data_8S8C # _model_server_result.job_id vErrJ-TjFNfD3RV0N16fQQ _model_server_result.datetime_utc '2025-03-04 17:51:14' _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 8s8c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 8S8C # _exptl.entry_id 8S8C _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 120 _cell.entry_id 8S8C _cell.length_a 93.853 _cell.length_b 93.853 _cell.length_c 121.021 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8S8C _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # 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 covale ? covale1 A SG CYS 13 A CYS 12 1_555 D C43 A1H5U . A A1H5U 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.825 ? metalc ? metalc1 A OG SER 18 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc2 B O2B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc3 C MG MG . A MG 202 1_555 E O HOH . A HOH 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc4 C MG MG . A MG 202 1_555 E O HOH . A HOH 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc5 C MG MG . A MG 202 1_555 E O HOH . A HOH 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc6 C MG MG . A MG 202 1_555 E O HOH . A HOH 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? # _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 166 n n PB O2B GDP sing 167 n n PB O3B GDP sing 168 n n PB O3A GDP sing 169 n n O2B HOB2 GDP sing 170 n n O3B HOB3 GDP sing 171 n n O3A PA GDP sing 172 n n PA O1A GDP doub 173 n n PA O2A GDP sing 174 n n PA O5' GDP sing 175 n n O2A HOA2 GDP sing 176 n n O5' C5' GDP sing 177 n n C5' C4' GDP sing 178 n n C5' H5' GDP sing 179 n n C5' "H5''" GDP sing 180 n n C4' O4' GDP sing 181 n n C4' C3' GDP sing 182 n n C4' H4' GDP sing 183 n n O4' C1' GDP sing 184 n n C3' O3' GDP sing 185 n n C3' C2' GDP sing 186 n n C3' H3' GDP sing 187 n n O3' HO3' GDP sing 188 n n C2' O2' GDP sing 189 n n C2' C1' GDP sing 190 n n C2' H2' GDP sing 191 n n O2' HO2' GDP sing 192 n n C1' N9 GDP sing 193 n n C1' H1' GDP sing 194 n n N9 C8 GDP sing 195 n y N9 C4 GDP sing 196 n y C8 N7 GDP doub 197 n y C8 H8 GDP sing 198 n n N7 C5 GDP sing 199 n y C5 C6 GDP sing 200 n n C5 C4 GDP doub 201 n y C6 O6 GDP doub 202 n n C6 N1 GDP sing 203 n n N1 C2 GDP sing 204 n n N1 HN1 GDP sing 205 n n C2 N2 GDP sing 206 n n C2 N3 GDP doub 207 n n N2 HN21 GDP sing 208 n n N2 HN22 GDP sing 209 n n N3 C4 GDP sing 210 n n # _atom_sites.entry_id 8S8C _atom_sites.fract_transf_matrix[1][1] 0.010655 _atom_sites.fract_transf_matrix[1][2] 0.006152 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012303 _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] 0.008263 _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 1 201 201 GDP GDP . C 3 MG A 1 202 202 MG MG . D 4 A1H5U A 1 203 1 A1H5U L01 . E 5 HOH A 1 301 118 HOH HOH . E 5 HOH A 2 302 152 HOH HOH . E 5 HOH A 3 303 179 HOH HOH . E 5 HOH A 4 304 44 HOH HOH . E 5 HOH A 5 305 109 HOH HOH . E 5 HOH A 6 306 132 HOH HOH . E 5 HOH A 7 307 106 HOH HOH . E 5 HOH A 8 308 24 HOH HOH . E 5 HOH A 9 309 21 HOH HOH . E 5 HOH A 10 310 93 HOH HOH . E 5 HOH A 11 311 1 HOH HOH . E 5 HOH A 12 312 116 HOH HOH . E 5 HOH A 13 313 50 HOH HOH . E 5 HOH A 14 314 175 HOH HOH . E 5 HOH A 15 315 148 HOH HOH . E 5 HOH A 16 316 48 HOH HOH . E 5 HOH A 17 317 111 HOH HOH . E 5 HOH A 18 318 177 HOH HOH . E 5 HOH A 19 319 70 HOH HOH . E 5 HOH A 20 320 26 HOH HOH . E 5 HOH A 21 321 11 HOH HOH . E 5 HOH A 22 322 39 HOH HOH . E 5 HOH A 23 323 20 HOH HOH . E 5 HOH A 24 324 121 HOH HOH . E 5 HOH A 25 325 18 HOH HOH . E 5 HOH A 26 326 176 HOH HOH . E 5 HOH A 27 327 171 HOH HOH . E 5 HOH A 28 328 7 HOH HOH . E 5 HOH A 29 329 47 HOH HOH . E 5 HOH A 30 330 63 HOH HOH . E 5 HOH A 31 331 15 HOH HOH . E 5 HOH A 32 332 13 HOH HOH . E 5 HOH A 33 333 3 HOH HOH . E 5 HOH A 34 334 84 HOH HOH . E 5 HOH A 35 335 69 HOH HOH . E 5 HOH A 36 336 77 HOH HOH . E 5 HOH A 37 337 38 HOH HOH . E 5 HOH A 38 338 74 HOH HOH . E 5 HOH A 39 339 125 HOH HOH . E 5 HOH A 40 340 29 HOH HOH . E 5 HOH A 41 341 83 HOH HOH . E 5 HOH A 42 342 173 HOH HOH . E 5 HOH A 43 343 155 HOH HOH . E 5 HOH A 44 344 56 HOH HOH . E 5 HOH A 45 345 60 HOH HOH . E 5 HOH A 46 346 17 HOH HOH . E 5 HOH A 47 347 46 HOH HOH . E 5 HOH A 48 348 10 HOH HOH . E 5 HOH A 49 349 4 HOH HOH . E 5 HOH A 50 350 32 HOH HOH . E 5 HOH A 51 351 72 HOH HOH . E 5 HOH A 52 352 98 HOH HOH . E 5 HOH A 53 353 30 HOH HOH . E 5 HOH A 54 354 33 HOH HOH . E 5 HOH A 55 355 25 HOH HOH . E 5 HOH A 56 356 2 HOH HOH . E 5 HOH A 57 357 36 HOH HOH . E 5 HOH A 58 358 110 HOH HOH . E 5 HOH A 59 359 82 HOH HOH . E 5 HOH A 60 360 145 HOH HOH . E 5 HOH A 61 361 90 HOH HOH . E 5 HOH A 62 362 136 HOH HOH . E 5 HOH A 63 363 41 HOH HOH . E 5 HOH A 64 364 12 HOH HOH . E 5 HOH A 65 365 5 HOH HOH . E 5 HOH A 66 366 40 HOH HOH . E 5 HOH A 67 367 126 HOH HOH . E 5 HOH A 68 368 35 HOH HOH . E 5 HOH A 69 369 92 HOH HOH . E 5 HOH A 70 370 157 HOH HOH . E 5 HOH A 71 371 167 HOH HOH . E 5 HOH A 72 372 174 HOH HOH . E 5 HOH A 73 373 52 HOH HOH . E 5 HOH A 74 374 100 HOH HOH . E 5 HOH A 75 375 34 HOH HOH . E 5 HOH A 76 376 22 HOH HOH . E 5 HOH A 77 377 96 HOH HOH . E 5 HOH A 78 378 71 HOH HOH . E 5 HOH A 79 379 103 HOH HOH . E 5 HOH A 80 380 170 HOH HOH . E 5 HOH A 81 381 57 HOH HOH . E 5 HOH A 82 382 59 HOH HOH . E 5 HOH A 83 383 23 HOH HOH . E 5 HOH A 84 384 67 HOH HOH . E 5 HOH A 85 385 122 HOH HOH . E 5 HOH A 86 386 51 HOH HOH . E 5 HOH A 87 387 172 HOH HOH . E 5 HOH A 88 388 130 HOH HOH . E 5 HOH A 89 389 166 HOH HOH . E 5 HOH A 90 390 73 HOH HOH . E 5 HOH A 91 391 85 HOH HOH . E 5 HOH A 92 392 31 HOH HOH . E 5 HOH A 93 393 159 HOH HOH . E 5 HOH A 94 394 28 HOH HOH . E 5 HOH A 95 395 123 HOH HOH . E 5 HOH A 96 396 112 HOH HOH . E 5 HOH A 97 397 37 HOH HOH . E 5 HOH A 98 398 137 HOH HOH . E 5 HOH A 99 399 86 HOH HOH . E 5 HOH A 100 400 164 HOH HOH . E 5 HOH A 101 401 6 HOH HOH . E 5 HOH A 102 402 91 HOH HOH . E 5 HOH A 103 403 8 HOH HOH . E 5 HOH A 104 404 129 HOH HOH . E 5 HOH A 105 405 88 HOH HOH . E 5 HOH A 106 406 150 HOH HOH . E 5 HOH A 107 407 75 HOH HOH . E 5 HOH A 108 408 156 HOH HOH . E 5 HOH A 109 409 55 HOH HOH . E 5 HOH A 110 410 76 HOH HOH . E 5 HOH A 111 411 49 HOH HOH . E 5 HOH A 112 412 61 HOH HOH . E 5 HOH A 113 413 107 HOH HOH . E 5 HOH A 114 414 117 HOH HOH . E 5 HOH A 115 415 147 HOH HOH . E 5 HOH A 116 416 124 HOH HOH . E 5 HOH A 117 417 161 HOH HOH . E 5 HOH A 118 418 54 HOH HOH . E 5 HOH A 119 419 158 HOH HOH . E 5 HOH A 120 420 87 HOH HOH . E 5 HOH A 121 421 160 HOH HOH . E 5 HOH A 122 422 128 HOH HOH . E 5 HOH A 123 423 151 HOH HOH . E 5 HOH A 124 424 114 HOH HOH . E 5 HOH A 125 425 42 HOH HOH . E 5 HOH A 126 426 140 HOH HOH . E 5 HOH A 127 427 101 HOH HOH . E 5 HOH A 128 428 102 HOH HOH . E 5 HOH A 129 429 139 HOH HOH . E 5 HOH A 130 430 120 HOH HOH . E 5 HOH A 131 431 134 HOH HOH . E 5 HOH A 132 432 143 HOH HOH . E 5 HOH A 133 433 65 HOH HOH . E 5 HOH A 134 434 141 HOH HOH . E 5 HOH A 135 435 105 HOH HOH . E 5 HOH A 136 436 53 HOH HOH . E 5 HOH A 137 437 127 HOH HOH . E 5 HOH A 138 438 27 HOH HOH . E 5 HOH A 139 439 138 HOH HOH . E 5 HOH A 140 440 79 HOH HOH . E 5 HOH A 141 441 115 HOH HOH . E 5 HOH A 142 442 97 HOH HOH . E 5 HOH A 143 443 142 HOH HOH . E 5 HOH A 144 444 66 HOH HOH . E 5 HOH A 145 445 43 HOH HOH . E 5 HOH A 146 446 19 HOH HOH . E 5 HOH A 147 447 9 HOH HOH . E 5 HOH A 148 448 104 HOH HOH . E 5 HOH A 149 449 178 HOH HOH . E 5 HOH A 150 450 146 HOH HOH . E 5 HOH A 151 451 119 HOH HOH . E 5 HOH A 152 452 64 HOH HOH . E 5 HOH A 153 453 135 HOH HOH . E 5 HOH A 154 454 80 HOH HOH . E 5 HOH A 155 455 144 HOH HOH . E 5 HOH A 156 456 14 HOH HOH . E 5 HOH A 157 457 99 HOH HOH . E 5 HOH A 158 458 168 HOH HOH . E 5 HOH A 159 459 45 HOH HOH . E 5 HOH A 160 460 133 HOH HOH . E 5 HOH A 161 461 81 HOH HOH . E 5 HOH A 162 462 94 HOH HOH . E 5 HOH A 163 463 163 HOH HOH . E 5 HOH A 164 464 108 HOH HOH . E 5 HOH A 165 465 113 HOH HOH . E 5 HOH A 166 466 131 HOH HOH . E 5 HOH A 167 467 62 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 -8.531 13.69 -21.385 1 28.45 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 -9.222 12.991 -22.509 1 28.62 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 -9.424 14.822 -20.959 1 32.44 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 -7.954 12.809 -20.342 1 28.82 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 -7.276 14.462 -22.088 1 29.64 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 -6.873 16.043 -22.059 1 30.83 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 -7.794 16.912 -22.862 1 30.29 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 -6.563 16.366 -20.633 1 31.97 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 -5.54 15.989 -22.959 1 31.5 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 -4.448 15.155 -22.611 1 31.95 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 -3.155 15.789 -23.097 1 31.75 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 -3.215 15.78 -24.529 1 28.26 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 -3.053 17.234 -22.617 1 33.31 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 -1.695 17.551 -22.264 1 37 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 -3.556 18.032 -23.809 1 32.73 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 -3.019 19.343 -23.947 1 35.08 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 -3.17 17.155 -24.991 1 28.99 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 -4.056 17.289 -26.159 1 26.37 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 -5.399 17.123 -26.224 1 25.66 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 -5.903 17.322 -27.461 1 23.9 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 -4.845 17.623 -28.209 1 25.04 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 -4.668 17.948 -29.626 1 25.16 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 -5.664 17.978 -30.391 1 24.64 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 -3.432 18.201 -30.045 1 25.96 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 -2.343 18.172 -29.23 1 26.98 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 -1.142 18.444 -29.757 1 27.82 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 -2.413 17.881 -27.909 1 27.56 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 -3.636 17.603 -27.37 1 26.96 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #