data_6XBU # _model_server_result.job_id FlAQqMvy_OgIWkfqAK2Qzw _model_server_result.datetime_utc '2024-10-19 03:53:54' _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 6xbu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2601}' # _entry.id 6XBU # _exptl.entry_id 6XBU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 491.182 _entity.id 4 _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 6XBU _cell.length_a 99.52 _cell.length_b 99.52 _cell.length_c 193.15 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XBU _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_554 x-y,-y,-z-1/3 1 0 0 0 -1 0 0 0 -1 0 0 -64.383333 # _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 hydrog 'DT-G MISPAIR' hydrog1 B O4 DT 8 F DT 8 1_555 C N1 G 9 E G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-G PAIR' hydrog2 B N3 DC 9 F DC 9 1_555 C N2 G 9 E G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N1 DA 10 F DA 10 1_555 C N3 U 8 E U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N6 DA 10 F DA 10 1_555 C O4 U 8 E U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N3 DT 11 F DT 11 1_555 C N1 A 7 E A 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O4 DT 11 F DT 11 1_555 C N6 A 7 E A 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N3 DT 12 F DT 12 1_555 C N1 A 6 E A 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O4 DT 12 F DT 12 1_555 C N6 A 6 E A 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DG 13 F DG 13 1_555 C N3 C 5 E C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N2 DG 13 F DG 13 1_555 C O2 C 5 E C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O6 DG 13 F DG 13 1_555 C N4 C 5 E C 5 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 270 n n PG O2G DG3 sing 271 n n PG O3G DG3 sing 272 n n PG O3B DG3 sing 273 n n O2G HOG2 DG3 sing 274 n n O3G HOG3 DG3 sing 275 n n O3B PB DG3 sing 276 n n PB O1B DG3 doub 277 n n PB O2B DG3 sing 278 n n PB O3A DG3 sing 279 n n O2B HOB2 DG3 sing 280 n n O3A PA DG3 sing 281 n n PA O1A DG3 doub 282 n n PA O2A DG3 sing 283 n n PA O5' DG3 sing 284 n n O2A HOA2 DG3 sing 285 n n O5' C5' DG3 sing 286 n n C5' C4' DG3 sing 287 n n C5' "H5'1" DG3 sing 288 n n C5' "H5'2" DG3 sing 289 n n C4' O4' DG3 sing 290 n n C4' C3' DG3 sing 291 n n C4' H4' DG3 sing 292 n n O4' C1' DG3 sing 293 n n C3' C2' DG3 sing 294 n n C3' "H3'1" DG3 sing 295 n n C3' "H3'2" DG3 sing 296 n n C2' C1' DG3 sing 297 n n C2' "H2'1" DG3 sing 298 n n C2' "H2'2" DG3 sing 299 n n C1' N9 DG3 sing 300 n n C1' H1' DG3 sing 301 n n N9 C8 DG3 sing 302 n y N9 C4 DG3 sing 303 n y C8 N7 DG3 doub 304 n y C8 H8 DG3 sing 305 n n N7 C5 DG3 sing 306 n y C5 C6 DG3 sing 307 n n C5 C4 DG3 doub 308 n y C6 O6 DG3 doub 309 n n C6 N1 DG3 sing 310 n n N1 C2 DG3 sing 311 n n N1 HN1 DG3 sing 312 n n C2 N2 DG3 sing 313 n n C2 N3 DG3 doub 314 n n N2 HN21 DG3 sing 315 n n N2 HN22 DG3 sing 316 n n N3 C4 DG3 sing 317 n n # _atom_sites.entry_id 6XBU _atom_sites.fract_transf_matrix[1][1] 0.010048 _atom_sites.fract_transf_matrix[1][2] 0.005801 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011603 _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] 0.005177 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id D _pdbx_nonpoly_scheme.entity_id 4 _pdbx_nonpoly_scheme.mon_id DG3 _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 2601 _pdbx_nonpoly_scheme.auth_seq_num 2604 _pdbx_nonpoly_scheme.pdb_mon_id DG3 _pdbx_nonpoly_scheme.auth_mon_id DG3 _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . D 4 26.212 -16.759 14.315 1 191.74 ? PG DG3 2601 A 1 HETATM 2 O O1G DG3 . . . D 4 25.281 -17.679 13.564 1 190.99 ? O1G DG3 2601 A 1 HETATM 3 O O2G DG3 . . . D 4 27.527 -17.418 14.659 1 187.58 -1 O2G DG3 2601 A 1 HETATM 4 O O3G DG3 . . . D 4 25.553 -16.114 15.51 1 192.97 ? O3G DG3 2601 A 1 HETATM 5 O O3B DG3 . . . D 4 26.56 -15.552 13.295 1 190.47 ? O3B DG3 2601 A 1 HETATM 6 P PB DG3 . . . D 4 25.679 -14.415 12.587 1 217.87 ? PB DG3 2601 A 1 HETATM 7 O O1B DG3 . . . D 4 24.32 -14.411 13.209 1 204.58 -1 O1B DG3 2601 A 1 HETATM 8 O O2B DG3 . . . D 4 26.473 -13.15 12.552 1 182.62 ? O2B DG3 2601 A 1 HETATM 9 O O3A DG3 . . . D 4 25.563 -15.001 11.098 1 176.73 ? O3A DG3 2601 A 1 HETATM 10 P PA DG3 . . . D 4 26.412 -14.723 9.765 1 133.8 ? PA DG3 2601 A 1 HETATM 11 O O1A DG3 . . . D 4 27.633 -13.968 10.171 1 132.04 -1 O1A DG3 2601 A 1 HETATM 12 O O2A DG3 . . . D 4 25.509 -14.107 8.747 1 143.44 ? O2A DG3 2601 A 1 HETATM 13 O O5' DG3 . . . D 4 26.828 -16.202 9.284 1 129.85 ? O5' DG3 2601 A 1 HETATM 14 C C5' DG3 . . . D 4 26.324 -17.371 9.987 1 136.1 ? C5' DG3 2601 A 1 HETATM 15 C C4' DG3 . . . D 4 26.931 -18.635 9.417 1 122.42 ? C4' DG3 2601 A 1 HETATM 16 O O4' DG3 . . . D 4 28.249 -18.346 8.896 1 115.92 ? O4' DG3 2601 A 1 HETATM 17 C C3' DG3 . . . D 4 27.087 -19.757 10.418 1 120.59 ? C3' DG3 2601 A 1 HETATM 18 C C2' DG3 . . . D 4 28.496 -20.284 10.217 1 113.21 ? C2' DG3 2601 A 1 HETATM 19 C C1' DG3 . . . D 4 29.232 -19.13 9.565 1 110.23 ? C1' DG3 2601 A 1 HETATM 20 N N9 DG3 . . . D 4 29.948 -18.263 10.5 1 117.07 ? N9 DG3 2601 A 1 HETATM 21 C C8 DG3 . . . D 4 29.56 -17.035 10.977 1 126.64 ? C8 DG3 2601 A 1 HETATM 22 N N7 DG3 . . . D 4 30.422 -16.502 11.806 1 120.05 ? N7 DG3 2601 A 1 HETATM 23 C C5 DG3 . . . D 4 31.442 -17.439 11.881 1 116.68 ? C5 DG3 2601 A 1 HETATM 24 C C6 DG3 . . . D 4 32.642 -17.41 12.63 1 116.78 ? C6 DG3 2601 A 1 HETATM 25 O O6 DG3 . . . D 4 33.046 -16.521 13.393 1 114.74 ? O6 DG3 2601 A 1 HETATM 26 N N1 DG3 . . . D 4 33.399 -18.566 12.422 1 121.37 ? N1 DG3 2601 A 1 HETATM 27 C C2 DG3 . . . D 4 33.045 -19.611 11.601 1 122.7 ? C2 DG3 2601 A 1 HETATM 28 N N2 DG3 . . . D 4 33.904 -20.638 11.53 1 122.03 ? N2 DG3 2601 A 1 HETATM 29 N N3 DG3 . . . D 4 31.915 -19.642 10.894 1 119.53 ? N3 DG3 2601 A 1 HETATM 30 C C4 DG3 . . . D 4 31.165 -18.528 11.083 1 117.81 ? C4 DG3 2601 A 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 30 #