data_8D9D # _model_server_result.job_id Q0B2MGMqrpuT5vPbGeWUOQ _model_server_result.datetime_utc '2024-11-22 21:56:26' _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 8d9d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1504}' # _entry.id 8D9D # _exptl.entry_id 8D9D _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 491.182 _entity.id 10 _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 8D9D _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8D9D _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 10 _struct_asym.id L _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 E O3' GTP 1 E GTP 1 1_555 E P G 2 E G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? metalc ? metalc1 A SG CYS 121 A CYS 121 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc2 A SG CYS 122 A CYS 122 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc3 A SG CYS 128 A CYS 128 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc4 A SG CYS 131 A CYS 131 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc5 B SG CYS 287 B CYS 287 1_555 H FE4 SF4 . B SF4 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc6 B SG CYS 367 B CYS 367 1_555 H FE1 SF4 . B SF4 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc7 B SG CYS 384 B CYS 384 1_555 H FE2 SF4 . B SF4 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc8 B SG CYS 424 B CYS 424 1_555 H FE3 SF4 . B SF4 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc9 C OD2 ASP 860 C ASP 860 1_555 I MG MG . C MG 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc10 C O PHE 861 C PHE 861 1_555 I MG MG . C MG 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc11 C OD1 ASP 1004 C ASP 1004 1_555 I MG MG . C MG 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc12 C SG CYS 1283 C CYS 1283 1_555 J ZN ZN . C ZN 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc13 C SG CYS 1286 C CYS 1286 1_555 J ZN ZN . C ZN 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc14 C SG CYS 1310 C CYS 1310 1_555 J ZN ZN . C ZN 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc15 C SG CYS 1315 C CYS 1315 1_555 J ZN ZN . C ZN 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc16 C SG CYS 1348 C CYS 1348 1_555 K ZN ZN . C ZN 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc17 C SG CYS 1353 C CYS 1353 1_555 K ZN ZN . C ZN 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc18 C SG CYS 1371 C CYS 1371 1_555 K ZN ZN . C ZN 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc19 C SG CYS 1374 C CYS 1374 1_555 K ZN ZN . C ZN 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc20 I MG MG . C MG 1501 1_555 L O2B DTP . C DTP 1504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc21 E O1G GTP 1 E GTP 1 1_555 M MG MG . E MG 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.767 ? metalc ? metalc22 E O1A GTP 1 E GTP 1 1_555 M MG MG . E MG 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.838 ? hydrog 'GTP-DC MISPAIR' hydrog1 E O6 GTP 1 E GTP 1 1_555 F N4 DC 14 F DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 E N1 G 2 E G 2 1_555 F N3 DC 13 F DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 E N2 G 2 E G 2 1_555 F O2 DC 13 F DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 E O6 G 2 E G 2 1_555 F N4 DC 13 F DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-DG PAIR' hydrog5 E N4 C 3 E C 3 1_555 F O6 DG 12 F DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-DC PAIR' hydrog6 E N1 G 4 E G 4 1_555 F O2 DC 11 F DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 E N1 G 5 E G 5 1_555 F N3 DC 10 F DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 E N2 G 5 E G 5 1_555 F O2 DC 10 F DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 E O6 G 5 E G 5 1_555 F N4 DC 10 F DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 E N3 C 6 E C 6 1_555 F N1 DG 9 F DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 E N4 C 6 E C 6 1_555 F O6 DG 9 F DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 E O2 C 6 E C 6 1_555 F N2 DG 9 F DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-DT PAIR' hydrog13 E N1 A 7 E A 7 1_555 F N3 DT 8 F DT 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 E N3 C 8 E C 8 1_555 F N1 DG 7 F DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 E N4 C 8 E C 8 1_555 F O6 DG 7 F DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 E O2 C 8 E C 8 1_555 F N2 DG 7 F DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-DC PAIR' hydrog17 E N2 G 9 E G 9 1_555 F O2 DC 6 F DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 E N1 DA 10 E DA 10 1_555 F N3 DT 5 F DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 E N6 DA 10 E DA 10 1_555 F O4 DT 5 F DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 E N3 DC 11 E DC 11 1_555 F N1 DG 4 F DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 E N4 DC 11 E DC 11 1_555 F O6 DG 4 F DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 E O2 DC 11 E DC 11 1_555 F N2 DG 4 F DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 E N3 DC 12 E DC 12 1_555 F N1 DG 3 F DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 E N4 DC 12 E DC 12 1_555 F O6 DG 3 F DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 E O2 DC 12 E DC 12 1_555 F N2 DG 3 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 8D9D _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 G 7 ZN A 1 501 501 ZN ZN . H 8 SF4 B 1 601 501 SF4 SF4 . I 9 MG C 1 1501 1501 MG MG . J 7 ZN C 1 1502 1502 ZN ZN . K 7 ZN C 1 1503 1503 ZN ZN . L 10 DTP C 1 1504 1 DTP DTP . M 9 MG E 1 101 101 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 . . . L 10 128.08 164.465 115.563 1 75.51 ? PG DTP 1504 C 1 HETATM 2 O O1G DTP . . . L 10 128.91 163.299 115.149 1 75.51 ? O1G DTP 1504 C 1 HETATM 3 O O2G DTP . . . L 10 126.851 164.69 114.68 1 75.51 ? O2G DTP 1504 C 1 HETATM 4 O O3G DTP . . . L 10 127.639 164.416 117.028 1 75.51 ? O3G DTP 1504 C 1 HETATM 5 P PB DTP . . . L 10 130.391 166.351 115.649 1 75.51 ? PB DTP 1504 C 1 HETATM 6 O O1B DTP . . . L 10 131.096 166.543 114.368 1 75.51 ? O1B DTP 1504 C 1 HETATM 7 O O2B DTP . . . L 10 130.308 167.575 116.56 1 75.51 ? O2B DTP 1504 C 1 HETATM 8 O O3B DTP . . . L 10 128.914 165.819 115.443 1 75.51 ? O3B DTP 1504 C 1 HETATM 9 P PA DTP . . . L 10 132.161 165.024 117.607 1 75.51 ? PA DTP 1504 C 1 HETATM 10 O O1A DTP . . . L 10 131.682 165.466 118.932 1 75.51 ? O1A DTP 1504 C 1 HETATM 11 O O2A DTP . . . L 10 132.644 163.575 117.557 1 75.51 ? O2A DTP 1504 C 1 HETATM 12 O O3A DTP . . . L 10 131.033 165.172 116.504 1 75.51 ? O3A DTP 1504 C 1 HETATM 13 O O5' DTP . . . L 10 133.315 165.953 117.061 1 75.51 ? O5' DTP 1504 C 1 HETATM 14 C C5' DTP . . . L 10 133.433 167.327 117.484 1 75.51 ? C5' DTP 1504 C 1 HETATM 15 C C4' DTP . . . L 10 134.47 167.999 116.624 1 75.51 ? C4' DTP 1504 C 1 HETATM 16 O O4' DTP . . . L 10 135.753 167.376 116.84 1 75.51 ? O4' DTP 1504 C 1 HETATM 17 C C3' DTP . . . L 10 134.215 167.897 115.125 1 75.51 ? C3' DTP 1504 C 1 HETATM 18 O O3' DTP . . . L 10 133.429 169.004 114.682 1 75.51 ? O3' DTP 1504 C 1 HETATM 19 C C2' DTP . . . L 10 135.622 167.969 114.552 1 75.51 ? C2' DTP 1504 C 1 HETATM 20 C C1' DTP . . . L 10 136.466 167.28 115.616 1 75.51 ? C1' DTP 1504 C 1 HETATM 21 N N9 DTP . . . L 10 136.746 165.874 115.36 1 75.51 ? N9 DTP 1504 C 1 HETATM 22 C C8 DTP . . . L 10 136.179 164.789 115.976 1 75.51 ? C8 DTP 1504 C 1 HETATM 23 N N7 DTP . . . L 10 136.626 163.634 115.545 1 75.51 ? N7 DTP 1504 C 1 HETATM 24 C C5 DTP . . . L 10 137.556 163.983 114.577 1 75.51 ? C5 DTP 1504 C 1 HETATM 25 C C6 DTP . . . L 10 138.387 163.217 113.739 1 75.51 ? C6 DTP 1504 C 1 HETATM 26 N N6 DTP . . . L 10 138.419 161.881 113.742 1 75.51 ? N6 DTP 1504 C 1 HETATM 27 N N1 DTP . . . L 10 139.198 163.878 112.885 1 75.51 ? N1 DTP 1504 C 1 HETATM 28 C C2 DTP . . . L 10 139.173 165.213 112.877 1 75.51 ? C2 DTP 1504 C 1 HETATM 29 N N3 DTP . . . L 10 138.433 166.04 113.619 1 75.51 ? N3 DTP 1504 C 1 HETATM 30 C C4 DTP . . . L 10 137.641 165.36 114.454 1 75.51 ? C4 DTP 1504 C 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 30 #