data_8GI3 # _model_server_result.job_id rR2HpeQe5BJuEgg2o_7lIw _model_server_result.datetime_utc '2024-10-11 06:21:11' _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 8gi3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 8GI3 # _exptl.entry_id 8GI3 _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 8GI3 _cell.length_a 32.048 _cell.length_b 64.081 _cell.length_c 82.504 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GI3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,D _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 metalc ? metalc1 A OG1 THR 22 A THR 19 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc2 A O PRO 39 A PRO 36 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc3 B O1B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc4 C MG MG . A MG 202 1_555 D O HOH . A HOH 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc5 C MG MG . A MG 202 1_555 D O HOH . A HOH 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc6 C MG MG . A MG 202 1_555 D O HOH . A HOH 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? # _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 8GI3 _atom_sites.fract_transf_matrix[1][1] 0.031203 _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] 0.015605 _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] 0.012121 _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 HOH A 1 301 382 HOH HOH . D 4 HOH A 2 302 327 HOH HOH . D 4 HOH A 3 303 386 HOH HOH . D 4 HOH A 4 304 356 HOH HOH . D 4 HOH A 5 305 344 HOH HOH . D 4 HOH A 6 306 384 HOH HOH . D 4 HOH A 7 307 288 HOH HOH . D 4 HOH A 8 308 290 HOH HOH . D 4 HOH A 9 309 319 HOH HOH . D 4 HOH A 10 310 278 HOH HOH . D 4 HOH A 11 311 281 HOH HOH . D 4 HOH A 12 312 273 HOH HOH . D 4 HOH A 13 313 390 HOH HOH . D 4 HOH A 14 314 389 HOH HOH . D 4 HOH A 15 315 302 HOH HOH . D 4 HOH A 16 316 257 HOH HOH . D 4 HOH A 17 317 296 HOH HOH . D 4 HOH A 18 318 346 HOH HOH . D 4 HOH A 19 319 336 HOH HOH . D 4 HOH A 20 320 315 HOH HOH . D 4 HOH A 21 321 348 HOH HOH . D 4 HOH A 22 322 237 HOH HOH . D 4 HOH A 23 323 260 HOH HOH . D 4 HOH A 24 324 352 HOH HOH . D 4 HOH A 25 325 338 HOH HOH . D 4 HOH A 26 326 328 HOH HOH . D 4 HOH A 27 327 342 HOH HOH . D 4 HOH A 28 328 345 HOH HOH . D 4 HOH A 29 329 391 HOH HOH . D 4 HOH A 30 330 379 HOH HOH . D 4 HOH A 31 331 362 HOH HOH . D 4 HOH A 32 332 230 HOH HOH . D 4 HOH A 33 333 305 HOH HOH . D 4 HOH A 34 334 232 HOH HOH . D 4 HOH A 35 335 353 HOH HOH . D 4 HOH A 36 336 265 HOH HOH . D 4 HOH A 37 337 238 HOH HOH . D 4 HOH A 38 338 216 HOH HOH . D 4 HOH A 39 339 279 HOH HOH . D 4 HOH A 40 340 297 HOH HOH . D 4 HOH A 41 341 246 HOH HOH . D 4 HOH A 42 342 321 HOH HOH . D 4 HOH A 43 343 203 HOH HOH . D 4 HOH A 44 344 205 HOH HOH . D 4 HOH A 45 345 370 HOH HOH . D 4 HOH A 46 346 277 HOH HOH . D 4 HOH A 47 347 351 HOH HOH . D 4 HOH A 48 348 242 HOH HOH . D 4 HOH A 49 349 256 HOH HOH . D 4 HOH A 50 350 292 HOH HOH . D 4 HOH A 51 351 323 HOH HOH . D 4 HOH A 52 352 204 HOH HOH . D 4 HOH A 53 353 214 HOH HOH . D 4 HOH A 54 354 334 HOH HOH . D 4 HOH A 55 355 243 HOH HOH . D 4 HOH A 56 356 369 HOH HOH . D 4 HOH A 57 357 335 HOH HOH . D 4 HOH A 58 358 360 HOH HOH . D 4 HOH A 59 359 373 HOH HOH . D 4 HOH A 60 360 208 HOH HOH . D 4 HOH A 61 361 385 HOH HOH . D 4 HOH A 62 362 251 HOH HOH . D 4 HOH A 63 363 363 HOH HOH . D 4 HOH A 64 364 270 HOH HOH . D 4 HOH A 65 365 275 HOH HOH . D 4 HOH A 66 366 234 HOH HOH . D 4 HOH A 67 367 322 HOH HOH . D 4 HOH A 68 368 287 HOH HOH . D 4 HOH A 69 369 316 HOH HOH . D 4 HOH A 70 370 219 HOH HOH . D 4 HOH A 71 371 212 HOH HOH . D 4 HOH A 72 372 207 HOH HOH . D 4 HOH A 73 373 221 HOH HOH . D 4 HOH A 74 374 209 HOH HOH . D 4 HOH A 75 375 376 HOH HOH . D 4 HOH A 76 376 250 HOH HOH . D 4 HOH A 77 377 354 HOH HOH . D 4 HOH A 78 378 285 HOH HOH . D 4 HOH A 79 379 349 HOH HOH . D 4 HOH A 80 380 211 HOH HOH . D 4 HOH A 81 381 333 HOH HOH . D 4 HOH A 82 382 388 HOH HOH . D 4 HOH A 83 383 236 HOH HOH . D 4 HOH A 84 384 326 HOH HOH . D 4 HOH A 85 385 247 HOH HOH . D 4 HOH A 86 386 225 HOH HOH . D 4 HOH A 87 387 210 HOH HOH . D 4 HOH A 88 388 241 HOH HOH . D 4 HOH A 89 389 213 HOH HOH . D 4 HOH A 90 390 274 HOH HOH . D 4 HOH A 91 391 227 HOH HOH . D 4 HOH A 92 392 330 HOH HOH . D 4 HOH A 93 393 240 HOH HOH . D 4 HOH A 94 394 331 HOH HOH . D 4 HOH A 95 395 294 HOH HOH . D 4 HOH A 96 396 304 HOH HOH . D 4 HOH A 97 397 233 HOH HOH . D 4 HOH A 98 398 231 HOH HOH . D 4 HOH A 99 399 244 HOH HOH . D 4 HOH A 100 400 259 HOH HOH . D 4 HOH A 101 401 222 HOH HOH . D 4 HOH A 102 402 280 HOH HOH . D 4 HOH A 103 403 266 HOH HOH . D 4 HOH A 104 404 300 HOH HOH . D 4 HOH A 105 405 215 HOH HOH . D 4 HOH A 106 406 341 HOH HOH . D 4 HOH A 107 407 245 HOH HOH . D 4 HOH A 108 408 295 HOH HOH . D 4 HOH A 109 409 339 HOH HOH . D 4 HOH A 110 410 320 HOH HOH . D 4 HOH A 111 411 224 HOH HOH . D 4 HOH A 112 412 380 HOH HOH . D 4 HOH A 113 413 261 HOH HOH . D 4 HOH A 114 414 377 HOH HOH . D 4 HOH A 115 415 299 HOH HOH . D 4 HOH A 116 416 252 HOH HOH . D 4 HOH A 117 417 310 HOH HOH . D 4 HOH A 118 418 298 HOH HOH . D 4 HOH A 119 419 276 HOH HOH . D 4 HOH A 120 420 217 HOH HOH . D 4 HOH A 121 421 206 HOH HOH . D 4 HOH A 122 422 223 HOH HOH . D 4 HOH A 123 423 307 HOH HOH . D 4 HOH A 124 424 293 HOH HOH . D 4 HOH A 125 425 365 HOH HOH . D 4 HOH A 126 426 314 HOH HOH . D 4 HOH A 127 427 301 HOH HOH . D 4 HOH A 128 428 254 HOH HOH . D 4 HOH A 129 429 268 HOH HOH . D 4 HOH A 130 430 350 HOH HOH . D 4 HOH A 131 431 312 HOH HOH . D 4 HOH A 132 432 220 HOH HOH . D 4 HOH A 133 433 272 HOH HOH . D 4 HOH A 134 434 311 HOH HOH . D 4 HOH A 135 435 218 HOH HOH . D 4 HOH A 136 436 226 HOH HOH . D 4 HOH A 137 437 235 HOH HOH . D 4 HOH A 138 438 228 HOH HOH . D 4 HOH A 139 439 358 HOH HOH . D 4 HOH A 140 440 284 HOH HOH . D 4 HOH A 141 441 248 HOH HOH . D 4 HOH A 142 442 262 HOH HOH . D 4 HOH A 143 443 313 HOH HOH . D 4 HOH A 144 444 387 HOH HOH . D 4 HOH A 145 445 283 HOH HOH . D 4 HOH A 146 446 239 HOH HOH . D 4 HOH A 147 447 364 HOH HOH . D 4 HOH A 148 448 267 HOH HOH . D 4 HOH A 149 449 337 HOH HOH . D 4 HOH A 150 450 258 HOH HOH . D 4 HOH A 151 451 378 HOH HOH . D 4 HOH A 152 452 332 HOH HOH . D 4 HOH A 153 453 289 HOH HOH . D 4 HOH A 154 454 372 HOH HOH . D 4 HOH A 155 455 343 HOH HOH . D 4 HOH A 156 456 383 HOH HOH . D 4 HOH A 157 457 264 HOH HOH . D 4 HOH A 158 458 282 HOH HOH . D 4 HOH A 159 459 309 HOH HOH . D 4 HOH A 160 460 286 HOH HOH . D 4 HOH A 161 461 263 HOH HOH . D 4 HOH A 162 462 255 HOH HOH . D 4 HOH A 163 463 291 HOH HOH . D 4 HOH A 164 464 366 HOH HOH . D 4 HOH A 165 465 318 HOH HOH . D 4 HOH A 166 466 340 HOH HOH . D 4 HOH A 167 467 317 HOH HOH . D 4 HOH A 168 468 347 HOH HOH . D 4 HOH A 169 469 371 HOH HOH . D 4 HOH A 170 470 303 HOH HOH . D 4 HOH A 171 471 367 HOH HOH . D 4 HOH A 172 472 269 HOH HOH . D 4 HOH A 173 473 368 HOH HOH . D 4 HOH A 174 474 229 HOH HOH . D 4 HOH A 175 475 308 HOH HOH . D 4 HOH A 176 476 355 HOH HOH . D 4 HOH A 177 477 271 HOH HOH . D 4 HOH A 178 478 249 HOH HOH . D 4 HOH A 179 479 357 HOH HOH . D 4 HOH A 180 480 374 HOH HOH . D 4 HOH A 181 481 306 HOH HOH . D 4 HOH A 182 482 359 HOH HOH . D 4 HOH A 183 483 375 HOH HOH . D 4 HOH A 184 484 325 HOH HOH . D 4 HOH A 185 485 329 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 -3.23 -1.941 12.274 1 6.74 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 -2.798 -1.836 10.85 1 6.56 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 -4.669 -1.589 12.456 1 6.51 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 -2.32 -1.175 13.197 1 7.36 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 -3.093 -3.5 12.687 1 6.66 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 -2.307 -4.722 12.01 1 6.69 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 -3.038 -5.205 10.815 1 6.77 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 -0.871 -4.36 11.851 1 7.17 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 -2.443 -5.819 13.165 1 6.85 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 -2.044 -5.489 14.506 1 7.06 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 -1.77 -6.774 15.247 1 7.7 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 -2.981 -7.574 15.294 1 8.03 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 -0.709 -7.685 14.621 1 8.28 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 0.02 -8.358 15.637 1 9.93 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 -1.55 -8.661 13.794 1 8.81 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 -0.896 -9.891 13.577 1 10.61 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 -2.771 -8.828 14.69 1 7.84 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 -3.981 -9.192 13.966 1 7.23 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 -4.455 -8.609 12.819 1 7.56 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 -5.575 -9.137 12.394 1 7.15 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 -5.867 -10.121 13.329 1 6.85 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 -6.958 -11.019 13.399 1 7.04 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 -7.912 -11.128 12.628 1 7.8 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 -6.864 -11.848 14.514 1 7.54 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 -5.855 -11.82 15.44 1 7.84 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 -5.942 -12.703 16.441 1 9.52 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 -4.823 -10.982 15.377 1 7.47 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 -4.893 -10.165 14.301 1 7.09 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #