data_1YZG # _model_server_result.job_id P0A_bU4SdTa23eNBBYZNKA _model_server_result.datetime_utc '2024-10-19 11:48:43' _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 1yzg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":181}' # _entry.id 1YZG # _exptl.entry_id 1YZG _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 103.45 _cell.angle_gamma 90 _cell.entry_id 1YZG _cell.length_a 37.725 _cell.length_b 48.137 _cell.length_c 51.371 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YZG _symmetry.cell_setting monoclinic _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 1YZG _atom_sites.fract_transf_matrix[1][1] 0.026508 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006339 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020774 _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] 0.020015 _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 1 181 181 GDP GDP . C 3 HOH A 1 201 201 HOH HOH . C 3 HOH A 2 202 202 HOH HOH . C 3 HOH A 3 203 203 HOH HOH . C 3 HOH A 4 204 204 HOH HOH . C 3 HOH A 5 205 205 HOH HOH . C 3 HOH A 6 206 206 HOH HOH . C 3 HOH A 7 207 207 HOH HOH . C 3 HOH A 8 208 208 HOH HOH . C 3 HOH A 9 209 209 HOH HOH . C 3 HOH A 10 210 210 HOH HOH . C 3 HOH A 11 211 211 HOH HOH . C 3 HOH A 12 212 212 HOH HOH . C 3 HOH A 13 213 213 HOH HOH . C 3 HOH A 14 214 214 HOH HOH . C 3 HOH A 15 215 215 HOH HOH . C 3 HOH A 16 216 216 HOH HOH . C 3 HOH A 17 217 217 HOH HOH . C 3 HOH A 18 218 218 HOH HOH . C 3 HOH A 19 219 219 HOH HOH . C 3 HOH A 20 220 220 HOH HOH . C 3 HOH A 21 221 221 HOH HOH . C 3 HOH A 22 222 222 HOH HOH . C 3 HOH A 23 223 223 HOH HOH . C 3 HOH A 24 224 224 HOH HOH . C 3 HOH A 25 225 225 HOH HOH . C 3 HOH A 26 226 226 HOH HOH . C 3 HOH A 27 227 227 HOH HOH . C 3 HOH A 28 228 228 HOH HOH . C 3 HOH A 29 229 229 HOH HOH . C 3 HOH A 30 230 230 HOH HOH . C 3 HOH A 31 231 231 HOH HOH . C 3 HOH A 32 232 232 HOH HOH . C 3 HOH A 33 233 233 HOH HOH . C 3 HOH A 34 234 234 HOH HOH . C 3 HOH A 35 235 235 HOH HOH . C 3 HOH A 36 236 236 HOH HOH . C 3 HOH A 37 237 237 HOH HOH . C 3 HOH A 38 238 238 HOH HOH . C 3 HOH A 39 239 239 HOH HOH . C 3 HOH A 40 240 240 HOH HOH . C 3 HOH A 41 241 241 HOH HOH . C 3 HOH A 42 242 242 HOH HOH . C 3 HOH A 43 243 243 HOH HOH . C 3 HOH A 44 244 244 HOH HOH . C 3 HOH A 45 245 245 HOH HOH . C 3 HOH A 46 246 246 HOH HOH . C 3 HOH A 47 247 247 HOH HOH . C 3 HOH A 48 248 248 HOH HOH . C 3 HOH A 49 249 249 HOH HOH . C 3 HOH A 50 250 250 HOH HOH . C 3 HOH A 51 251 251 HOH HOH . C 3 HOH A 52 252 252 HOH HOH . C 3 HOH A 53 253 253 HOH HOH . C 3 HOH A 54 254 254 HOH HOH . C 3 HOH A 55 255 255 HOH HOH . C 3 HOH A 56 256 256 HOH HOH . C 3 HOH A 57 257 257 HOH HOH . C 3 HOH A 58 258 258 HOH HOH . C 3 HOH A 59 259 259 HOH HOH . C 3 HOH A 60 260 260 HOH HOH . C 3 HOH A 61 261 261 HOH HOH . C 3 HOH A 62 262 262 HOH HOH . C 3 HOH A 63 263 263 HOH HOH . C 3 HOH A 64 264 264 HOH HOH . C 3 HOH A 65 265 265 HOH HOH . C 3 HOH A 66 266 266 HOH HOH . C 3 HOH A 67 267 267 HOH HOH . C 3 HOH A 68 268 268 HOH HOH . C 3 HOH A 69 269 269 HOH HOH . C 3 HOH A 70 270 270 HOH HOH . C 3 HOH A 71 271 271 HOH HOH . C 3 HOH A 72 272 272 HOH HOH . C 3 HOH A 73 273 273 HOH HOH . C 3 HOH A 74 274 274 HOH HOH . C 3 HOH A 75 275 275 HOH HOH . C 3 HOH A 76 276 276 HOH HOH . C 3 HOH A 77 277 277 HOH HOH . C 3 HOH A 78 278 278 HOH HOH . C 3 HOH A 79 279 279 HOH HOH . C 3 HOH A 80 280 280 HOH HOH . C 3 HOH A 81 281 281 