data_9D6O # _model_server_result.job_id fA_Rp7ob7-wQzUuJtaAgpg _model_server_result.datetime_utc '2025-08-21 21:32:32' _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 9d6o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":2602}' # _entry.id 9D6O # _exptl.entry_id 9D6O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 491.182 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-3'-DIDEOXYGUANOSINE-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 120 _cell.entry_id 9D6O _cell.length_a 172.356 _cell.length_b 172.356 _cell.length_c 62.415 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9D6O _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_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 x,y,z _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 5 _struct_asym.id E _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 metalc ? metalc1 A OD1 ASP 401 A ASP 2330 1_555 D MG MG . A MG 2601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? metalc ? metalc2 A OD2 ASP 401 A ASP 2330 1_555 D MG MG . A MG 2601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.906 ? metalc ? metalc3 A OD2 ASP 602 A ASP 2540 1_555 D MG MG . A MG 2601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc4 D MG MG . A MG 2601 1_555 E O2B DG3 . A DG3 2602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc5 D MG MG . A MG 2601 1_555 E O3B DG3 . A DG3 2602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? hydrog WATSON-CRICK hydrog1 B N1 DG 11 E DG 11 1_555 C N3 DC 14 F DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 11 E DG 11 1_555 C O2 DC 14 F DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 11 E DG 11 1_555 C N4 DC 14 F DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DC 12 E DC 12 1_555 C N1 DG 13 F DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N4 DC 12 E DC 12 1_555 C O6 DG 13 F DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O2 DC 12 E DC 12 1_555 C N2 DG 13 F DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N1 DG 13 E DG 13 1_555 C N3 DC 12 F DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N2 DG 13 E DG 13 1_555 C O2 DC 12 F DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O6 DG 13 E DG 13 1_555 C N4 DC 12 F DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N3 DC 14 E DC 14 1_555 C N1 DG 11 F DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N4 DC 14 E DC 14 1_555 C O6 DG 11 F DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B O2 DC 14 E DC 14 1_555 C N2 DG 11 F DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N3 DT 15 E DT 15 1_555 C N1 DA 10 F DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O4 DT 15 E DT 15 1_555 C N6 DA 10 F DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N1 DG 16 E DG 16 1_555 C N3 DC 9 F DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N2 DG 16 E DG 16 1_555 C O2 DC 9 F DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B O6 DG 16 E DG 16 1_555 C N4 DC 9 F DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N3 DC 17 E DC 17 1_555 C N1 DG 8 F DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N4 DC 17 E DC 17 1_555 C O6 DG 8 F DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O2 DC 17 E DC 17 1_555 C N2 DG 8 F DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N1 DG 18 E DG 18 1_555 C N3 DC 7 F DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N2 DG 18 E DG 18 1_555 C O2 DC 7 F DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O6 DG 18 E DG 18 1_555 C N4 DC 7 F DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N1 DA 19 E DA 19 1_555 C N3 DT 6 F DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N6 DA 19 E DA 19 1_555 C O4 DT 6 F DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H16 N5 O12 P3' _chem_comp.formula_weight 491.182 _chem_comp.id DG3 _chem_comp.mon_nstd_flag . _chem_comp.name "2'-3'-DIDEOXYGUANOSINE-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 DG3 doub 250 n n PG O2G DG3 sing 251 n n PG