data_2QU8 # _model_server_result.job_id ccuoJDJjZIdzxIrGX2GRJw _model_server_result.datetime_utc '2024-11-05 00:35:22' _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 2qu8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":229}' # _entry.id 2QU8 # _exptl.entry_id 2QU8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 2QU8 _cell.length_a 56.377 _cell.length_b 77.162 _cell.length_c 40.196 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2QU8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 2QU8 _atom_sites.fract_transf_matrix[1][1] 0.017738 _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] 0.01296 _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] 0.024878 _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 B 2 GDP A 1 229 1 GDP GDP . C 3 HOH A 1 230 5 HOH HOH . C 3 HOH A 2 231 6 HOH HOH . C 3 HOH A 3 232 16 HOH HOH . C 3 HOH A 4 233 22 HOH HOH . C 3 HOH A 5 234 23 HOH HOH . C 3 HOH A 6 235 26 HOH HOH . C 3 HOH A 7 236 28 HOH HOH . C 3 HOH A 8 237 29 HOH HOH . C 3 HOH A 9 238 30 HOH HOH . C 3 HOH A 10 239 33 HOH HOH . C 3 HOH A 11 240 43 HOH HOH . C 3 HOH A 12 241 45 HOH HOH . C 3 HOH A 13 242 46 HOH HOH . C 3 HOH A 14 243 50 HOH HOH . C 3 HOH A 15 244 51 HOH HOH . C 3 HOH A 16 245 54 HOH HOH . C 3 HOH A 17 246 55 HOH HOH . C 3 HOH A 18 247 61 HOH HOH . C 3 HOH A 19 248 62 HOH HOH . C 3 HOH A 20 249 65 HOH HOH . C 3 HOH A 21 250 66 HOH HOH . C 3 HOH A 22 251 75 HOH HOH . C 3 HOH A 23 252 77 HOH HOH . C 3 HOH A 24 253 78 HOH HOH . C 3 HOH A 25 254 81 HOH HOH . C 3 HOH A 26 255 86 HOH HOH . C 3 HOH A 27 256 87 HOH HOH . C 3 HOH A 28 257 89 HOH HOH . C 3 HOH A 29 258 96 HOH HOH . C 3 HOH A 30 259 97 HOH HOH . C 3 HOH A 31 260 104 HOH HOH . C 3 HOH A 32 261 105 HOH HOH . C 3 HOH A 33 262 106 HOH HOH . C 3 HOH A 34 263 1 HOH HOH . C 3 HOH A 35 264 2 HOH HOH . C 3 HOH A 36 265 3 HOH HOH . C 3 HOH A 37 266 4 HOH HOH . C 3 HOH A 38 267 5 HOH HOH . C 3 HOH A 39 268 6 HOH HOH . C 3 HOH A 40 269 7 HOH HOH . C 3 HOH A 41 270 11 HOH HOH . C 3 HOH A 42 271 12 HOH HOH . C 3 HOH A 43 272 13 HOH HOH . C 3 HOH A 44 273 14 HOH HOH . C 3 HOH A 45 274 15 HOH HOH . C 3 HOH A 46 275 17 HOH HOH . C 3 HOH A 47 276 18 HOH HOH . C 3 HOH A 48 277 2 HOH HOH . C 3 HOH A 49 278 6 HOH HOH . C 3 HOH A 50 279 7 HOH HOH . C 3 HOH A 51 280 8 HOH HOH . C 3 HOH A 52 281 9 HOH HOH . C 3 HOH A 53 282 15 HOH HOH . C 3 HOH A 54 283 16 HOH HOH . C 3 HOH A 55 284 22 HOH HOH . C 3 HOH A 56 285 23 HOH HOH . C 3 HOH A 57 286 29 HOH HOH . C 3 HOH A 58 287 31 HOH HOH . C 3 HOH A 59 288 32 HOH HOH . C 3 HOH A 60 289 35 HOH HOH . C 3 HOH A 61 290 38 HOH HOH . C 3 HOH A 62 291 42 HOH HOH . C 3 HOH A 63 292 50 HOH HOH . C 3 HOH A 64 293 52 HOH HOH . C 3 HOH A 65 294 73 HOH HOH . C 3 HOH A 66 295 2 HOH HOH . C 3 HOH A 67 296 3 HOH HOH . C 3 HOH A 68 297 4 HOH HOH . C 3 HOH A 69 298 5 HOH HOH . C 3 HOH A 70 299 11 HOH HOH . C 3 HOH A 71 300 16 HOH HOH . C 3 HOH A 72 301 30 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 P PB GDP . . . B 2 34.45 12.431 -0.161 1 22.92 ? PB GDP 229 A 1 HETATM 2 O O1B GDP . . . B 2 34.413 11.88 -1.577 1 21.35 ? O1B GDP 229 A 1 HETATM 3 O O2B GDP . . . B 2 35.773 12.073 0.458 1 20.98 ? O2B GDP 229 A 1 HETATM 4 O O3B GDP . . . B 2 34.337 13.918 -0.281 1 23.39 ? O3B GDP 229 A 1 HETATM 5 O O3A GDP . . . B 2 33.263 11.8 0.712 1 22.47 ? O3A GDP 229 A 1 HETATM 6 P PA GDP . . . B 2 31.741 12.355 0.741 1 22.99 ? PA GDP 229 A 1 HETATM 7 O O1A GDP . . . B 2 31.285 12.708 -0.663 1 22.6 ? O1A GDP 229 A 1 HETATM 8 O O2A GDP . . . B 2 31.619 13.533 1.658 1 23.61 ? O2A GDP 229 A 1 HETATM 9 O O5' GDP . . . B 2 30.982 11.063 1.297 1 22.92 ? O5' GDP 229 A 1 HETATM 10 C C5' GDP . . . B 2 30.875 9.888 0.479 1 24.53 ? C5' GDP 229 A 1 HETATM 11 C C4' GDP . . . B 2 29.638 9.087 0.862 1 25.38 ? C4' GDP 229 A 1 HETATM 12 O O4' GDP . . . B 2 29.697 8.769 2.259 1 25.7 ? O4' GDP 229 A 1 HETATM 13 C C3' GDP . . . B 2 28.358 9.89 0.674 1 25.73 ? C3' GDP 229 A 1 HETATM 14 O O3' GDP . . . B 2 27.317 9.012 0.247 1 25.7 ? O3' GDP 229 A 1 HETATM 15 C C2' GDP . . . B 2 28.062 10.407 2.064 1 25.29 ? C2' GDP 229 A 1 HETATM 16 O O2' GDP . . . B 2 26.682 10.727 2.239 1 25.68 ? O2' GDP 229 A 1 HETATM 17 C C1' GDP . . . B 2 28.528 9.249 2.927 1 25.63 ? C1' GDP 229 A 1 HETATM 18 N N9 GDP . . . B 2 28.948 9.618 4.292 1 25.52 ? N9 GDP 229 A 1 HETATM 19 C C8 GDP . . . B 2 29.622 10.734 4.638 1 25.79 ? C8 GDP 229 A 1 HETATM 20 N N7 GDP . . . B 2 29.872 10.745 5.97 1 25.73 ? N7 GDP 229 A 1 HETATM 21 C C5 GDP . . . B 2 29.353 9.615 6.49 1 25.35 ? C5 GDP 229 A 1 HETATM 22 C C6 GDP . . . B 2 29.276 9 7.836 1 25.38 ? C6 GDP 229 A 1 HETATM 23 O O6 GDP . . . B 2 29.775 9.588 8.823 1 25.62 ? O6 GDP 229 A 1 HETATM 24 N N1 GDP . . . B 2 28.648 7.816 7.959 1 25.57 ? N1 GDP 229 A 1 HETATM 25 C C2 GDP . . . B 2 28.104 7.171 6.905 1 26.22 ? C2 GDP 229 A 1 HETATM 26 N N2 GDP . . . B 2 27.494 5.975 7.11 1 25.98 ? N2 GDP 229 A 1 HETATM 27 N N3 GDP . . . B 2 28.151 7.678 5.642 1 26.31 ? N3 GDP 229 A 1 HETATM 28 C C4 GDP . . . B 2 28.753 8.87 5.377 1 25.23 ? C4 GDP 229 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #