data_1Z22 # _model_server_result.job_id ZF35Yd-s7qtnUblPCLRKlw _model_server_result.datetime_utc '2024-11-06 08:47:49' _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 1z22 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 1Z22 # _exptl.entry_id 1Z22 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 1Z22 _cell.length_a 67.01 _cell.length_b 71.333 _cell.length_c 65.684 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Z22 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 3 _struct_asym.id C _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 OD2 ASP 60 A ASP 64 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? metalc ? metalc2 C O3B GDP . A GDP 201 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.777 ? metalc ? metalc3 B MG MG . A MG 300 1_555 D O HOH . A HOH 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.977 ? # _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 1Z22 _atom_sites.fract_transf_matrix[1][1] 0.014923 _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] 0.014019 _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] 0.015224 _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 MG A 1 300 300 MG MG . C 3 GDP A 1 201 201 GDP GDP . D 4 HOH A 1 301 5 HOH HOH . D 4 HOH A 2 302 7 HOH HOH . D 4 HOH A 3 303 8 HOH HOH . D 4 HOH A 4 304 13 HOH HOH . D 4 HOH A 5 305 14 HOH HOH . D 4 HOH A 6 306 15 HOH HOH . D 4 HOH A 7 307 16 HOH HOH . D 4 HOH A 8 308 17 HOH HOH . D 4 HOH A 9 309 18 HOH HOH . D 4 HOH A 10 310 20 HOH HOH . D 4 HOH A 11 311 21 HOH HOH . D 4 HOH A 12 312 22 HOH HOH . D 4 HOH A 13 313 23 HOH HOH . D 4 HOH A 14 314 24 HOH HOH . D 4 HOH A 15 315 29 HOH HOH . D 4 HOH A 16 316 30 HOH HOH . D 4 HOH A 17 317 32 HOH HOH . D 4 HOH A 18 318 35 HOH HOH . D 4 HOH A 19 319 38 HOH HOH . D 4 HOH A 20 320 44 HOH HOH . D 4 HOH A 21 321 45 HOH HOH . D 4 HOH A 22 322 46 HOH HOH . D 4 HOH A 23 323 49 HOH HOH . D 4 HOH A 24 324 52 HOH HOH . D 4 HOH A 25 325 55 HOH HOH . D 4 HOH A 26 326 57 HOH HOH . D 4 HOH A 27 327 61 HOH HOH . D 4 HOH A 28 328 62 HOH HOH . D 4 HOH A 29 329 63 HOH HOH . D 4 HOH A 30 330 67 HOH HOH . D 4 HOH A 31 331 68 HOH HOH . D 4 HOH A 32 332 69 HOH HOH . D 4 HOH A 33 333 71 HOH HOH . D 4 HOH A 34 334 73 HOH HOH . D 4 HOH A 35 335 74 HOH HOH . D 4 HOH A 36 336 76 HOH HOH . D 4 HOH A 37 337 77 HOH HOH . D 4 HOH A 38 338 81 HOH HOH . D 4 HOH A 39 339 83 HOH HOH . D 4 HOH A 40 340 84 HOH HOH . D 4 HOH A 41 341 85 HOH HOH . D 4 HOH A 42 342 87 HOH HOH . D 4 HOH A 43 343 88 HOH HOH . D 4 HOH A 44 344 91 HOH HOH . D 4 HOH A 45 345 92 HOH HOH . D 4 HOH A 46 346 93 HOH HOH . D 4 HOH A 47 347 94 HOH HOH . D 4 HOH A 48 348 95 HOH HOH . D 4 HOH A 49 349 96 HOH HOH . D 4 HOH A 50 350 99 HOH HOH . D 4 HOH A 51 351 100 HOH HOH . D 4 HOH A 52 352 101 HOH HOH . D 4 HOH A 53 353 102 HOH HOH . D 4 HOH A 54 354 103 HOH HOH . D 4 HOH A 55 355 104 HOH HOH . D 4 HOH A 56 356 105 HOH HOH . D 4 HOH A 57 357 106 HOH HOH . D 4 HOH A 58 358 107 HOH HOH . D 4 HOH A 59 359 109 HOH HOH . D 4 HOH A 60 360 111 HOH HOH . D 4 HOH A 61 361 112 HOH HOH . D 4 HOH A 62 362 114 HOH HOH . D 4 HOH A 63 363 115 HOH HOH . D 4 HOH A 64 364 116 HOH HOH . D 4 HOH A 65 365 117 HOH HOH . D 4 HOH A 66 366 118 HOH HOH . D 4 HOH A 67 367 119 HOH HOH . D 4 HOH A 68 368 120 HOH HOH . D 4 HOH A 69 369 122 HOH HOH . D 4 HOH A 70 370 123 HOH HOH . D 4 HOH A 71 371 124 HOH HOH . D 4 HOH A 72 372 125 HOH HOH . D 4 HOH A 73 373 126 HOH HOH . D 4 HOH A 74 374 128 HOH HOH . D 4 HOH A 75 375 129 HOH HOH . D 4 HOH A 76 376 130 HOH HOH . D 4 HOH A 77 377 132 HOH HOH . D 4 HOH A 78 378 135 HOH HOH . D 4 HOH A 79 379 136 HOH HOH . D 4 HOH A 80 380 139 HOH HOH . D 4 HOH A 81 381 140 HOH HOH . D 4 HOH A 82 382 141 HOH HOH . D 4 HOH A 83 383 142 HOH HOH . D 4 HOH A 84 384 143 HOH HOH . D 4 HOH A 85 385 145 HOH HOH . D 4 HOH A 86 386 146 HOH HOH . D 4 HOH A 87 387 147 HOH HOH . D 4 HOH A 88 388 148 HOH HOH . D 4 HOH A 89 389 149 HOH HOH . D 4 HOH A 90 390 150 HOH HOH . D 4 HOH A 91 391 152 HOH HOH . D 4 HOH A 92 392 153 HOH HOH . D 4 HOH A 93 393 156 HOH HOH . D 4 HOH A 94 394 158 HOH HOH . D 4 HOH A 95 395 160 HOH HOH . D 4 HOH A 96 396 161 HOH HOH . D 4 HOH A 97 397 163 HOH HOH . D 4 HOH A 98 398 168 HOH HOH . D 4 HOH A 99 399 169 HOH HOH . D 4 HOH A 100 400 170 HOH HOH . D 4 HOH A 101 401 174 HOH HOH . D 4 HOH A 102 402 175 HOH HOH . D 4 HOH A 103 403 178 HOH HOH . D 4 HOH A 104 404 181 HOH HOH . D 4 HOH A 105 405 182 HOH HOH . D 4 HOH A 106 406 184 HOH HOH . D 4 HOH A 107 407 185 HOH HOH . D 4 HOH A 108 408 186 HOH HOH . D 4 HOH A 109 409 187 HOH HOH . D 4 HOH A 110 410 188 HOH HOH . D 4 HOH A 111 411 189 HOH HOH . D 4 HOH A 112 412 190 HOH HOH . D 4 HOH A 113 413 192 HOH HOH . D 4 HOH A 114 414 193 HOH HOH . D 4 HOH A 115 415 194 HOH HOH . D 4 HOH A 116 416 195 HOH HOH . D 4 HOH A 117 417 196 HOH HOH . D 4 HOH A 118 418 198 HOH HOH . D 4 HOH A 119 419 200 HOH HOH . D 4 HOH A 120 420 204 HOH HOH . D 4 HOH A 121 421 206 HOH HOH . D 4 HOH A 122 422 207 HOH HOH . D 4 HOH A 123 423 211 HOH HOH . D 4 HOH A 124 424 212 HOH HOH . D 4 HOH A 125 425 213 HOH HOH . D 4 HOH A 126 426 217 HOH HOH . D 4 HOH A 127 427 218 HOH HOH . D 4 HOH A 128 428 219 HOH HOH . D 4 HOH A 129 429 220 HOH HOH . D 4 HOH A 130 430 222 HOH HOH . D 4 HOH A 131 431 225 HOH HOH . D 4 HOH A 132 432 228 HOH HOH . D 4 HOH A 133 433 229 HOH HOH . D 4 HOH A 134 434 232 HOH HOH . D 4 HOH A 135 435 234 HOH HOH . D 4 HOH A 136 436 236 HOH HOH . D 4 HOH A 137 437 238 HOH HOH . D 4 HOH A 138 438 241 HOH HOH . D 4 HOH A 139 439 242 HOH HOH . D 4 HOH A 140 440 244 HOH HOH . D 4 HOH A 141 441 247 HOH HOH . D 4 HOH A 142 442 248 HOH HOH . D 4 HOH A 143 443 250 HOH HOH . D 4 HOH A 144 444 251 HOH HOH . D 4 HOH A 145 445 257 HOH HOH . D 4 HOH A 146 446 258 HOH HOH . D 4 HOH A 147 447 260 HOH HOH . D 4 HOH A 148 448 263 HOH HOH . D 4 HOH A 149 449 264 HOH HOH . D 4 HOH A 150 450 265 HOH HOH . D 4 HOH A 151 451 267 HOH HOH . D 4 HOH A 152 452 270 HOH HOH . D 4 HOH A 153 453 271 HOH HOH . D 4 HOH A 154 454 272 HOH HOH . D 4 HOH A 155 455 282 HOH HOH . D 4 HOH A 156 456 284 HOH HOH . D 4 HOH A 157 457 286 HOH HOH . D 4 HOH A 158 458 287 HOH HOH . D 4 HOH A 159 459 288 HOH HOH . D 4 HOH A 160 460 291 HOH HOH . D 4 HOH A 161 461 297 HOH HOH . D 4 HOH A 162 462 298 HOH HOH . D 4 HOH A 163 463 299 HOH HOH . D 4 HOH A 164 464 301 HOH HOH . D 4 HOH A 165 465 302 HOH HOH . D 4 HOH A 166 466 310 HOH HOH . D 4 HOH A 167 467 320 HOH HOH . D 4 HOH A 168 468 321 HOH HOH . D 4 HOH A 169 469 322 HOH HOH . D 4 HOH A 170 470 331 HOH HOH . D 4 HOH A 171 471 332 HOH HOH . D 4 HOH A 172 472 333 HOH HOH . D 4 HOH A 173 473 334 HOH HOH . D 4 HOH A 174 474 336 HOH HOH . D 4 HOH A 175 475 344 HOH HOH . D 4 HOH A 176 476 346 HOH HOH . D 4 HOH A 177 477 349 HOH HOH . D 4 HOH A 178 478 355 HOH HOH . D 4 HOH A 179 479 356 HOH HOH . D 4 HOH A 180 480 360 HOH HOH . D 4 HOH A 181 481 361 HOH HOH . D 4 HOH A 182 482 363 HOH HOH . D 4 HOH A 183 483 367 HOH HOH . D 4 HOH A 184 484 384 HOH HOH . D 4 HOH A 185 485 387 HOH HOH . D 4 HOH A 186 486 388 HOH HOH . D 4 HOH A 187 487 396 HOH HOH . D 4 HOH A 188 488 400 HOH HOH . D 4 HOH A 189 489 401 HOH HOH . D 4 HOH A 190 490 412 HOH HOH . D 4 HOH A 191 491 413 HOH HOH . D 4 HOH A 192 492 423 HOH HOH . D 4 HOH A 193 493 464 HOH HOH . D 4 HOH A 194 494 478 HOH HOH . D 4 HOH A 195 495 479 HOH HOH . D 4 HOH A 196 496 487 HOH HOH . D 4 HOH A 197 497 489 HOH HOH . D 4 HOH A 198 498 492 HOH HOH . D 4 HOH A 199 499 504 HOH HOH . D 4 HOH A 200 500 516 HOH HOH . D 4 HOH A 201 501 551 HOH HOH . D 4 HOH A 202 502 554 HOH HOH . D 4 HOH A 203 503 556 HOH HOH . D 4 HOH A 204 504 565 HOH HOH . D 4 HOH A 205 505 581 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 3 16.14 23.898 10.608 1 15.03 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . C 3 15.189 23.112 9.756 1 15.47 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . C 3 15.379 24.521 11.752 1 15.94 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . C 3 17.238 23.001 11.138 1 16.07 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . C 3 16.758 25.1 9.736 1 16.38 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . C 3 18.268 25.134 9.179 1 16.86 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . C 3 18.536 23.942 8.305 1 17.28 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . C 3 19.251 25.237 10.313 1 16.86 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . C 3 18.27 26.49 8.312 1 16.07 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . C 3 17.35 26.677 7.235 1 16.42 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . C 3 17.887 27.745 6.291 1 16.15 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . C 3 17.945 29.009 6.974 1 16.19 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . C 3 19.306 27.424 5.842 1 16.52 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . C 3 19.479 27.861 4.488 1 17.53 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . C 3 20.162 28.272 6.756 1 16.38 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . C 3 21.428 28.599 6.174 1 18.75 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . C 3 19.286 29.495 6.967 1 14.84 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . C 3 19.61 30.197 8.231 1 14.82 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . C 3 19.79 29.667 9.456 1 14.27 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . C 3 20.069 30.639 10.366 1 14.33 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . C 3 20.078 31.815 9.705 1 13.93 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . C 3 20.296 33.238 10.043 1 13.99 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . C 3 20.566 33.594 11.211 1 14.3 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . C 3 20.197 34.136 9.053 1 14.89 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . C 3 19.911 33.802 7.773 1 14.56 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . C 3 19.836 34.786 6.846 1 14.22 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . C 3 19.7 32.52 7.386 1 13.01 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . C 3 19.769 31.514 8.298 1 14.24 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #