Project name: P0DO15

Status: done

Started: 2025-06-28 12:56:50
Chain sequence(s) A: MMRARFPLLLLGLVFLASVSVSFGIAYWEKENPKHNKCLQSCNSERDSYRNQACHARCNLLKVEKEECEEGEIPRPRPRPQHPEREPQQPGEKEEDEDEQPRPIPFPRPQPRQEEEHEQREEQEWPRKEEKRGEKGSEEEDEDEDEEQDERQFPFPRPPHQKEERKQEEDEDEEQQRESEESEDSELRRHKNKNPFLFGSNRFETLFKNQYGRIRVLQRFNQRSPQLQNLRDYRILEFNSKPNTLLLPNHADADYLIVILNGTAILSLVNNDDRDSYRLQSGDALRVPSGTTYYVVNPDNNENLRLITLAIPVNKPGRFESFFLSSTEAQQSYLQGFSRNILEASYDTKFEEINKVLFSREEGQQQGEQRLQESVIVEISKEQIRALSKRAKSSSRKTISSEDKPFNLRSRDPIYSNKLGKFFEITPEKNPQLRDLDIFLSIVDMNEGALLLPHFNSKAIVILVINEGDANIELVGLKEQQQEQQQEEQPLEVRKYRAELSEQDIFVIPAGYPVVVNATSNLNFFAIGINAENNQRNFLAGSQDNVISQIPSQVQELAFPGSAQAVEKLLKNQRESYFVDAQPKKKEEGNKGRKGPLSSILRAFY
input PDB
Selected Chain(s) A
Distance of aggregation 10 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]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       PDB:      Running AlphaCutter                                                         (00:00:01)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:13)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:13)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:10:34)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/a3bf2db547da905/tmp/folded.pdb                (00:10:34)
[INFO]       Main:     Simulation completed successfully.                                          (00:17:01)
Show buried residues

Minimal score value
-5.6501
Maximal score value
2.374
Average score
-1.3259
Total score value
-613.8958

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 -3.2114
30 K A -3.6460
31 E A -3.8456
32 N A -3.1227
33 P A -2.5209
34 K A -2.7439
35 H A 0.0000
36 N A -2.9367
37 K A -2.8875
38 C A -2.1708
39 L A -1.7279
40 Q A -2.4964
41 S A -1.9677
42 C A 0.0000
43 N A -2.2738
44 S A -1.8959
45 E A -2.4863
46 R A -2.6704
47 D A -1.6804
48 S A -0.9357
49 Y A 0.0083
50 R A -1.0172
51 N A -1.8204
52 Q A -1.3522
53 A A -0.8331
54 C A -0.8590
55 H A -0.9827
56 A A -0.6177
57 R A -0.5841
58 C A 0.0000
59 N A -0.4600
60 L A 0.3534
61 L A -1.0956
62 K A -2.5179
63 V A -1.8190
64 E A -3.4352
65 K A -4.3332
66 E A -4.8883
67 E A -4.6400
68 C A -3.3866
69 E A -4.6307
70 E A -4.4672
71 G A -3.1417
72 E A -2.8780
187 L A -1.3487
188 R A -3.0858
189 R A -3.5419
190 H A 0.0000
191 K A -3.9039
192 N A -3.5742
193 K A -3.4185
194 N A 0.0000
195 P A -1.2809
196 F A 0.0000
197 L A 0.0000
198 F A 0.0000
199 G A -1.5637
200 S A -1.4914
201 N A -2.0878
202 R A -2.0588
203 F A -1.6343
204 E A -2.0324
205 T A -0.9893
206 L A -0.0235
207 F A -0.5571
208 K A -1.9350
209 N A -1.8565
210 Q A -2.1532
211 Y A -1.6220
212 G A -1.6047
213 R A -1.4143
214 I A 0.0000
215 R A 0.0000
216 V A 0.0000
217 L A 0.0000
218 Q A -1.6872
219 R A -1.9805
220 F A 0.0000
221 N A -2.4009
222 Q A -2.1692
223 R A -1.4836
224 S A 0.0000
225 P A -1.6567
226 Q A -1.8437
227 L A 0.0000
228 Q A -2.7872
229 N A -2.3946
230 L A 0.0000
231 R A -2.9368
232 D A -2.1274
233 Y A -1.0776
234 R A -0.8581
235 I A 0.0000
236 L A 0.0000
237 E A 0.0000
238 F A 0.0000
239 N A -0.9665
240 S A 0.0000
241 K A -2.4792
242 P A -2.3490
243 N A -2.1968
244 T A 0.0000
245 L A -0.4058
246 L A 0.0000
247 L A 0.0000
248 P A 0.2063
249 N A 0.0000
250 H A -0.2733
251 A A 0.0000
252 D A -1.2320
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 -0.9875
262 G A -1.2842
263 T A -0.9775
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 -1.3440
270 N A -2.6099
271 N A -3.0052
272 D A -3.5542
273 D A -3.6234
274 R A -2.6854
275 D A -2.3340
276 S A 0.0000
277 Y A 0.0000
278 R A -1.8046
279 L A 0.0000
280 Q A -1.0832
281 S A -0.7247
282 G A 0.0000
283 D A 0.0000
284 A A 0.0000
285 L A 0.0000
286 R A -1.2392
287 V A 0.0000
288 P A -0.4566
289 S A -0.1927
290 G A -0.2002
291 T A 0.0000
292 T A -0.2358
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 -1.7573
299 D A -2.2166
300 N A -2.8464
301 N A -2.8236
302 E A -2.6599
303 N A -2.2072
304 L A 0.0000
305 R A -0.8582
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 -0.5828
312 P A 0.0000
313 V A -1.0090
314 N A -2.4517
315 K A -3.0136
316 P A -2.2022
317 G A 0.0000
318 R A -3.1634
319 F A -2.0668
320 E A -2.2192
321 S A -0.5866
322 F A -0.0007
323 F A 0.0000
324 L A 0.6564
325 S A 0.1747
326 S A -0.9092
327 T A 0.0000
328 E A -3.0838
329 A A -1.8276
330 Q A -1.2936
331 Q A -1.4177
332 S A 0.0000
333 Y A 0.5678
334 L A 0.5276
335 Q A -0.3374
336 G A -0.1622
337 F A 0.9068
338 S A -0.2840
339 R A -2.1514
340 N A -1.4208
341 I A 0.8075
342 L A 0.0000
343 E A -2.0675
344 A A -0.9233
345 S A -0.4404
346 Y A -0.5771
347 D A -1.8607
348 T A -2.1868
349 K A -3.3472
350 F A -2.6843
351 E A -3.8551
352 E A -2.5570
353 I A 0.0000
354 N A -2.3798
355 K A -2.6041
356 V A 0.3856
357 L A 0.6880
358 F A 0.0000
359 S A -1.9616
360 R A -3.0627
361 E A -4.4931
362 E A -3.9725
363 G A -2.9361
364 Q A -3.6809
365 Q A -3.2640
366 Q A -3.1704
367 G A -3.0893
368 E A -3.6139
369 Q A -3.7578
370 R A -3.8305
371 L A -2.6283
372 Q A -2.7212
373 E A -3.1523
374 S A 0.0000
375 V A 0.0000
376 I A 0.0000
377 V A -1.3748
378 E A -2.2362
379 I A 0.0000
380 S A -2.4691
381 K A -3.6767
382 E A -3.7006
383 Q A -3.0170
384 I A 0.0000
385 R A -3.7906
386 A A -2.6125
387 L A -1.9119
388 S A -2.6324
389 K A -3.1949
390 R A -3.5363
391 A A -2.5955
392 K A -2.9704
393 S A -1.7844
394 S A -1.6806
395 S A -1.9362
396 R A -3.1923
397 K A -2.7634
398 T A 0.0000
399 I A 0.0000
400 S A -2.1328
401 S A -2.2840
402 E A -3.4091
403 D A -3.2589
404 K A -2.7973
405 P A 0.0000
406 F A 0.0000
407 N A -1.2161
408 L A 0.0000
409 R A -2.1297
410 S A -2.5300
411 R A -3.1604
412 D A -2.7151
413 P A -1.2851
414 I A 0.2857
415 Y A 0.0281
416 S A -0.9551
417 N A -1.4102
418 K A -2.2120
419 L A -1.8085
420 G A -1.7134
421 K A -1.5616
422 F A 0.0000
423 F A 0.0000
424 E A -0.7431
425 I A 0.0000
426 T A -1.6836
427 P A 0.0000
428 E A -2.9753
429 K A -2.3684
430 N A 0.0000
431 P A -2.6912
432 Q A 0.0000
433 L A 0.0000
434 R A -3.6689
435 D A -2.9432
436 L A 0.0000
437 D A -2.2020
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 -1.6107
445 M A 0.0000
446 N A -2.9411
447 E A -3.1425
448 G A -1.7868
449 A A 0.0000
450 L A -0.4291
451 L A 0.0000
452 L A 0.0000
453 P A 0.1341
454 H A 0.0000
455 F A 0.0734
456 N A 0.0000
457 S A -1.0310
458 K A -1.2686
459 A A 0.0000
460 I A -0.2509
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 -2.1719
468 G A -2.2133
469 D A -2.2876
470 A A 0.0000
471 N A -1.4595
472 I A 0.0000
473 E A -1.8059
474 L A 0.0000
475 V A -0.0115
476 G A 0.0000
477 L A -0.1411
478 K A -2.0808
479 E A -3.1602
480 Q A -3.6041
481 Q A -3.6764
482 Q A -3.8415
483 E A -3.9696
484 Q A -3.6445
485 Q A -3.9480
486 Q A -3.8446
487 E A -4.1777
488 E A -3.5956
489 Q A -3.1127
490 P A -1.2913
491 L A -0.1593
492 E A -1.2256
493 V A 0.5954
494 R A -0.8238
495 K A -1.5724
496 Y A 0.0000
497 R A -2.3690
498 A A 0.0000
499 E A -1.9789
500 L A 0.0000
501 S A -1.6810
502 E A -1.9918
503 Q A -1.2667
504 D A -1.3722
505 I A 0.0000
506 F A 0.0000
507 V A 0.0000
508 I A 0.0000
509 P A -0.2353
510 A A -0.2138
511 G A -0.1985
512 Y A 0.3741
513 P A 0.0694
514 V A 0.0000
515 V A -0.2285
516 V A 0.0000
517 N A -1.0914
518 A A 0.0000
519 T A -1.6409
520 S A -2.2608
521 N A -2.9831
522 L A 0.0000
523 N A -1.5112
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 -1.3484
531 A A 0.0000
532 E A -2.6296
533 N A -2.5478
534 N A -1.9746
535 Q A -1.9320
536 R A -1.2205
537 N A -0.8419
538 F A 0.0000
539 L A 0.1695
540 A A -0.8559
541 G A 0.0000
542 S A -2.4724
543 Q A -2.3427
544 D A -2.2425
545 N A 0.0000
546 V A -0.1578
547 I A 0.1511
548 S A -0.9512
549 Q A -0.9608
550 I A -0.0826
551 P A -0.5373
552 S A -1.0863
553 Q A -0.9527
554 V A 0.5885
555 Q A 0.0000
556 E A -1.2243
557 L A 0.8654
558 A A 0.6526
559 F A 0.4884
560 P A -0.1628
561 G A -0.6828
562 S A -1.3929
563 A A 0.0000
564 Q A -2.0390
565 A A -1.3995
566 V A 0.0000
567 E A -2.0786
568 K A -2.5552
569 L A -0.6304
570 L A -1.5035
571 K A -3.2593
572 N A -2.8592
573 Q A -2.6160
574 R A -3.4075
575 E A -2.6835
576 S A 0.0000
577 Y A -0.4516
578 F A 0.0000
579 V A 0.0000
580 D A -1.7153
581 A A -1.2499
582 Q A -2.2658
583 P A -3.0296
584 K A -4.4606
585 K A -4.9690
586 K A -5.4048
587 E A -5.6501
588 E A -5.5990
589 G A -4.6129
590 N A -4.9670
591 K A -4.8000
592 G A -3.8788
593 R A -4.2018
594 K A -3.3216
595 G A -1.6944
596 P A -0.4946
597 L A 1.1940
598 S A 0.9937
599 S A 1.1349
600 I A 2.3740
601 L A 1.8412
602 R A 0.1853
603 A A 1.1378
604 F A 2.3312
605 Y A 1.9627
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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 -1.306 4.3351 View CSV PDB
4.5 -1.3913 4.3351 View CSV PDB
5.0 -1.5003 4.3351 View CSV PDB
5.5 -1.6102 4.3351 View CSV PDB
6.0 -1.6956 4.3351 View CSV PDB
6.5 -1.7368 4.3351 View CSV PDB
7.0 -1.7297 4.3351 View CSV PDB
7.5 -1.6876 4.335 View CSV PDB
8.0 -1.6268 4.3348 View CSV PDB
8.5 -1.5562 4.3342 View CSV PDB
9.0 -1.4795 4.3322 View CSV PDB