HOH HOH . C 3 HOH A 82 282 282 HOH HOH . C 3 HOH A 83 283 283 HOH HOH . C 3 HOH A 84 284 284 HOH HOH . C 3 HOH A 85 285 285 HOH HOH . C 3 HOH A 86 286 286 HOH HOH . C 3 HOH A 87 287 287 HOH HOH . C 3 HOH A 88 288 288 HOH HOH . C 3 HOH A 89 289 289 HOH HOH . C 3 HOH A 90 290 290 HOH HOH . C 3 HOH A 91 291 291 HOH HOH . C 3 HOH A 92 292 292 HOH HOH . C 3 HOH A 93 293 293 HOH HOH . C 3 HOH A 94 294 294 HOH HOH . C 3 HOH A 95 295 295 HOH HOH . C 3 HOH A 96 296 296 HOH HOH . C 3 HOH A 97 297 297 HOH HOH . C 3 HOH A 98 298 298 HOH HOH . C 3 HOH A 99 299 299 HOH HOH . C 3 HOH A 100 300 300 HOH HOH . C 3 HOH A 101 301 301 HOH HOH . C 3 HOH A 102 302 302 HOH HOH . C 3 HOH A 103 303 303 HOH HOH . C 3 HOH A 104 304 304 HOH HOH . C 3 HOH A 105 305 305 HOH HOH . C 3 HOH A 106 306 306 HOH HOH . C 3 HOH A 107 307 307 HOH HOH . C 3 HOH A 108 308 308 HOH HOH . C 3 HOH A 109 309 309 HOH HOH . C 3 HOH A 110 310 310 HOH HOH . C 3 HOH A 111 311 311 HOH HOH . C 3 HOH A 112 312 312 HOH HOH . C 3 HOH A 113 313 313 HOH HOH . C 3 HOH A 114 314 314 HOH HOH . C 3 HOH A 115 315 315 HOH HOH . C 3 HOH A 116 316 316 HOH HOH . C 3 HOH A 117 317 317 HOH HOH . C 3 HOH A 118 318 318 HOH HOH . C 3 HOH A 119 319 319 HOH HOH . C 3 HOH A 120 320 320 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 6.702 -4.326 0.841 1 13.01 ? PB GDP 181 A 1 HETATM 2 O O1B GDP . . . B 2 5.978 -5.354 1.671 1 11.07 ? O1B GDP 181 A 1 HETATM 3 O O2B GDP . . . B 2 7.173 -3.131 1.639 1 10.81 ? O2B GDP 181 A 1 HETATM 4 O O3B GDP . . . B 2 5.84 -3.775 -0.266 1 12.13 ? O3B GDP 181 A 1 HETATM 5 O O3A GDP . . . B 2 8.107 -4.882 0.268 1 14.91 ? O3A GDP 181 A 1 HETATM 6 P PA GDP . . . B 2 8.503 -6.413 -0.031 1 15.93 ? PA GDP 181 A 1 HETATM 7 O O1A GDP . . . B 2 8.844 -7.115 1.26 1 17.11 ? O1A GDP 181 A 1 HETATM 8 O O2A GDP . . . B 2 7.391 -7.12 -0.755 1 17.46 ? O2A GDP 181 A 1 HETATM 9 O O5' GDP . . . B 2 9.784 -6.185 -0.965 1 15.18 ? O5' GDP 181 A 1 HETATM 10 C C5' GDP . . . B 2 9.551 -5.626 -2.26 1 15.96 ? C5' GDP 181 A 1 HETATM 11 C C4' GDP . . . B 2 10.563 -6.108 -3.285 1 16.36 ? C4' GDP 181 A 1 HETATM 12 O O4' GDP . . . B 2 11.898 -5.649 -2.957 1 14.76 ? O4' GDP 181 A 1 HETATM 13 C C3' GDP . . . B 2 10.602 -7.629 -3.313 1 16 ? C3' GDP 181 A 1 HETATM 14 O O3' GDP . . . B 2 10.853 -8.083 -4.638 1 15.37 ? O3' GDP 181 A 1 HETATM 15 C C2' GDP . . . B 2 11.795 -7.944 -2.433 1 15.86 ? C2' GDP 181 A 1 HETATM 16 O O2' GDP . . . B 2 12.392 -9.198 -2.749 1 18.15 ? O2' GDP 181 A 1 HETATM 17 C C1' GDP . . . B 2 12.741 -6.77 -2.656 1 13.99 ? C1' GDP 181 A 1 HETATM 18 N N9 GDP . . . B 2 13.601 -6.508 -1.48 1 13.82 ? N9 GDP 181 A 1 HETATM 19 C C8 GDP . . . B 2 13.211 -6.455 -0.182 1 13.22 ? C8 GDP 181 A 1 HETATM 20 N N7 GDP . . . B 2 14.275 -6.18 0.62 1 14.36 ? N7 GDP 181 A 1 HETATM 21 C C5 GDP . . . B 2 15.361 -6.069 -0.179 1 10.71 ? C5 GDP 181 A 1 HETATM 22 C C6 GDP . . . B 2 16.79 -5.781 0.02 1 11.68 ? C6 GDP 181 A 1 HETATM 23 O O6 GDP . . . B 2 17.208 -5.594 1.174 1 13.35 ? O6 GDP 181 A 1 HETATM 24 N N1 GDP . . . B 2 17.597 -5.736 -1.059 1 12.38 ? N1 GDP 181 A 1 HETATM 25 C C2 GDP . . . B 2 17.129 -5.929 -2.313 1 13.55 ? C2 GDP 181 A 1 HETATM 26 N N2 GDP . . . B 2 17.974 -5.878 -3.378 1 14.41 ? N2 GDP 181 A 1 HETATM 27 N N3 GDP . . . B 2 15.82 -6.207 -2.555 1 14.33 ? N3 GDP 181 A 1 HETATM 28 C C4 GDP . . . B 2 14.915 -6.277 -1.549 1 10.85 ? C4 GDP 181 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #