTP sing 351 n y C2 N3 DTP doub 352 n y C2 H2 DTP sing 353 n n N3 C4 DTP sing 354 n y # _atom_sites.entry_id 8D96 _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 E 5 SF4 B 1 601 501 SF4 SF4 . F 6 MG B 1 602 101 MG MG . G 7 DTP C 1 1501 1 DTP DTP . # 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 . . . G 7 134.956 168.144 103.925 1 75.51 ? PG DTP 1501 C 1 HETATM 2 O O1G DTP . . . G 7 135.833 166.943 103.837 1 75.51 ? O1G DTP 1501 C 1 HETATM 3 O O2G DTP . . . G 7 133.873 168.196 102.846 1 75.51 ? O2G DTP 1501 C 1 HETATM 4 O O3G DTP . . . G 7 134.302 168.328 105.297 1 75.51 ? O3G DTP 1501 C 1 HETATM 5 P PB DTP . . . G 7 137.237 170.065 104.037 1 75.51 ? PB DTP 1501 C 1 HETATM 6 O O1B DTP . . . G 7 138.126 170.058 102.86 1 75.51 ? O1B DTP 1501 C 1 HETATM 7 O O2B DTP . . . G 7 137.025 171.42 104.711 1 75.51 ? O2B DTP 1501 C 1 HETATM 8 O O3B DTP . . . G 7 135.805 169.477 103.707 1 75.51 ? O3B DTP 1501 C 1 HETATM 9 P PA DTP . . . G 7 138.69 169.114 106.427 1 75.51 ? PA DTP 1501 C 1 HETATM 10 O O1A DTP . . . G 7 138.022 169.758 107.576 1 75.51 ? O1A DTP 1501 C 1 HETATM 11 O O2A DTP . . . G 7 139.169 167.686 106.69 1 75.51 ? O2A DTP 1501 C 1 HETATM 12 O O3A DTP . . . G 7 137.74 169.056 105.161 1 75.51 ? O3A DTP 1501 C 1 HETATM 13 O O5' DTP . . . G 7 139.917 169.963 105.911 1 75.51 ? O5' DTP 1501 C 1 HETATM 14 C C5' DTP . . . G 7 139.977 171.39 106.114 1 75.51 ? C5' DTP 1501 C 1 HETATM 15 C C4' DTP . . . G 7 141.134 171.932 105.317 1 75.51 ? C4' DTP 1501 C 1 HETATM 16 O O4' DTP . . . G 7 142.367 171.379 105.819 1 75.51 ? O4' DTP 1501 C 1 HETATM 17 C C3' DTP . . . G 7 141.104 171.58 103.834 1 75.51 ? C3' DTP 1501 C 1 HETATM 18 O O3' DTP . . . G 7 140.398 172.583 103.103 1 75.51 ? O3' DTP 1501 C 1 HETATM 19 C C2' DTP . . . G 7 142.581 171.585 103.471 1 75.51 ? C2' DTP 1501 C 1 HETATM 20 C C1' DTP . . . G 7 143.254 171.098 104.747 1 75.51 ? C1' DTP 1501 C 1 HETATM 21 N N9 DTP . . . G 7 143.562 169.675 104.771 1 75.51 ? N9 DTP 1501 C 1 HETATM 22 C C8 DTP . . . G 7 142.905 168.695 105.468 1 75.51 ? C8 DTP 1501 C 1 HETATM 23 N N7 DTP . . . G 7 143.406 167.494 105.305 1 75.51 ? N7 DTP 1501 C 1 HETATM 24 C C5 DTP . . . G 7 144.471 167.697 104.44 1 75.51 ? C5 DTP 1501 C 1 HETATM 25 C C6 DTP . . . G 7 145.414 166.821 103.873 1 75.51 ? C6 DTP 1501 C 1 HETATM 26 N N6 DTP . . . G 7 145.439 165.505 104.101 1 75.51 ? N6 DTP 1501 C 1 HETATM 27 N N1 DTP . . . G 7 146.346 167.349 103.05 1 75.51 ? N1 DTP 1501 C 1 HETATM 28 C C2 DTP . . . G 7 146.329 168.663 102.817 1 75.51 ? C2 DTP 1501 C 1 HETATM 29 N N3 DTP . . . G 7 145.49 169.586 103.295 1 75.51 ? N3 DTP 1501 C 1 HETATM 30 C C4 DTP . . . G 7 144.58 169.037 104.105 1 75.51 ? C4 DTP 1501 C 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 53 _model_server_stats.query_time_ms 364 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 30 #