data_3AF3 # _model_server_result.job_id 10q1Fj9L1LCha5G0prFqWg _model_server_result.datetime_utc '2025-02-24 12:30:52' _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 3af3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":313}' # _entry.id 3AF3 # _exptl.entry_id 3AF3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 521.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' _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 3AF3 _cell.length_a 103.11 _cell.length_b 103.11 _cell.length_c 91.05 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AF3 _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 _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' 6_555 -x,-x+y,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 30.35 # _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 'C11 H18 N5 O13 P3' _chem_comp.formula_weight 521.208 _chem_comp.id GCP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' _chem_comp.type non-polymer _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 PG O1G GCP doub 83 n n PG O2G GCP sing 84 n n PG O3G GCP sing 85 n n PG C3B GCP sing 86 n n O2G HOG2 GCP sing 87 n n O3G HOG3 GCP sing 88 n n C3B PB GCP sing 89 n n C3B H3B1 GCP sing 90 n n C3B H3B2 GCP sing 91 n n PB O1B GCP doub 92 n n PB O2B GCP sing 93 n n PB O3A GCP sing 94 n n O2B HOB2 GCP sing 95 n n O3A PA GCP sing 96 n n PA O1A GCP doub 97 n n PA O2A GCP sing 98 n n PA O5' GCP sing 99 n n O2A HOA2 GCP sing 100 n n O5' C5' GCP sing 101 n n C5' C4' GCP sing 102 n n C5' "H5'2" GCP sing 103 n n C5' "H5'1" GCP sing 104 n n C4' O4' GCP sing 105 n n C4' C3' GCP sing 106 n n C4' H4' GCP sing 107 n n O4' C1' GCP sing 108 n n C3' O3' GCP sing 109 n n C3' C2' GCP sing 110 n n C3' H3' GCP sing 111 n n O3' HO3' GCP sing 112 n n C2' O2' GCP sing 113 n n C2' C1' GCP sing 114 n n C2' H2' GCP sing 115 n n O2' HO2' GCP sing 116 n n C1' N9 GCP sing 117 n n C1' H1' GCP sing 118 n n N9 C8 GCP sing 119 n y N9 C4 GCP sing 120 n y C8 N7 GCP doub 121 n y C8 H8 GCP sing 122 n n N7 C5 GCP sing 123 n y C5 C6 GCP sing 124 n y C5 C4 GCP doub 125 n y C6 O6 GCP doub 126 n n C6 N1 GCP sing 127 n y N1 C2 GCP sing 128 n y N1 HN1 GCP sing 129 n n C2 N2 GCP sing 130 n n C2 N3 GCP doub 131 n y N2 HN21 GCP sing 132 n n N2 HN22 GCP sing 133 n n N3 C4 GCP sing 134 n y # _atom_sites.entry_id 3AF3 _atom_sites.fract_transf_matrix[1][1] 0.009698 _atom_sites.fract_transf_matrix[1][2] 0.005599 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011199 _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] 0.010983 _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 GCP A 1 313 313 GCP GCP . C 3 PAU A 1 314 314 PAU PAU . D 4 GOL A 1 315 315 GOL GOL . E 4 GOL A 1 316 316 GOL GOL . F 4 GOL A 1 317 317 GOL GOL . G 4 GOL A 1 318 318 GOL GOL . H 4 GOL A 1 319 319 GOL GOL . I 4 GOL A 1 320 320 GOL GOL . J 4 GOL A 1 321 321 GOL GOL . K 4 GOL A 1 322 322 GOL GOL . L 4 GOL A 1 323 323 GOL GOL . M 5 HOH A 1 324 324 HOH HOH . M 5 HOH A 2 325 325 HOH HOH . M 5 HOH A 3 326 326 HOH HOH . M 5 HOH A 4 327 327 HOH HOH . M 5 HOH A 5 328 328 HOH HOH . M 5 HOH A 6 329 329 HOH HOH . M 5 HOH A 7 330 330 HOH HOH . M 5 HOH A 8 331 331 HOH HOH . M 5 HOH A 9 332 332 HOH HOH . M 5 HOH A 10 333 333 HOH HOH . M 5 HOH A 11 334 334 HOH HOH . M 5 HOH A 12 335 335 HOH HOH . M 5 HOH A 13 336 336 HOH HOH . M 5 HOH A 14 337 337 HOH HOH . M 5 HOH A 15 338 338 HOH HOH . M 5 HOH A 16 339 339 HOH HOH . M 5 HOH A 17 340 340 HOH HOH . M 5 HOH A 18 341 341 HOH HOH . M 5 HOH A 19 342 342 HOH HOH . M 5 HOH A 20 343 343 HOH HOH . M 5 HOH A 21 344 344 HOH HOH . M 5 HOH A 22 345 345 HOH HOH . M 5 HOH A 23 346 346 HOH HOH . M 5 HOH A 24 347 347 HOH HOH . M 5 HOH A 25 348 348 HOH HOH . M 5 HOH A 26 349 349 HOH HOH . M 5 HOH A 27 350 350 HOH HOH . M 5 HOH A 28 351 351 HOH HOH . M 5 HOH A 29 352 352 HOH HOH . M 5 HOH A 30 353 353 HOH HOH . M 5 HOH A 31 354 354 HOH HOH . M 5 HOH A 32 355 355 HOH HOH . M 5 HOH A 33 356 356 HOH HOH . M 5 HOH A 34 357 357 HOH HOH . M 5 HOH A 35 358 358 HOH HOH . M 5 HOH A 36 359 359 HOH HOH . M 5 HOH A 37 360 360 HOH HOH . M 5 HOH A 38 361 361 HOH HOH . M 5 HOH A 39 362 362 HOH HOH . M 5 HOH A 40 363 363 HOH HOH . M 5 HOH A 41 364 364 HOH HOH . M 5 HOH A 42 365 365 HOH HOH . M 5 HOH A 43 366 366 HOH HOH . M 5 HOH A 44 367 367 HOH HOH . M 5 HOH A 45 368 368 HOH HOH . M 5 HOH A 46 369 369 HOH HOH . M 5 HOH A 47 370 370 HOH HOH . M 5 HOH A 48 371 371 HOH HOH . M 5 HOH A 49 372 372 HOH HOH . M 5 HOH A 50 373 373 HOH HOH . M 5 HOH A 51 374 374 HOH HOH . M 5 HOH A 52 375 375 HOH HOH . M 5 HOH A 53 376 376 HOH HOH . M 5 HOH A 54 377 377 HOH HOH . M 5 HOH A 55 378 378 HOH HOH . M 5 HOH A 56 379 379 HOH HOH . M 5 HOH A 57 380 380 HOH HOH . M 5 HOH A 58 381 381 HOH HOH . M 5 HOH A 59 382 382 HOH HOH . M 5 HOH A 60 383 383 HOH HOH . M 5 HOH A 61 384 384 HOH HOH . M 5 HOH A 62 385 385 HOH HOH . M 5 HOH A 63 386 386 HOH HOH . M 5 HOH A 64 387 387 HOH HOH . M 5 HOH A 65 388 388 HOH HOH . M 5 HOH A 66 389 389 HOH HOH . M 5 HOH A 67 390 390 HOH HOH . M 5 HOH A 68 391 391 HOH HOH . M 5 HOH A 69 392 392 HOH HOH . M 5 HOH A 70 393 393 HOH HOH . M 5 HOH A 71 394 394 HOH HOH . M 5 HOH A 72 395 395 HOH HOH . M 5 HOH A 73 396 396 HOH HOH . M 5 HOH A 74 397 397 HOH HOH . M 5 HOH A 75 398 398 HOH HOH . M 5 HOH A 76 399 399 HOH HOH . M 5 HOH A 77 400 400 HOH HOH . M 5 HOH A 78 401 401 HOH HOH . M 5 HOH A 79 402 402 HOH HOH . M 5 HOH A 80 403 403 HOH HOH . M 5 HOH A 81 404 404 HOH HOH . M 5 HOH A 82 405 405 HOH HOH . M 5 HOH A 83 406 406 HOH HOH . M 5 HOH A 84 407 407 HOH HOH . M 5 HOH A 85 408 408 HOH HOH . M 5 HOH A 86 409 409 HOH HOH . M 5 HOH A 87 410 410 HOH HOH . M 5 HOH A 88 411 411 HOH HOH . M 5 HOH A 89 412 412 HOH HOH . M 5 HOH A 90 413 413 HOH HOH . M 5 HOH A 91 414 414 HOH HOH . M 5 HOH A 92 415 415 HOH HOH . M 5 HOH A 93 416 416 HOH HOH . M 5 HOH A 94 417 417 HOH HOH . M 5 HOH A 95 418 418 HOH HOH . M 5 HOH A 96 419 419 HOH HOH . M 5 HOH A 97 420 420 HOH HOH . M 5 HOH A 98 421 421 HOH HOH . M 5 HOH A 99 422 422 HOH HOH . M 5 HOH A 100 423 423 HOH HOH . M 5 HOH A 101 424 424 HOH HOH . M 5 HOH A 102 425 425 HOH HOH . M 5 HOH A 103 426 426 HOH HOH . M 5 HOH A 104 427 427 HOH HOH . M 5 HOH A 105 428 428 HOH HOH . M 5 HOH A 106 429 429 HOH HOH . M 5 HOH A 107 430 430 HOH HOH . M 5 HOH A 108 431 431 HOH HOH . M 5 HOH A 109 432 432 HOH HOH . M 5 HOH A 110 433 433 HOH HOH . M 5 HOH A 111 434 434 HOH HOH . M 5 HOH A 112 435 435 HOH HOH . M 5 HOH A 113 436 436 HOH HOH . M 5 HOH A 114 437 437 HOH HOH . M 5 HOH A 115 438 438 HOH HOH . M 5 HOH A 116 439 439 HOH HOH . M 5 HOH A 117 440 440 HOH HOH . M 5 HOH A 118 441 441 HOH HOH . M 5 HOH A 119 442 442 HOH HOH . M 5 HOH A 120 443 443 HOH HOH . M 5 HOH A 121 444 444 HOH HOH . M 5 HOH A 122 445 445 HOH HOH . M 5 HOH A 123 446 446 HOH HOH . M 5 HOH A 124 447 447 HOH HOH . M 5 HOH A 125 448 448 HOH HOH . M 5 HOH A 126 449 449 HOH HOH . M 5 HOH A 127 450 450 HOH HOH . M 5 HOH A 128 451 451 HOH HOH . M 5 HOH A 129 452 452 HOH HOH . M 5 HOH A 130 453 453 HOH HOH . M 5 HOH A 131 454 454 HOH HOH . M 5 HOH A 132 455 455 HOH HOH . M 5 HOH A 133 456 456 HOH HOH . M 5 HOH A 134 457 457 HOH HOH . M 5 HOH A 135 458 458 HOH HOH . M 5 HOH A 136 459 459 HOH HOH . M 5 HOH A 137 460 460 HOH HOH . M 5 HOH A 138 461 461 HOH HOH . M 5 HOH A 139 462 462 HOH HOH . M 5 HOH A 140 463 463 HOH HOH . M 5 HOH A 141 464 464 HOH HOH . M 5 HOH A 142 465 465 HOH HOH . M 5 HOH A 143 466 466 HOH HOH . M 5 HOH A 144 467 467 HOH HOH . M 5 HOH A 145 468 468 HOH HOH . M 5 HOH A 146 469 469 HOH HOH . M 5 HOH A 147 470 470 HOH HOH . M 5 HOH A 148 471 471 HOH HOH . M 5 HOH A 149 472 472 HOH HOH . M 5 HOH A 150 473 473 HOH HOH . M 5 HOH A 151 474 474 HOH HOH . M 5 HOH A 152 475 475 HOH HOH . M 5 HOH A 153 476 476 HOH HOH . M 5 HOH A 154 477 477 HOH HOH . M 5 HOH A 155 478 478 HOH HOH . M 5 HOH A 156 479 479 HOH HOH . M 5 HOH A 157 480 480 HOH HOH . M 5 HOH A 158 481 481 HOH HOH . M 5 HOH A 159 482 482 HOH HOH . M 5 HOH A 160 483 483 HOH HOH . M 5 HOH A 161 484 484 HOH HOH . M 5 HOH A 162 485 485 HOH HOH . M 5 HOH A 163 486 486 HOH HOH . M 5 HOH A 164 487 487 HOH HOH . M 5 HOH A 165 488 488 HOH HOH . M 5 HOH A 166 489 489 HOH HOH . M 5 HOH A 167 490 490 HOH HOH . M 5 HOH A 168 491 491 HOH HOH . M 5 HOH A 169 492 492 HOH HOH . M 5 HOH A 170 493 493 HOH HOH . M 5 HOH A 171 494 494 HOH HOH . M 5 HOH A 172 495 495 HOH HOH . M 5 HOH A 173 496 496 HOH HOH . M 5 HOH A 174 497 497 HOH HOH . M 5 HOH A 175 498 498 HOH HOH . M 5 HOH A 176 499 499 HOH HOH . M 5 HOH A 177 500 500 HOH HOH . M 5 HOH A 178 501 501 HOH HOH . M 5 HOH A 179 502 502 HOH HOH . M 5 HOH A 180 503 503 HOH HOH . M 5 HOH A 181 504 504 HOH HOH . M 5 HOH A 182 505 505 HOH HOH . M 5 HOH A 183 506 506 HOH HOH . M 5 HOH A 184 507 507 HOH HOH . M 5 HOH A 185 508 508 HOH HOH . M 5 HOH A 186 509 509 HOH HOH . M 5 HOH A 187 510 510 HOH HOH . M 5 HOH A 188 511 511 HOH HOH . M 5 HOH A 189 512 512 HOH HOH . M 5 HOH A 190 513 513 HOH HOH . M 5 HOH A 191 514 514 HOH HOH . M 5 HOH A 192 515 515 HOH HOH . M 5 HOH A 193 516 516 HOH HOH . M 5 HOH A 194 517 517 HOH HOH . M 5 HOH A 195 518 518 HOH HOH . M 5 HOH A 196 519 519 HOH HOH . M 5 HOH A 197 520 520 HOH HOH . M 5 HOH A 198 521 521 HOH HOH . M 5 HOH A 199 522 522 HOH HOH . M 5 HOH A 200 523 523 HOH HOH . M 5 HOH A 201 524 524 HOH HOH . M 5 HOH A 202 525 525 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 PG GCP . . . B 2 -38.825 32.55 -1.953 0.75 49.54 ? PG GCP 313 A 1 HETATM 2 O O1G GCP . . . B 2 -37.694 32.904 -1.096 0.75 61.21 ? O1G GCP 313 A 1 HETATM 3 O O2G GCP . . . B 2 -39.425 33.721 -2.568 0.75 59.74 ? O2G GCP 313 A 1 HETATM 4 O O3G GCP . . . B 2 -39.699 31.516 -1.357 0.75 46.86 ? O3G GCP 313 A 1 HETATM 5 C C3B GCP . . . B 2 -38.127 31.831 -3.408 0.75 60.95 ? C3B GCP 313 A 1 HETATM 6 P PB GCP . . . B 2 -36.684 30.864 -3.009 0.75 62.76 ? PB GCP 313 A 1 HETATM 7 O O1B GCP . . . B 2 -35.67 31.334 -3.953 0.75 62.18 ? O1B GCP 313 A 1 HETATM 8 O O2B GCP . . . B 2 -36.251 30.87 -1.621 0.75 59.49 ? O2B GCP 313 A 1 HETATM 9 O O3A GCP . . . B 2 -37.291 29.411 -3.337 0.75 65.47 ? O3A GCP 313 A 1 HETATM 10 P PA GCP . . . B 2 -36.796 28.369 -4.469 0.75 64.99 ? PA GCP 313 A 1 HETATM 11 O O1A GCP . . . B 2 -35.428 27.939 -4.155 0.75 61.03 ? O1A GCP 313 A 1 HETATM 12 O O2A GCP . . . B 2 -37.068 28.931 -5.8 0.75 69.55 ? O2A GCP 313 A 1 HETATM 13 O O5' GCP . . . B 2 -37.826 27.208 -4.202 0.75 67.39 ? O5' GCP 313 A 1 HETATM 14 C C5' GCP . . . B 2 -39.067 27.667 -3.686 0.75 80.18 ? C5' GCP 313 A 1 HETATM 15 C C4' GCP . . . B 2 -39.837 26.681 -2.819 0.75 84.78 ? C4' GCP 313 A 1 HETATM 16 O O4' GCP . . . B 2 -40.158 27.168 -1.509 0.75 86.53 ? O4' GCP 313 A 1 HETATM 17 C C3' GCP . . . B 2 -41.165 26.519 -3.482 0.75 89.3 ? C3' GCP 313 A 1 HETATM 18 O O3' GCP . . . B 2 -41.082 25.446 -4.399 0.75 88.59 ? O3' GCP 313 A 1 HETATM 19 C C2' GCP . . . B 2 -42.08 26.251 -2.308 0.75 92.69 ? C2' GCP 313 A 1 HETATM 20 O O2' GCP . . . B 2 -41.876 24.909 -1.873 0.75 94.29 ? O2' GCP 313 A 1 HETATM 21 C C1' GCP . . . B 2 -41.562 27.185 -1.241 0.75 92.12 ? C1' GCP 313 A 1 HETATM 22 N N9 GCP . . . B 2 -42.133 28.549 -1.453 0.75 95.54 ? N9 GCP 313 A 1 HETATM 23 C C8 GCP . . . B 2 -41.475 29.683 -1.191 0.75 97.02 ? C8 GCP 313 A 1 HETATM 24 N N7 GCP . . . B 2 -42.251 30.735 -1.5 0.75 97.95 ? N7 GCP 313 A 1 HETATM 25 C C5 GCP . . . B 2 -43.42 30.266 -1.975 0.75 96.88 ? C5 GCP 313 A 1 HETATM 26 C C6 GCP . . . B 2 -44.562 30.875 -2.452 0.75 95.4 ? C6 GCP 313 A 1 HETATM 27 O O6 GCP . . . B 2 -44.706 32.09 -2.516 0.75 93.84 ? O6 GCP 313 A 1 HETATM 28 N N1 GCP . . . B 2 -45.576 30.168 -2.853 0.75 95.73 ? N1 GCP 313 A 1 HETATM 29 C C2 GCP . . . B 2 -45.535 28.857 -2.826 0.75 97.61 ? C2 GCP 313 A 1 HETATM 30 N N2 GCP . . . B 2 -46.646 28.227 -3.263 0.75 96.21 ? N2 GCP 313 A 1 HETATM 31 N N3 GCP . . . B 2 -44.434 28.203 -2.376 0.75 98.01 ? N3 GCP 313 A 1 HETATM 32 C C4 GCP . . . B 2 -43.348 28.892 -1.94 0.75 97.05 ? C4 GCP 313 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 436 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 32 #