data_7WQY # _model_server_result.job_id mdzHUquMxN3m81OYL7Rf1A _model_server_result.datetime_utc '2024-11-13 00:03:34' _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 7wqy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 7WQY # _exptl.entry_id 7WQY _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 131.53 _cell.angle_gamma 90 _cell.entry_id 7WQY _cell.length_a 121.571 _cell.length_b 43.688 _cell.length_c 87.841 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7WQY _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 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' 3_445 x-1/2,y-1/2,z 1 0 0 0 1 0 0 0 1 -60.7855 -21.844 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N 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 7WQY _atom_sites.fract_transf_matrix[1][1] 0.008226 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007286 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02289 _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] 0.015208 _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 C 2 GDP A 1 201 201 GDP LIG . D 2 GDP B 1 201 1 GDP GDP . E 3 HOH A 1 301 155 HOH HOH . E 3 HOH A 2 302 138 HOH HOH . E 3 HOH A 3 303 4 HOH HOH . E 3 HOH A 4 304 163 HOH HOH . E 3 HOH A 5 305 134 HOH HOH . E 3 HOH A 6 306 56 HOH HOH . E 3 HOH A 7 307 85 HOH HOH . E 3 HOH A 8 308 222 HOH HOH . E 3 HOH A 9 309 164 HOH HOH . E 3 HOH A 10 310 249 HOH HOH . E 3 HOH A 11 311 88 HOH HOH . E 3 HOH A 12 312 50 HOH HOH . E 3 HOH A 13 313 227 HOH HOH . E 3 HOH A 14 314 65 HOH HOH . E 3 HOH A 15 315 69 HOH HOH . E 3 HOH A 16 316 79 HOH HOH . E 3 HOH A 17 317 132 HOH HOH . E 3 HOH A 18 318 90 HOH HOH . E 3 HOH A 19 319 5 HOH HOH . E 3 HOH A 20 320 18 HOH HOH . E 3 HOH A 21 321 94 HOH HOH . E 3 HOH A 22 322 238 HOH HOH . E 3 HOH A 23 323 103 HOH HOH . E 3 HOH A 24 324 93 HOH HOH . E 3 HOH A 25 325 182 HOH HOH . E 3 HOH A 26 326 47 HOH HOH . E 3 HOH A 27 327 51 HOH HOH . E 3 HOH A 28 328 248 HOH HOH . E 3 HOH A 29 329 8 HOH HOH . E 3 HOH A 30 330 34 HOH HOH . E 3 HOH A 31 331 96 HOH HOH . E 3 HOH A 32 332 64 HOH HOH . E 3 HOH A 33 333 14 HOH HOH . E 3 HOH A 34 334 28 HOH HOH . E 3 HOH A 35 335 49 HOH HOH . E 3 HOH A 36 336 10 HOH HOH . E 3 HOH A 37 337 126 HOH HOH . E 3 HOH A 38 338 147 HOH HOH . E 3 HOH A 39 339 58 HOH HOH . E 3 HOH A 40 340 9 HOH HOH . E 3 HOH A 41 341 241 HOH HOH . E 3 HOH A 42 342 127 HOH HOH . E 3 HOH A 43 343 2 HOH HOH . E 3 HOH A 44 344 152 HOH HOH . E 3 HOH A 45 345 195 HOH HOH . E 3 HOH A 46 346 130 HOH HOH . E 3 HOH A 47 347 106 HOH HOH . E 3 HOH A 48 348 63 HOH HOH . E 3 HOH A 49 349 191 HOH HOH . E 3 HOH A 50 350 55 HOH HOH . E 3 HOH A 51 351 76 HOH HOH . E 3 HOH A 52 352 142 HOH HOH . E 3 HOH A 53 353 160 HOH HOH . E 3 HOH A 54 354 207 HOH HOH . E 3 HOH A 55 355 225 HOH HOH . E 3 HOH A 56 356 133 HOH HOH . E 3 HOH A 57 357 224 HOH HOH . E 3 HOH A 58 358 24 HOH HOH . E 3 HOH A 59 359 86 HOH HOH . E 3 HOH A 60 360 116 HOH HOH . E 3 HOH A 61 361 19 HOH HOH . E 3 HOH A 62 362 44 HOH HOH . E 3 HOH A 63 363 52 HOH HOH . E 3 HOH A 64 364 214 HOH HOH . E 3 HOH A 65 365 250 HOH HOH . E 3 HOH A 66 366 40 HOH HOH . E 3 HOH A 67 367 119 HOH HOH . E 3 HOH A 68 368 97 HOH HOH . E 3 HOH A 69 369 109 HOH HOH . E 3 HOH A 70 370 20 HOH HOH . E 3 HOH A 71 371 12 HOH HOH . E 3 HOH A 72 372 251 HOH HOH . E 3 HOH A 73 373 91 HOH HOH . E 3 HOH A 74 374 220 HOH HOH . E 3 HOH A 75 375 206 HOH HOH . E 3 HOH A 76 376 107 HOH HOH . E 3 HOH A 77 377 252 HOH HOH . E 3 HOH A 78 378 124 HOH HOH . E 3 HOH A 79 379 123 HOH HOH . E 3 HOH A 80 380 237 HOH HOH . E 3 HOH A 81 381 175 HOH HOH . E 3 HOH A 82 382 35 HOH HOH . E 3 HOH A 83 383 67 HOH HOH . E 3 HOH A 84 384 239 HOH HOH . E 3 HOH A 85 385 262 HOH HOH . E 3 HOH A 86 386 186 HOH HOH . E 3 HOH A 87 387 39 HOH HOH . E 3 HOH A 88 388 144 HOH HOH . E 3 HOH A 89 389 234 HOH HOH . E 3 HOH A 90 390 203 HOH HOH . E 3 HOH A 91 391 258 HOH HOH . E 3 HOH A 92 392 193 HOH HOH . E 3 HOH A 93 393 101 HOH HOH . E 3 HOH A 94 394 255 HOH HOH . E 3 HOH A 95 395 99 HOH HOH . E 3 HOH A 96 396 259 HOH HOH . E 3 HOH A 97 397 190 HOH HOH . E 3 HOH A 98 398 82 HOH HOH . E 3 HOH A 99 399 211 HOH HOH . E 3 HOH A 100 400 81 HOH HOH . E 3 HOH A 101 401 118 HOH HOH . E 3 HOH A 102 402 242 HOH HOH . E 3 HOH A 103 403 114 HOH HOH . E 3 HOH A 104 404 202 HOH HOH . E 3 HOH A 105 405 102 HOH HOH . E 3 HOH A 106 406 228 HOH HOH . E 3 HOH A 107 407 61 HOH HOH . E 3 HOH A 108 408 223 HOH HOH . E 3 HOH A 109 409 37 HOH HOH . E 3 HOH A 110 410 226 HOH HOH . E 3 HOH A 111 411 33 HOH HOH . E 3 HOH A 112 412 43 HOH HOH . E 3 HOH A 113 413 110 HOH HOH . E 3 HOH A 114 414 217 HOH HOH . E 3 HOH A 115 415 231 HOH HOH . E 3 HOH A 116 416 235 HOH HOH . F 3 HOH B 1 301 247 HOH HOH . F 3 HOH B 2 302 213 HOH HOH . F 3 HOH B 3 303 187 HOH HOH . F 3 HOH B 4 304 184 HOH HOH . F 3 HOH B 5 305 158 HOH HOH . F 3 HOH B 6 306 229 HOH HOH . F 3 HOH B 7 307 17 HOH HOH . F 3 HOH B 8 308 145 HOH HOH . F 3 HOH B 9 309 154 HOH HOH . F 3 HOH B 10 310 7 HOH HOH . F 3 HOH B 11 311 23 HOH HOH . F 3 HOH B 12 312 53 HOH HOH . F 3 HOH B 13 313 74 HOH HOH . F 3 HOH B 14 314 111 HOH HOH . F 3 HOH B 15 315 254 HOH HOH . F 3 HOH B 16 316 87 HOH HOH . F 3 HOH B 17 317 6 HOH HOH . F 3 HOH B 18 318 261 HOH HOH . F 3 HOH B 19 319 181 HOH HOH . F 3 HOH B 20 320 45 HOH HOH . F 3 HOH B 21 321 21 HOH HOH . F 3 HOH B 22 322 188 HOH HOH . F 3 HOH B 23 323 136 HOH HOH . F 3 HOH B 24 324 165 HOH HOH . F 3 HOH B 25 325 36 HOH HOH . F 3 HOH B 26 326 113 HOH HOH . F 3 HOH B 27 327 11 HOH HOH . F 3 HOH B 28 328 70 HOH HOH . F 3 HOH B 29 329 108 HOH HOH . F 3 HOH B 30 330 72 HOH HOH . F 3 HOH B 31 331 137 HOH HOH . F 3 HOH B 32 332 1 HOH HOH . F 3 HOH B 33 333 13 HOH HOH . F 3 HOH B 34 334 42 HOH HOH . F 3 HOH B 35 335 78 HOH HOH . F 3 HOH B 36 336 32 HOH HOH . F 3 HOH B 37 337 41 HOH HOH . F 3 HOH B 38 338 232 HOH HOH . F 3 HOH B 39 339 100 HOH HOH . F 3 HOH B 40 340 89 HOH HOH . F 3 HOH B 41 341 135 HOH HOH . F 3 HOH B 42 342 29 HOH HOH . F 3 HOH B 43 343 26 HOH HOH . F 3 HOH B 44 344 71 HOH HOH . F 3 HOH B 45 345 16 HOH HOH . F 3 HOH B 46 346 161 HOH HOH . F 3 HOH B 47 347 162 HOH HOH . F 3 HOH B 48 348 60 HOH HOH . F 3 HOH B 49 349 157 HOH HOH . F 3 HOH B 50 350 77 HOH HOH . F 3 HOH B 51 351 230 HOH HOH . F 3 HOH B 52 352 48 HOH HOH . F 3 HOH B 53 353 131 HOH HOH . F 3 HOH B 54 354 240 HOH HOH . F 3 HOH B 55 355 174 HOH HOH . F 3 HOH B 56 356 31 HOH HOH . F 3 HOH B 57 357 143 HOH HOH . F 3 HOH B 58 358 122 HOH HOH . F 3 HOH B 59 359 98 HOH HOH . F 3 HOH B 60 360 139 HOH HOH . F 3 HOH B 61 361 22 HOH HOH . F 3 HOH B 62 362 115 HOH HOH . F 3 HOH B 63 363 68 HOH HOH . F 3 HOH B 64 364 62 HOH HOH . F 3 HOH B 65 365 15 HOH HOH . F 3 HOH B 66 366 121 HOH HOH . F 3 HOH B 67 367 80 HOH HOH . F 3 HOH B 68 368 149 HOH HOH . F 3 HOH B 69 369 30 HOH HOH . F 3 HOH B 70 370 38 HOH HOH . F 3 HOH B 71 371 59 HOH HOH . F 3 HOH B 72 372 205 HOH HOH . F 3 HOH B 73 373 73 HOH HOH . F 3 HOH B 74 374 185 HOH HOH . F 3 HOH B 75 375 120 HOH HOH . F 3 HOH B 76 376 125 HOH HOH . F 3 HOH B 77 377 221 HOH HOH . F 3 HOH B 78 378 244 HOH HOH . F 3 HOH B 79 379 95 HOH HOH . F 3 HOH B 80 380 129 HOH HOH . F 3 HOH B 81 381 246 HOH HOH . F 3 HOH B 82 382 57 HOH HOH . F 3 HOH B 83 383 46 HOH HOH . F 3 HOH B 84 384 201 HOH HOH . F 3 HOH B 85 385 92 HOH HOH . F 3 HOH B 86 386 112 HOH HOH . F 3 HOH B 87 387 148 HOH HOH . F 3 HOH B 88 388 54 HOH HOH . F 3 HOH B 89 389 105 HOH HOH . F 3 HOH B 90 390 104 HOH HOH . F 3 HOH B 91 391 140 HOH HOH . F 3 HOH B 92 392 27 HOH HOH . F 3 HOH B 93 393 128 HOH HOH . F 3 HOH B 94 394 173 HOH HOH . F 3 HOH B 95 395 192 HOH HOH . F 3 HOH B 96 396 25 HOH HOH . F 3 HOH B 97 397 219 HOH HOH . F 3 HOH B 98 398 209 HOH HOH . F 3 HOH B 99 399 84 HOH HOH . F 3 HOH B 100 400 75 HOH HOH . F 3 HOH B 101 401 3 HOH HOH . F 3 HOH B 102 402 218 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 . . . C 2 -13.722 0.346 52.73 1 17.37 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . C 2 -14.465 -0.872 52.128 1 19.61 -1 O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . C 2 -14.445 1.611 52.241 1 20.18 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . C 2 -12.285 0.376 52.321 1 15.63 -1 O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . C 2 -13.797 0.271 54.344 1 15.62 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . C 2 -14.668 1.281 55.295 1 20.84 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . C 2 -16.104 1.123 54.9 1 18.64 -1 O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . C 2 -14.273 2.773 55.209 1 17.73 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . C 2 -14.348 0.618 56.762 1 22.42 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . C 2 -14.526 -0.758 56.843 1 16.73 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . C 2 -14.606 -1.175 58.365 1 26.4 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . C 2 -13.451 -0.995 58.965 1 16.29 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . C 2 -15.675 -0.345 59.193 1 26.78 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . C 2 -16.302 -1.133 60.144 1 32.29 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . C 2 -14.751 0.739 59.724 1 25.98 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . C 2 -15.445 1.356 60.907 1 22.68 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . C 2 -13.664 0.125 60.102 1 18.74 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . C 2 -12.458 0.936 60.184 1 21.03 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . C 2 -11.974 1.842 59.331 1 18.64 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . C 2 -10.833 2.348 59.804 1 20.8 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . C 2 -10.566 1.738 60.986 1 20.14 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . C 2 -9.539 1.806 61.959 1 18.32 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . C 2 -8.473 2.678 61.831 1 18.48 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . C 2 -9.581 1.014 63.021 1 19.86 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . C 2 -10.594 0.176 63.202 1 25.12 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . C 2 -10.561 -0.602 64.404 1 20.66 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . C 2 -11.594 0.046 62.322 1 19.22 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . C 2 -11.595 0.829 61.222 1 18.49 ? C4 GDP 201 A 1 HETATM 29 H H5' GDP . . . C 2 -13.688 -1.261 56.372 1 20.1 ? H5' GDP 201 A 1 HETATM 30 H "H5''" GDP . . . C 2 -15.447 -1.035 56.342 1 20.1 ? "H5''" GDP 201 A 1 HETATM 31 H H4' GDP . . . C 2 -14.893 -2.219 58.421 1 31.71 ? H4' GDP 201 A 1 HETATM 32 H H3' GDP . . . C 2 -16.494 0.078 58.624 1 32.16 ? H3' GDP 201 A 1 HETATM 33 H HO3' GDP . . . C 2 -17.044 -1.563 59.726 1 38.78 ? HO3' GDP 201 A 1 HETATM 34 H H2' GDP . . . C 2 -14.492 1.47 58.965 1 31.2 ? H2' GDP 201 A 1 HETATM 35 H HO2' GDP . . . C 2 -15.648 2.256 60.72 1 27.24 ? HO2' GDP 201 A 1 HETATM 36 H H1' GDP . . . C 2 -13.852 -0.263 61.098 1 22.51 ? H1' GDP 201 A 1 HETATM 37 H H8 GDP . . . C 2 -12.439 2.125 58.395 1 22.4 ? H8 GDP 201 A 1 HETATM 38 H HN21 GDP . . . C 2 -11.205 -0.405 65.147 1 24.82 ? HN21 GDP 201 A 1 HETATM 39 H HN22 GDP . . . C 2 -9.881 -1.335 64.504 1 24.82 ? HN22 GDP 201 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 39 #