Project name: seed_prop_1

Status: done

Started: 2025-06-28 11:06:33
Chain sequence(s) A: MMRARFPLLLLGLVFLASVSVSFGIAYWEKENPKHNKCLQSCNSERDSYRNQACHARCNLLKVEKEECEEGEIPRPRPRPQHPEREPQQPGEKEEDEDEQPRPIPFPRPQPRQEEEHEQREEQEWPRKEEKRGEKGSEEEDEDEDEEQDERQFPFPRPPHQKEERKQEEDEDEEQQRESEESEDSELRRHKNKNPFLFGSNRFETLFKNQYGRIRVLQRFNQRSPQLQNLRDYRILEFNSKPNTLLLPNHADADYLIVILNGTAILSLVNNDDRDSYRLQSGDALRVPSGTTYYVVNPDNNENLRLITLAIPVNKPGRFESFFLSSTEAQQSYLQGFSRNILEASYDTKFEEINKVLFSREEGQQQGEQRLQESVIVEISKEQIRALSKRAKSSSRKTISSEDKPFNLRSRDPIYSNKLGKFFEITPEKNPQLRDLDIFLSIVDMNEGALLLPHFNSKAIVILVINEGDANIELVGLKEQQQEQQQEEQPLEVRKYRAELSEQDIFVIPAGYPVVVNATSNLNFFAIGINAENNQRNFLAGSQDNVISQIPSQVQELAFPGSAQAVEKLLKNQRESYFVDAQPKKKEEGNKGRKGPLSSILRAFY
input PDB
Selected Chain(s) A
Distance of aggregation 5 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage A:

MMRARFPLLLLGLVFLASVSVSFGIAYW

EKENPKHNKCLQSCNSERDSYRNQACHARCNLLKVEKEECEEG

EIPRPRPRPQHPEREPQQPGEKEEDEDEQPRPIPFPRPQPRQEEEHEQREEQEWPRKEEKRGEKGSEEEDEDEDEEQDERQFPFPRPPHQKEERKQEEDEDEEQQRESEESEDS

ELRRHKNKNPFLFGSNRFETLFKNQYGRIRVLQRFNQRSPQLQNLRDYRILEFNSKPNTLLLPNHADADYLIVILNGTAILSLVNNDDRDSYRLQSGDALRVPSGTTYYVVNPDNNENLRLITLAIPVNKPGRFESFFLSSTEAQQSYLQGFSRNILEASYDTKFEEINKVLFSREEGQQQGEQRLQESVIVEISKEQIRALSKRAKSSSRKTISSEDKPFNLRSRDPIYSNKLGKFFEITPEKNPQLRDLDIFLSIVDMNEGALLLPHFNSKAIVILVINEGDANIELVGLKEQQQEQQQEEQPLEVRKYRAELSEQDIFVIPAGYPVVVNATSNLNFFAIGINAENNQRNFLAGSQDNVISQIPSQVQELAFPGSAQAVEKLLKNQRESYFVDAQPKKKEEGNKGRKGPLSSILRAFY
(Red indicates removed residues)
Dynamic mode No
Automated mutations No
Downloads Download all the data
Simulation log
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       PDB:      Running AlphaCutter                                                         (00:00:01)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:12)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:12)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:10:27)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/97b9229d7136a9c/tmp/folded.pdb                (00:10:27)
[INFO]       Main:     Simulation completed successfully.                                          (00:14:15)
Show buried residues

Minimal score value
-2.4524
Maximal score value
2.2521
Average score
-0.5252
Total score value
-243.1626

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan4D score mutation
29 E A -2.1226
30 K A -2.3572
31 E A -2.1674
32 N A -0.5756
33 P A -0.5324
34 K A -1.3974
35 H A 0.0000
36 N A -1.0816
37 K A -1.7863
38 C A -0.1242
39 L A 0.2053
40 Q A -1.1434
41 S A -0.3164
42 C A 0.0000
43 N A -1.3110
44 S A -0.5506
45 E A -0.9862
46 R A -2.0440
47 D A -0.8615
48 S A -0.0629
49 Y A 1.2081
50 R A -0.2006
51 N A -0.6096
52 Q A -1.2550
53 A A -0.2168
54 C A 0.0775
55 H A -0.2820
56 A A -0.1266
57 R A -0.5744
58 C A 0.0000
59 N A -0.3755
60 L A 1.4816
61 L A 0.3435
62 K A -1.0051
63 V A 0.1072
64 E A -2.0091
65 K A -2.3496
66 E A -2.4482
67 E A -2.0137
68 C A 0.0851
69 E A -2.0088
70 E A -2.2206
71 G A -1.1086
72 E A -1.9025
187 L A 0.8446
188 R A -1.9620
189 R A -2.1720
190 H A 0.0000
191 K A -1.8577
192 N A -1.8631
193 K A -1.9240
194 N A 0.0000
195 P A -0.0312
196 F A 0.0000
197 L A 0.0000
198 F A 0.0000
199 G A -0.1439
200 S A -0.3352
201 N A -1.4418
202 R A -1.0534
203 F A -0.2880
204 E A -1.7925
205 T A -0.2562
206 L A 0.7728
207 F A 0.1915
208 K A -1.7456
209 N A -0.7398
210 Q A -1.1942
211 Y A 0.0135
212 G A -0.0977
213 R A -0.7571
214 I A 0.0000
215 R A 0.0000
216 V A 0.0000
217 L A 0.0000
218 Q A -0.4742
219 R A -0.5131
220 F A 0.0000
221 N A -0.5570
222 Q A -1.3084
223 R A -0.6097
224 S A 0.0000
225 P A -0.3863
226 Q A -0.7799
227 L A 0.0000
228 Q A -1.2947
229 N A -1.4591
230 L A 0.0000
231 R A -1.2376
232 D A -0.8205
233 Y A -0.0040
234 R A -0.1619
235 I A 0.0000
236 L A 0.0000
237 E A 0.0000
238 F A 0.0000
239 N A -0.1793
240 S A 0.0000
241 K A -1.1522
242 P A -0.2680
243 N A -0.1964
244 T A 0.0000
245 L A 0.1630
246 L A 0.0000
247 L A 0.0000
248 P A -0.0726
249 N A 0.0000
250 H A -0.1624
251 A A 0.0000
252 D A -0.2238
253 A A 0.0000
254 D A 0.0000
255 Y A 0.0000
256 L A 0.0000
257 I A 0.0000
258 V A 0.0000
259 I A 0.0000
260 L A 0.0000
261 N A -0.3445
262 G A -0.1279
263 T A -0.1185
264 A A 0.0000
265 I A 0.0000
266 L A 0.0000
267 S A 0.0000
268 L A 0.0000
269 V A 0.3064
270 N A -0.9349
271 N A -1.7397
272 D A -2.3418
273 D A -2.2378
274 R A -1.0692
275 D A -0.8558
276 S A 0.0000
277 Y A 0.0000
278 R A -0.8291
279 L A 0.0000
280 Q A -0.7403
281 S A -0.2139
282 G A 0.0000
283 D A 0.0000
284 A A 0.0000
285 L A 0.0000
286 R A -0.3088
287 V A 0.0000
288 P A -0.0552
289 S A -0.0581
290 G A -0.1591
291 T A 0.0000
292 T A -0.0342
293 Y A 0.0000
294 Y A 0.0000
295 V A 0.0000
296 V A 0.0000
297 N A 0.0000
298 P A -0.1018
299 D A -0.6591
300 N A -1.5793
301 N A -1.6722
302 E A -1.2781
303 N A -0.8939
304 L A 0.0000
305 R A -0.2640
306 L A 0.0000
307 I A 0.0000
308 T A 0.0000
309 L A 0.0000
310 A A 0.0000
311 I A 0.2023
312 P A 0.0000
313 V A 0.2660
314 N A -1.4877
315 K A -1.9469
316 P A -0.4865
317 G A 0.0000
318 R A -1.7921
319 F A -0.3833
320 E A -1.7791
321 S A -0.3183
322 F A 0.4039
323 F A 0.0000
324 L A 0.5999
325 S A 0.0724
326 S A -0.0265
327 T A 0.0000
328 E A -1.8094
329 A A -0.2880
330 Q A -0.3250
331 Q A -1.2196
332 S A 0.0000
333 Y A 0.6498
334 L A 0.1982
335 Q A -0.4623
336 G A -0.2999
337 F A 1.2320
338 S A -0.2039
339 R A -1.9690
340 N A -1.2239
341 I A 1.7744
342 L A 0.0000
343 E A -0.7056
344 A A -0.1093
345 S A -0.0864
346 Y A 0.2870
347 D A -1.6794
348 T A -0.6582
349 K A -1.6611
350 F A -0.3983
351 E A -1.9440
352 E A -1.2563
353 I A 0.0000
354 N A -0.4629
355 K A -1.4181
356 V A 1.5684
357 L A 0.8873
358 F A 0.0000
359 S A -0.4072
360 R A -1.0073
361 E A -2.2691
362 E A -2.2318
363 G A -1.0064
364 Q A -1.5016
365 Q A -1.6343
366 Q A -1.4985
367 G A -1.0259
368 E A -2.1192
369 Q A -1.8520
370 R A -2.0301
371 L A -0.3027
372 Q A -0.9683
373 E A -1.9316
374 S A 0.0000
375 V A 0.0000
376 I A 0.0000
377 V A -0.1567
378 E A -1.7876
379 I A 0.0000
380 S A -0.3534
381 K A -1.8353
382 E A -2.2873
383 Q A -1.4303
384 I A 0.0000
385 R A -1.8353
386 A A -0.2369
387 L A 0.2704
388 S A -0.2858
389 K A -2.0343
390 R A -2.1455
391 A A -0.6284
392 K A -1.7364
393 S A -0.6097
394 S A -0.0735
395 S A -0.4150
396 R A -2.1611
397 K A -2.0285
398 T A 0.0000
399 I A 0.0000
400 S A -0.2169
401 S A -0.3919
402 E A -2.1452
403 D A -2.2668
404 K A -1.1704
405 P A 0.0000
406 F A 0.0000
407 N A -0.1442
408 L A 0.0000
409 R A -0.8657
410 S A -0.4859
411 R A -2.0761
412 D A -2.1202
413 P A -0.1644
414 I A 1.1681
415 Y A 0.3120
416 S A -0.3138
417 N A -0.5930
418 K A -1.7150
419 L A -0.1348
420 G A -0.1793
421 K A -0.9362
422 F A 0.0000
423 F A 0.0000
424 E A -0.2312
425 I A 0.0000
426 T A -0.0095
427 P A 0.0000
428 E A -1.7289
429 K A -1.5499
430 N A 0.0000
431 P A -0.2245
432 Q A 0.0000
433 L A 0.0000
434 R A -2.0315
435 D A -2.0940
436 L A 0.0000
437 D A -0.4671
438 I A 0.0000
439 F A 0.0000
440 L A 0.0000
441 S A 0.0000
442 I A 0.0000
443 V A 0.0000
444 D A -0.5032
445 M A 0.0000
446 N A -1.4783
447 E A -2.2019
448 G A -0.4515
449 A A 0.0000
450 L A 0.2392
451 L A 0.0000
452 L A 0.0000
453 P A -0.0533
454 H A 0.0000
455 F A 0.3922
456 N A 0.0000
457 S A -0.2209
458 K A -0.5062
459 A A 0.0000
460 I A 0.2199
461 V A 0.0000
462 I A 0.0000
463 L A 0.0000
464 V A 0.0000
465 I A 0.0000
466 N A 0.0000
467 E A -1.1410
468 G A -0.4582
469 D A -0.8213
470 A A 0.0000
471 N A -0.4730
472 I A 0.0000
473 E A -1.1222
474 L A 0.0000
475 V A 0.3419
476 G A 0.0000
477 L A 0.6948
478 K A -1.2533
479 E A -2.2165
480 Q A -1.6779
481 Q A -1.6192
482 Q A -1.7372
483 E A -2.2624
484 Q A -1.7576
485 Q A -1.6246
486 Q A -1.7382
487 E A -2.3626
488 E A -2.3664
489 Q A -1.5753
490 P A -0.1887
491 L A 1.1705
492 E A -1.2145
493 V A 1.4143
494 R A -0.4518
495 K A -1.2094
496 Y A 0.0000
497 R A -1.3082
498 A A 0.0000
499 E A -1.1504
500 L A 0.0000
501 S A -0.4303
502 E A -1.2091
503 Q A -0.4409
504 D A -0.2540
505 I A 0.0000
506 F A 0.0000
507 V A 0.0000
508 I A 0.0000
509 P A 0.0026
510 A A -0.0637
511 G A -0.2589
512 Y A 0.1761
513 P A 0.0328
514 V A 0.0000
515 V A 0.1908
516 V A 0.0000
517 N A -0.2483
518 A A 0.0000
519 T A -0.0820
520 S A -0.5574
521 N A -1.6475
522 L A 0.0000
523 N A -0.1814
524 F A 0.0000
525 F A 0.0000
526 A A 0.0000
527 I A 0.0000
528 G A 0.0000
529 I A 0.0000
530 N A -0.5618
531 A A 0.0000
532 E A -1.1231
533 N A -1.4647
534 N A -0.6228
535 Q A -1.2663
536 R A -0.4485
537 N A -0.2193
538 F A 0.0000
539 L A 0.3317
540 A A 0.0726
541 G A 0.0000
542 S A -0.3663
543 Q A -1.5195
544 D A -1.8602
545 N A 0.0000
546 V A 0.6069
547 I A 0.4606
548 S A -0.2663
549 Q A -1.1119
550 I A 0.3480
551 P A -0.1442
552 S A -0.3485
553 Q A -1.0221
554 V A 0.8534
555 Q A 0.0000
556 E A -1.5428
557 L A 1.2324
558 A A 0.4469
559 F A 0.5755
560 P A -0.1791
561 G A -0.2600
562 S A -0.1903
563 A A 0.0000
564 Q A -1.1906
565 A A -0.1736
566 V A 0.0000
567 E A -1.1391
568 K A -1.5709
569 L A 1.2756
570 L A 0.1679
571 K A -1.8927
572 N A -1.6480
573 Q A -0.9632
574 R A -2.0716
575 E A -1.1900
576 S A 0.0000
577 Y A 0.1697
578 F A 0.0000
579 V A 0.0000
580 D A -0.4757
581 A A -0.1935
582 Q A -0.7502
583 P A -0.6834
584 K A -2.0466
585 K A -2.3043
586 K A -2.3305
587 E A -2.4524
588 E A -2.2298
589 G A -1.0186
590 N A -1.6591
591 K A -2.0089
592 G A -1.0895
593 R A -2.2455
594 K A -2.1335
595 G A -0.8299
596 P A -0.0556
597 L A 1.4616
598 S A 0.0331
599 S A 0.1351
600 I A 2.2521
601 L A 1.5778
602 R A -1.5524
603 A A 0.0690
604 F A 2.1998
605 Y A 1.6814
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Calculations for various pH values

This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is globular. Max score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -0.5213 4.5872 View CSV PDB
4.5 -0.5563 4.5872 View CSV PDB
5.0 -0.6009 4.5872 View CSV PDB
5.5 -0.6459 4.5872 View CSV PDB
6.0 -0.6811 4.5872 View CSV PDB
6.5 -0.6985 4.5872 View CSV PDB
7.0 -0.6965 4.5872 View CSV PDB
7.5 -0.6805 4.5872 View CSV PDB
8.0 -0.657 4.5871 View CSV PDB
8.5 -0.6297 4.5869 View CSV PDB
9.0 -0.5997 4.5861 View CSV PDB