data_3AF0 # _model_server_result.job_id p7N2olsTWhyTIFvSpUSj2Q _model_server_result.datetime_utc '2025-02-24 11:58:38' _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 3af0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":313}' # _entry.id 3AF0 # _exptl.entry_id 3AF0 _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 3AF0 _cell.length_a 104.73 _cell.length_b 104.73 _cell.length_c 90.4 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AF0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 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 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 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 3AF0 _atom_sites.fract_transf_matrix[1][1] 0.009548 _atom_sites.fract_transf_matrix[1][2] 0.005513 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011025 _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] 0.011062 _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 1 313 1 GDP GDP . C 3 PAU A 1 314 2 PAU PAU . D 4 CL A 1 315 1 CL CL . E 5 GOL A 1 316 1 GOL GOL . F 5 GOL A 1 317 2 GOL GOL . G 5 GOL A 1 318 3 GOL GOL . H 5 GOL A 1 319 4 GOL GOL . I 5 GOL A 1 320 5 GOL GOL . J 5 GOL A 1 321 6 GOL GOL . K 5 GOL A 1 322 7 GOL GOL . L 5 GOL A 1 323 8 GOL GOL . M 5 GOL A 1 324 9 GOL GOL . N 6 HOH A 1 325 1 HOH HOH . N 6 HOH A 2 326 2 HOH HOH . N 6 HOH A 3 327 3 HOH HOH . N 6 HOH A 4 328 4 HOH HOH . N 6 HOH A 5 329 5 HOH HOH . N 6 HOH A 6 330 6 HOH HOH . N 6 HOH A 7 331 7 HOH HOH . N 6 HOH A 8 332 8 HOH HOH . N 6 HOH A 9 333 9 HOH HOH . N 6 HOH A 10 334 10 HOH HOH . N 6 HOH A 11 335 11 HOH HOH . N 6 HOH A 12 336 12 HOH HOH . N 6 HOH A 13 337 13 HOH HOH . N 6 HOH A 14 338 14 HOH HOH . N 6 HOH A 15 339 15 HOH HOH . N 6 HOH A 16 340 16 HOH HOH . N 6 HOH A 17 341 17 HOH HOH . N 6 HOH A 18 342 18 HOH HOH . N 6 HOH A 19 343 19 HOH HOH . N 6 HOH A 20 344 20 HOH HOH . N 6 HOH A 21 345 21 HOH HOH . N 6 HOH A 22 346 22 HOH HOH . N 6 HOH A 23 347 23 HOH HOH . N 6 HOH A 24 348 24 HOH HOH . N 6 HOH A 25 349 25 HOH HOH . N 6 HOH A 26 350 26 HOH HOH . N 6 HOH A 27 351 27 HOH HOH . N 6 HOH A 28 352 28 HOH HOH . N 6 HOH A 29 353 29 HOH HOH . N 6 HOH A 30 354 30 HOH HOH . N 6 HOH A 31 355 31 HOH HOH . N 6 HOH A 32 356 32 HOH HOH . N 6 HOH A 33 357 33 HOH HOH . N 6 HOH A 34 358 34 HOH HOH . N 6 HOH A 35 359 35 HOH HOH . N 6 HOH A 36 360 36 HOH HOH . N 6 HOH A 37 361 37 HOH HOH . N 6 HOH A 38 362 38 HOH HOH . N 6 HOH A 39 363 39 HOH HOH . N 6 HOH A 40 364 40 HOH HOH . N 6 HOH A 41 365 41 HOH HOH . N 6 HOH A 42 366 42 HOH HOH . N 6 HOH A 43 367 43 HOH HOH . N 6 HOH A 44 368 44 HOH HOH . N 6 HOH A 45 369 45 HOH HOH . N 6 HOH A 46 370 46 HOH HOH . N 6 HOH A 47 371 47 HOH HOH . N 6 HOH A 48 372 48 HOH HOH . N 6 HOH A 49 373 49 HOH HOH . N 6 HOH A 50 374 50 HOH HOH . N 6 HOH A 51 375 51 HOH HOH . N 6 HOH A 52 376 52 HOH HOH . N 6 HOH A 53 377 53 HOH HOH . N 6 HOH A 54 378 54 HOH HOH . N 6 HOH A 55 379 55 HOH HOH . N 6 HOH A 56 380 56 HOH HOH . N 6 HOH A 57 381 57 HOH HOH . N 6 HOH A 58 382 58 HOH HOH . N 6 HOH A 59 383 59 HOH HOH . N 6 HOH A 60 384 60 HOH HOH . N 6 HOH A 61 385 61 HOH HOH . N 6 HOH A 62 386 62 HOH HOH . N 6 HOH A 63 387 63 HOH HOH . N 6 HOH A 64 388 64 HOH HOH . N 6 HOH A 65 389 65 HOH HOH . N 6 HOH A 66 390 66 HOH HOH . N 6 HOH A 67 391 67 HOH HOH . N 6 HOH A 68 392 68 HOH HOH . N 6 HOH A 69 393 69 HOH HOH . N 6 HOH A 70 394 70 HOH HOH . N 6 HOH A 71 395 71 HOH HOH . N 6 HOH A 72 396 72 HOH HOH . N 6 HOH A 73 397 73 HOH HOH . N 6 HOH A 74 398 74 HOH HOH . N 6 HOH A 75 399 75 HOH HOH . N 6 HOH A 76 400 76 HOH HOH . N 6 HOH A 77 401 77 HOH HOH . N 6 HOH A 78 402 78 HOH HOH . N 6 HOH A 79 403 79 HOH HOH . N 6 HOH A 80 404 80 HOH HOH . N 6 HOH A 81 405 81 HOH HOH . N 6 HOH A 82 406 82 HOH HOH . N 6 HOH A 83 407 83 HOH HOH . N 6 HOH A 84 408 84 HOH HOH . N 6 HOH A 85 409 85 HOH HOH . N 6 HOH A 86 410 86 HOH HOH . N 6 HOH A 87 411 87 HOH HOH . N 6 HOH A 88 412 88 HOH HOH . N 6 HOH A 89 413 89 HOH HOH . N 6 HOH A 90 414 90 HOH HOH . N 6 HOH A 91 415 91 HOH HOH . N 6 HOH A 92 416 92 HOH HOH . N 6 HOH A 93 417 93 HOH HOH . N 6 HOH A 94 418 94 HOH HOH . N 6 HOH A 95 419 95 HOH HOH . N 6 HOH A 96 420 96 HOH HOH . N 6 HOH A 97 421 97 HOH HOH . N 6 HOH A 98 422 98 HOH HOH . N 6 HOH A 99 423 99 HOH HOH . N 6 HOH A 100 424 100 HOH HOH . N 6 HOH A 101 425 101 HOH HOH . N 6 HOH A 102 426 102 HOH HOH . N 6 HOH A 103 427 103 HOH HOH . N 6 HOH A 104 428 104 HOH HOH . N 6 HOH A 105 429 105 HOH HOH . N 6 HOH A 106 430 106 HOH HOH . N 6 HOH A 107 431 107 HOH HOH . N 6 HOH A 108 432 108 HOH HOH . N 6 HOH A 109 433 109 HOH HOH . N 6 HOH A 110 434 110 HOH HOH . N 6 HOH A 111 435 111 HOH HOH . N 6 HOH A 112 436 112 HOH HOH . N 6 HOH A 113 437 113 HOH HOH . N 6 HOH A 114 438 114 HOH HOH . N 6 HOH A 115 439 115 HOH HOH . N 6 HOH A 116 440 116 HOH HOH . N 6 HOH A 117 441 117 HOH HOH . N 6 HOH A 118 442 118 HOH HOH . N 6 HOH A 119 443 119 HOH HOH . N 6 HOH A 120 444 120 HOH HOH . N 6 HOH A 121 445 121 HOH HOH . N 6 HOH A 122 446 122 HOH HOH . N 6 HOH A 123 447 123 HOH HOH . N 6 HOH A 124 448 124 HOH HOH . N 6 HOH A 125 449 125 HOH HOH . N 6 HOH A 126 450 126 HOH HOH . N 6 HOH A 127 451 127 HOH HOH . N 6 HOH A 128 452 128 HOH HOH . N 6 HOH A 129 453 129 HOH HOH . N 6 HOH A 130 454 130 HOH HOH . N 6 HOH A 131 455 131 HOH HOH . N 6 HOH A 132 456 132 HOH HOH . N 6 HOH A 133 457 133 HOH HOH . N 6 HOH A 134 458 134 HOH HOH . N 6 HOH A 135 459 135 HOH HOH . N 6 HOH A 136 460 136 HOH HOH . N 6 HOH A 137 461 137 HOH HOH . N 6 HOH A 138 462 138 HOH HOH . N 6 HOH A 139 463 139 HOH HOH . N 6 HOH A 140 464 140 HOH HOH . N 6 HOH A 141 465 141 HOH HOH . N 6 HOH A 142 466 142 HOH HOH . N 6 HOH A 143 467 143 HOH HOH . N 6 HOH A 144 468 144 HOH HOH . N 6 HOH A 145 469 145 HOH HOH . N 6 HOH A 146 470 146 HOH HOH . N 6 HOH A 147 471 147 HOH HOH . N 6 HOH A 148 472 148 HOH HOH . N 6 HOH A 149 473 149 HOH HOH . N 6 HOH A 150 474 150 HOH HOH . N 6 HOH A 151 475 151 HOH HOH . N 6 HOH A 152 476 152 HOH HOH . N 6 HOH A 153 477 153 HOH HOH . N 6 HOH A 154 478 154 HOH HOH . N 6 HOH A 155 479 155 HOH HOH . N 6 HOH A 156 480 156 HOH HOH . N 6 HOH A 157 481 157 HOH HOH . N 6 HOH A 158 482 158 HOH HOH . N 6 HOH A 159 483 159 HOH HOH . N 6 HOH A 160 484 160 HOH HOH . N 6 HOH A 161 485 161 HOH HOH . N 6 HOH A 162 486 162 HOH HOH . N 6 HOH A 163 487 163 HOH HOH . N 6 HOH A 164 488 164 HOH HOH . N 6 HOH A 165 489 165 HOH HOH . N 6 HOH A 166 490 166 HOH HOH . N 6 HOH A 167 491 167 HOH HOH . N 6 HOH A 168 492 168 HOH HOH . N 6 HOH A 169 493 169 HOH HOH . N 6 HOH A 170 494 170 HOH HOH . N 6 HOH A 171 495 171 HOH HOH . N 6 HOH A 172 496 172 HOH HOH . N 6 HOH A 173 497 173 HOH HOH . N 6 HOH A 174 498 174 HOH HOH . N 6 HOH A 175 499 175 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 8.637 47.783 -16.844 1 33.51 ? PB GDP 313 A 1 HETATM 2 O O1B GDP . . . B 2 8.632 48.381 -18.339 1 35.98 ? O1B GDP 313 A 1 HETATM 3 O O2B GDP . . . B 2 7.259 46.961 -16.626 1 32.1 ? O2B GDP 313 A 1 HETATM 4 O O3B GDP . . . B 2 9.813 46.936 -16.532 1 38.32 ? O3B GDP 313 A 1 HETATM 5 O O3A GDP . . . B 2 8.508 48.973 -15.784 1 36.93 ? O3A GDP 313 A 1 HETATM 6 P PA GDP . . . B 2 8.399 50.548 -16.005 1 34.41 ? PA GDP 313 A 1 HETATM 7 O O1A GDP . . . B 2 8.535 51.144 -14.66 1 44.8 ? O1A GDP 313 A 1 HETATM 8 O O2A GDP . . . B 2 9.324 51.007 -17.062 1 40.1 ? O2A GDP 313 A 1 HETATM 9 O O5' GDP . . . B 2 6.884 50.723 -16.455 1 40.6 ? O5' GDP 313 A 1 HETATM 10 C C5' GDP . . . B 2 5.84 50.294 -15.583 1 42.9 ? C5' GDP 313 A 1 HETATM 11 C C4' GDP . . . B 2 4.478 50.656 -16.179 1 46.98 ? C4' GDP 313 A 1 HETATM 12 O O4' GDP . . . B 2 4.387 52.057 -15.873 1 47.8 ? O4' GDP 313 A 1 HETATM 13 C C3' GDP . . . B 2 4.523 50.534 -17.709 1 50.47 ? C3' GDP 313 A 1 HETATM 14 O O3' GDP . . . B 2 3.581 49.552 -18.164 1 54.86 ? O3' GDP 313 A 1 HETATM 15 C C2' GDP . . . B 2 4.049 51.884 -18.225 1 53.32 ? C2' GDP 313 A 1 HETATM 16 O O2' GDP . . . B 2 2.795 51.676 -18.868 1 68.87 ? O2' GDP 313 A 1 HETATM 17 C C1' GDP . . . B 2 3.76 52.718 -16.98 1 49.75 ? C1' GDP 313 A 1 HETATM 18 N N9 GDP . . . B 2 4.577 53.923 -17.168 1 47.84 ? N9 GDP 313 A 1 HETATM 19 C C8 GDP . . . B 2 5.909 53.98 -17.239 1 46.18 ? C8 GDP 313 A 1 HETATM 20 N N7 GDP . . . B 2 6.282 55.239 -17.453 1 43.61 ? N7 GDP 313 A 1 HETATM 21 C C5 GDP . . . B 2 5.18 55.984 -17.493 1 42.13 ? C5 GDP 313 A 1 HETATM 22 C C6 GDP . . . B 2 4.973 57.353 -17.603 1 44.02 ? C6 GDP 313 A 1 HETATM 23 O O6 GDP . . . B 2 5.942 58.112 -17.726 1 49.45 ? O6 GDP 313 A 1 HETATM 24 N N1 GDP . . . B 2 3.65 57.828 -17.53 1 37.01 ? N1 GDP 313 A 1 HETATM 25 C C2 GDP . . . B 2 2.596 56.919 -17.359 1 40 ? C2 GDP 313 A 1 HETATM 26 N N2 GDP . . . B 2 1.334 57.337 -17.33 1 40.95 ? N2 GDP 313 A 1 HETATM 27 N N3 GDP . . . B 2 2.836 55.601 -17.295 1 42.23 ? N3 GDP 313 A 1 HETATM 28 C C4 GDP . . . B 2 4.09 55.14 -17.343 1 42.43 ? C4 GDP 313 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 1091 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #