data_6OIW # _model_server_result.job_id Ni21PTUvOwEAkJHWEGHBgw _model_server_result.datetime_utc '2024-11-21 12:50:43' _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 6oiw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":602}' # _entry.id 6OIW # _exptl.entry_id 6OIW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-deoxyguanosine-5'-O-(1-thiotriphosphate)" _entity.pdbx_number_of_molecules 6 _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 6OIW _cell.length_a 191.24 _cell.length_b 191.24 _cell.length_c 298.61 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6OIW _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 I N N ? 4 K N N ? 4 M N N ? 4 O N N ? 4 R N N ? 4 U N 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 NE2 HIS 69 A HIS 69 1_555 H MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc2 A NE2 HIS 117 A HIS 117 1_555 H MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc3 A OD1 ASP 268 A ASP 268 1_555 H MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc4 A OD1 ASP 269 A ASP 269 1_555 G MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.692 ? metalc ? metalc5 G MG MG . A MG 601 1_555 I O2B T8T . A T8T 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc6 B NE2 HIS 117 B HIS 117 1_555 J MN MN . B MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc7 B OD1 ASP 268 B ASP 268 1_555 J MN MN . B MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc8 C NE2 HIS 117 C HIS 117 1_555 L MN MN . C MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc9 C OD1 ASP 268 C ASP 268 1_555 L MN MN . C MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc10 D NE2 HIS 117 D HIS 117 1_555 N MN MN . D MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.69 ? metalc ? metalc11 D OD1 ASP 268 D ASP 268 1_555 N MN MN . D MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc12 E NE2 HIS 117 E HIS 117 1_555 Q MN MN . E MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc13 E OD1 ASP 268 E ASP 268 1_555 Q MN MN . E MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc14 E OD1 ASP 269 E ASP 269 1_555 P MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc15 F NE2 HIS 69 F HIS 69 1_555 T MN MN . F MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.721 ? metalc ? metalc16 F NE2 HIS 117 F HIS 117 1_555 T MN MN . F MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? metalc ? metalc17 F OD2 ASP 268 F ASP 268 1_555 S MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc18 F OD1 ASP 268 F ASP 268 1_555 T MN MN . F MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? # _chem_comp.formula 'C10 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id T8T _chem_comp.mon_nstd_flag . _chem_comp.name "2'-deoxyguanosine-5'-O-(1-thiotriphosphate)" _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 N1 C2 T8T doub 290 n n N1 C6 T8T sing 291 n n N2 C2 T8T sing 292 n n C2 N3 T8T sing 293 n n N2 HN2 T8T sing 294 n n N2 HN2A T8T sing 295 n n N3 C4 T8T sing 296 n n N3 HN3 T8T sing 297 n n C5 C4 T8T doub 298 n y C4 N9 T8T sing 299 n y C6 C5 T8T sing 300 n n C5 N7 T8T sing 301 n y O6 C6 T8T doub 302 n n N7 C8 T8T doub 303 n y N9 C8 T8T sing 304 n y C8 H8 T8T sing 305 n n N9 C1' T8T sing 306 n n S1A PA T8T sing 307 n n PA O5' T8T sing 308 n n PA O2A T8T doub 309 n n PA O3A T8T sing 310 n n O3B PB T8T sing 311 n n O3A PB T8T sing 312 n n PB O1B T8T doub 313 n n PB O2B T8T sing 314 n n O3G PG T8T doub 315 n n O3B PG T8T sing 316 n n PG O1G T8T sing 317 n n PG O2G T8T sing 318 n n O4' C1' T8T sing 319 n n C1' C2' T8T sing 320 n n C1' H1' T8T sing 321 n n S1A HS1A T8T sing 322 n n O1G HO1G T8T sing 323 n n C2' C3' T8T sing 324 n n C2' H2' T8T sing 325 n n C2' "H2'A" T8T sing 326 n n O2B HO2B T8T sing 327 n n O2G HO2G T8T sing 328 n n C4' C3' T8T sing 329 n n C3' O3' T8T sing 330 n n C3' H3' T8T sing 331 n n O3' HO3' T8T sing 332 n n O4' C4' T8T sing 333 n n C4' C5' T8T sing 334 n n C4' H4' T8T sing 335 n n C5' O5' T8T sing 336 n n C5' H5' T8T sing 337 n n C5' "H5'A" T8T sing 338 n n # _atom_sites.entry_id 6OIW _atom_sites.fract_transf_matrix[1][1] 0.005229 _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] 0.005229 _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] 0.003349 _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 2 MG A 1 601 601 MG MG . H 3 MN A 1 602 602 MN MN . I 4 T8T A 1 603 603 T8T T8T . J 3 MN B 1 601 601 MN MN . K 4 T8T B 1 602 602 T8T T8T . L 3 MN C 1 601 601 MN MN . M 4 T8T C 1 602 602 T8T T8T . N 3 MN D 1 601 601 MN MN . O 4 T8T D 1 602 602 T8T T8T . P 2 MG E 1 601 601 MG MG . Q 3 MN E 1 602 602 MN MN . R 4 T8T E 1 603 603 T8T T8T . S 2 MG F 1 601 601 MG MG . T 3 MN F 1 602 602 MN MN . U 4 T8T F 1 603 603 T8T T8T . V 5 HOH A 1 701 701 HOH HOH . V 5 HOH A 2 702 702 HOH HOH . V 5 HOH A 3 703 703 HOH HOH . V 5 HOH A 4 704 704 HOH HOH . V 5 HOH A 5 705 705 HOH HOH . W 5 HOH B 1 702 701 HOH HOH . W 5 HOH B 2 703 703 HOH HOH . W 5 HOH B 3 704 704 HOH HOH . W 5 HOH B 4 705 705 HOH HOH . X 5 HOH C 1 701 701 HOH HOH . X 5 HOH C 2 702 702 HOH HOH . Y 5 HOH D 1 701 701 HOH HOH . Y 5 HOH D 2 702 702 HOH HOH . Y 5 HOH D 3 703 703 HOH HOH . Y 5 HOH D 4 704 704 HOH HOH . Y 5 HOH D 5 705 705 HOH HOH . Z 5 HOH E 1 701 701 HOH HOH . Z 5 HOH E 2 702 702 HOH HOH . Z 5 HOH E 3 703 703 HOH HOH . Z 5 HOH E 4 704 704 HOH HOH . AA 5 HOH F 1 701 701 HOH HOH . AA 5 HOH F 2 702 702 HOH HOH . AA 5 HOH F 3 703 703 HOH HOH . # 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 N N1 T8T . . . O 4 73.329 41.558 72.678 1 153.2 ? N1 T8T 602 D 1 HETATM 2 C C2 T8T . . . O 4 73.209 40.256 72.505 1 152.4 ? C2 T8T 602 D 1 HETATM 3 N N2 T8T . . . O 4 72.302 39.783 71.658 1 148.25 ? N2 T8T 602 D 1 HETATM 4 N N3 T8T . . . O 4 73.899 39.348 73.235 1 156.43 ? N3 T8T 602 D 1 HETATM 5 C C4 T8T . . . O 4 74.689 39.831 74.233 1 160.75 ? C4 T8T 602 D 1 HETATM 6 C C5 T8T . . . O 4 74.81 41.177 74.471 1 160.97 ? C5 T8T 602 D 1 HETATM 7 C C6 T8T . . . O 4 74.115 42.085 73.642 1 157.76 ? C6 T8T 602 D 1 HETATM 8 O O6 T8T . . . O 4 74.197 43.297 73.775 1 160.1 ? O6 T8T 602 D 1 HETATM 9 N N7 T8T . . . O 4 75.607 41.38 75.583 1 166.02 ? N7 T8T 602 D 1 HETATM 10 C C8 T8T . . . O 4 75.937 40.178 75.968 1 168.38 ? C8 T8T 602 D 1 HETATM 11 N N9 T8T . . . O 4 75.419 39.201 75.19 1 166.47 ? N9 T8T 602 D 1 HETATM 12 P PA T8T . . . O 4 76.753 38.542 80.024 1 203.55 ? PA T8T 602 D 1 HETATM 13 P PB T8T . . . O 4 76.344 37.014 82.152 1 224.97 ? PB T8T 602 D 1 HETATM 14 P PG T8T . . . O 4 77.39 38.775 84.258 1 226.86 ? PG T8T 602 D 1 HETATM 15 C C1' T8T . . . O 4 75.605 37.769 75.33 1 171.58 ? C1' T8T 602 D 1 HETATM 16 S S1A T8T . . . O 4 76.405 40.401 79.949 1 203.52 ? S1A T8T 602 D 1 HETATM 17 O O1B T8T . . . O 4 76.97 35.813 81.598 1 225.42 ? O1B T8T 602 D 1 HETATM 18 O O1G T8T . . . O 4 77.12 40.26 84.067 1 226.03 ? O1G T8T 602 D 1 HETATM 19 C C2' T8T . . . O 4 77.038 37.379 75.568 1 177.41 ? C2' T8T 602 D 1 HETATM 20 O O2A T8T . . . O 4 78.059 38.174 80.423 1 206.84 ? O2A T8T 602 D 1 HETATM 21 O O2B T8T . . . O 4 75.267 36.637 83.14 1 225.9 ? O2B T8T 602 D 1 HETATM 22 O O2G T8T . . . O 4 76.288 38.219 85.053 1 226.81 ? O2G T8T 602 D 1 HETATM 23 C C3' T8T . . . O 4 76.901 36.081 76.341 1 179.54 ? C3' T8T 602 D 1 HETATM 24 O O3' T8T . . . O 4 76.799 34.995 75.432 1 177.04 ? O3' T8T 602 D 1 HETATM 25 O O3A T8T . . . O 4 75.807 37.907 80.961 1 213.06 ? O3A T8T 602 D 1 HETATM 26 O O3B T8T . . . O 4 77.364 38.012 82.86 1 226.69 ? O3B T8T 602 D 1 HETATM 27 O O3G T8T . . . O 4 78.676 38.44 84.819 1 228.19 ? O3G T8T 602 D 1 HETATM 28 C C4' T8T . . . O 4 75.604 36.268 77.11 1 180.2 ? C4' T8T 602 D 1 HETATM 29 O O4' T8T . . . O 4 74.92 37.365 76.478 1 175.26 ? O4' T8T 602 D 1 HETATM 30 C C5' T8T . . . O 4 75.78 36.579 78.573 1 186.84 ? C5' T8T 602 D 1 HETATM 31 O O5' T8T . . . O 4 76.359 37.889 78.698 1 193.06 ? O5' T8T 602 D 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 73 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 31 #