O3G DG3 sing 252 n n PG O3B DG3 sing 253 n n O2G HOG2 DG3 sing 254 n n O3G HOG3 DG3 sing 255 n n O3B PB DG3 sing 256 n n PB O1B DG3 doub 257 n n PB O2B DG3 sing 258 n n PB O3A DG3 sing 259 n n O2B HOB2 DG3 sing 260 n n O3A PA DG3 sing 261 n n PA O1A DG3 doub 262 n n PA O2A DG3 sing 263 n n PA O5' DG3 sing 264 n n O2A HOA2 DG3 sing 265 n n O5' C5' DG3 sing 266 n n C5' C4' DG3 sing 267 n n C5' "H5'1" DG3 sing 268 n n C5' "H5'2" DG3 sing 269 n n C4' O4' DG3 sing 270 n n C4' C3' DG3 sing 271 n n C4' H4' DG3 sing 272 n n O4' C1' DG3 sing 273 n n C3' C2' DG3 sing 274 n n C3' "H3'1" DG3 sing 275 n n C3' "H3'2" DG3 sing 276 n n C2' C1' DG3 sing 277 n n C2' "H2'1" DG3 sing 278 n n C2' "H2'2" DG3 sing 279 n n C1' N9 DG3 sing 280 n n C1' H1' DG3 sing 281 n n N9 C8 DG3 sing 282 n y N9 C4 DG3 sing 283 n y C8 N7 DG3 doub 284 n y C8 H8 DG3 sing 285 n n N7 C5 DG3 sing 286 n y C5 C6 DG3 sing 287 n n C5 C4 DG3 doub 288 n y C6 O6 DG3 doub 289 n n C6 N1 DG3 sing 290 n n N1 C2 DG3 sing 291 n n N1 HN1 DG3 sing 292 n n C2 N2 DG3 sing 293 n n C2 N3 DG3 doub 294 n n N2 HN21 DG3 sing 295 n n N2 HN22 DG3 sing 296 n n N3 C4 DG3 sing 297 n n # _atom_sites.entry_id 9D6O _atom_sites.fract_transf_matrix[1][1] 0.005802 _atom_sites.fract_transf_matrix[1][2] 0.00335 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0067 _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] 0.016022 _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 MG A 1 2601 2603 MG MG . E 5 DG3 A 1 2602 2604 DG3 DG3 . F 6 A1A2D A 1 2603 2605 A1A2D 161 . # 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 DG3 . . . E 5 67.991 32.368 -2.361 1 134.18 ? PG DG3 2602 A 1 HETATM 2 O O1G DG3 . . . E 5 68.405 32.757 -3.762 1 156.09 ? O1G DG3 2602 A 1 HETATM 3 O O2G DG3 . . . E 5 67.913 30.884 -2.051 1 141.31 ? O2G DG3 2602 A 1 HETATM 4 O O3G DG3 . . . E 5 68.642 33.209 -1.277 1 134.41 ? O3G DG3 2602 A 1 HETATM 5 O O3B DG3 . . . E 5 66.304 32.84 -2.303 1 124.89 ? O3B DG3 2602 A 1 HETATM 6 P PB DG3 . . . E 5 65.036 33.411 -3.073 1 124.49 ? PB DG3 2602 A 1 HETATM 7 O O1B DG3 . . . E 5 65.507 34.443 -4.055 1 123.69 ? O1B DG3 2602 A 1 HETATM 8 O O2B DG3 . . . E 5 64.165 32.325 -3.67 1 142.88 ? O2B DG3 2602 A 1 HETATM 9 O O3A DG3 . . . E 5 64.167 34.135 -1.962 1 134.75 ? O3A DG3 2602 A 1 HETATM 10 P PA DG3 . . . E 5 63.257 34.014 -0.666 1 154.54 ? PA DG3 2602 A 1 HETATM 11 O O1A DG3 . . . E 5 63.531 35.16 0.257 1 115.77 ? O1A DG3 2602 A 1 HETATM 12 O O2A DG3 . . . E 5 63.108 32.597 -0.182 1 161.83 ? O2A DG3 2602 A 1 HETATM 13 O O5' DG3 . . . E 5 61.945 34.525 -1.395 1 110.76 ? O5' DG3 2602 A 1 HETATM 14 C C5' DG3 . . . E 5 61.219 33.578 -2.2 1 133.37 ? C5' DG3 2602 A 1 HETATM 15 C C4' DG3 . . . E 5 60.14 34.287 -3.044 1 113.78 ? C4' DG3 2602 A 1 HETATM 16 O O4' DG3 . . . E 5 59.464 35.244 -2.233 1 120.52 ? O4' DG3 2602 A 1 HETATM 17 C C3' DG3 . . . E 5 60.662 35.041 -4.252 1 113.78 ? C3' DG3 2602 A 1 HETATM 18 C C2' DG3 . . . E 5 59.655 36.163 -4.423 1 126.27 ? C2' DG3 2602 A 1 HETATM 19 C C1' DG3 . . . E 5 59.192 36.399 -2.961 1 130.67 ? C1' DG3 2602 A 1 HETATM 20 N N9 DG3 . . . E 5 59.939 37.536 -2.359 1 117.62 ? N9 DG3 2602 A 1 HETATM 21 C C8 DG3 . . . E 5 60.942 37.555 -1.341 1 111.89 ? C8 DG3 2602 A 1 HETATM 22 N N7 DG3 . . . E 5 61.353 38.837 -1.098 1 112.46 ? N7 DG3 2602 A 1 HETATM 23 C C5 DG3 . . . E 5 60.609 39.634 -1.964 1 134.88 ? C5 DG3 2602 A 1 HETATM 24 C C6 DG3 . . . E 5 60.646 41.07 -2.123 1 140.61 ? C6 DG3 2602 A 1 HETATM 25 O O6 DG3 . . . E 5 61.352 41.835 -1.51 1 139.05 ? O6 DG3 2602 A 1 HETATM 26 N N1 DG3 . . . E 5 59.762 41.501 -3.081 1 129.55 ? N1 DG3 2602 A 1 HETATM 27 C C2 DG3 . . . E 5 58.93 40.66 -3.813 1 134.87 ? C2 DG3 2602 A 1 HETATM 28 N N2 DG3 . . . E 5 58.127 41.246 -4.71 1 127.38 ? N2 DG3 2602 A 1 HETATM 29 N N3 DG3 . . . E 5 58.851 39.324 -3.709 1 149.38 ? N3 DG3 2602 A 1 HETATM 30 C C4 DG3 . . . E 5 59.739 38.85 -2.741 1 139.52 ? C4 DG3 2602 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 30 #