Project name: Q96318

Status: done

Started: 2025-06-28 13:13:26
Chain sequence(s) A: MVKLSNLLVATFGVLLVLNGCLARQSLGVPPQLQNECNLDNLDVLQATETIKSEAGQIEYWDHNHPQLRCVGVSVARYVIEQGGLYLPTFFTSPKISYVVQGTGISGRVVPGCAETFMDSQPMQGQQQGQPWQGRQGQQGQPWEGQGQQGQQGRQGQPWEGQGQQGQQGRQGQQGQPWEGQGQQGQQGFRDMHQKVEHVRRGDVFANTPGSAHWIYNSGEQPLVIIALLDIANYQNQLDRNPRVFHLAGNNQQGGFGGSQQQQEQKNLWSGFDAQVIAQALKIDVQLAQQLQNQQDSRGNIVRVKGPFQVVRPPLRQPYESEEWRHPRSPQGNGLEETICSMRSHENIDDPARADVYKPSLGRVTSVNSYTLPILEYVRLSATRGVLQGNAMVLPKYNMNANEILYCTGGQGRIQVVNDNGQNVLDQQVQKGQLVVIPQGFAYVVQSHGNKFEWISFKTNENAMISTLAGRTSLLRALPLEVISNGFQISPEEARKIKFNTLETTLTRAAGRQQQQLIEEIVEA
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage A: MVKLSNLLVATFGVLLVLNGCLARQSLGVPPQLQNECNLDNLDVLQATETIKSEAGQIEYWDHNHPQLRCVGVSVARYVIEQGGLYLPTFFTSPKISYVVQGTGISGRVVPGCAETFMDS

QPMQGQQQGQPWQGRQGQQGQPWEGQGQQGQQGRQGQPWEGQGQQGQQGRQGQQGQPWEGQGQQGQ

QGFRDMHQKVEHVRRGDVFANTPGSAHWIYNSGEQPLVIIALLDIANYQNQLDRNPRVFHLAGNNQQGGFGGSQQQQEQKNLWSGFDAQVIAQALKIDVQLAQQLQNQQDSRGNIVRVKGPFQVVRPPLRQPYESEEWRHPRSPQGNGLEETICSMRSHENIDDPARADVYKPSLGRVTSVNSYTLPILEYVRLSATRGVLQGNAMVLPKYNMNANEILYCTGGQGRIQVVNDNGQNVLDQQVQKGQLVVIPQGFAYVVQSHGNKFEWISFKTNENAMISTLAGRTSLLRALPLEVISNGFQISPEEARKIKFNTLETTLTRAAGRQQQQLIEEIVEA
(Red indicates removed residues)
Dynamic mode No
Automated mutations No
Downloads Download all the data
Simulation log
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       PDB:      Running AlphaCutter                                                         (00:00:02)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:21)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:21)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:11:55)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/d7fabcd9023df1b/tmp/folded.pdb                (00:11:55)
[INFO]       Main:     Simulation completed successfully.                                          (00:18:18)
Show buried residues

Minimal score value
-4.1198
Maximal score value
4.2155
Average score
-0.6182
Total score value
-283.1576

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
1 M A 1.4759
2 V A 1.5811
3 K A -0.1045
4 L A 1.4246
5 S A 1.1662
6 N A 0.7208
7 L A 2.1521
8 L A 2.5253
9 V A 3.1360
10 A A 2.3988
11 T A 2.9369
12 F A 4.2155
13 G A 3.2791
14 V A 3.5855
15 L A 3.7561
16 L A 3.7999
17 V A 3.8833
18 L A 3.2451
19 N A 1.1975
20 G A 1.1673
21 C A 1.0953
22 L A 1.0762
23 A A -0.1154
24 R A -1.7223
25 Q A -1.1753
26 S A 0.0321
27 L A 0.7901
28 G A 0.5430
29 V A 1.0871
30 P A -0.0155
31 P A -0.9421
32 Q A -1.5483
33 L A -1.1233
34 Q A -2.0059
35 N A -2.3524
36 E A -2.0295
37 C A -1.6092
38 N A -2.8321
39 L A 0.0000
40 D A -3.3168
41 N A -3.0061
42 L A 0.0000
43 D A -2.4544
44 V A 0.0000
45 L A 0.0000
46 Q A -1.8238
47 A A -1.3649
48 T A -1.4410
49 E A -2.1484
50 T A -1.4996
51 I A 0.0000
52 K A -2.6099
53 S A -2.0771
54 E A -1.9396
55 A A 0.0000
56 G A -1.2306
57 Q A -1.1590
58 I A 0.0000
59 E A -1.2103
60 Y A 0.0000
61 W A 0.0000
62 D A -1.7280
63 H A 0.0000
64 N A -1.5383
65 H A -1.1541
66 P A -1.1214
67 Q A 0.0000
68 L A 0.0000
69 R A -1.5292
70 C A 0.0000
71 V A 0.0000
72 G A 0.0000
73 V A 0.0000
74 S A 0.0000
75 V A 0.0000
76 A A 0.0000
77 R A -0.2153
78 Y A 0.0000
79 V A -0.2547
80 I A 0.0000
81 E A -1.6601
82 Q A -2.2082
83 G A -1.4517
84 G A 0.0000
85 L A -0.0946
86 Y A 0.0000
87 L A 0.0000
88 P A 0.4279
89 T A 0.0000
90 F A 0.5197
91 F A 0.0000
92 T A -0.2528
93 S A 0.0000
94 P A 0.0000
95 K A 0.0000
96 I A 0.0000
97 S A 0.0000
98 Y A 0.0000
99 V A 0.0000
100 V A -0.7153
101 Q A -1.3453
102 G A -1.8712
103 T A -1.6515
104 G A 0.0000
105 I A 0.0000
106 S A 0.0000
107 G A 0.0000
108 R A 0.2598
109 V A 0.7460
110 V A 0.8269
111 P A 0.0135
112 G A -0.4454
113 C A -0.4095
114 A A -0.8446
115 E A -1.5413
116 T A -0.9348
117 F A -0.3920
118 M A -0.1103
119 D A -0.7380
120 S A -0.9000
121 Q A -1.6900
188 G A -0.7655
189 F A -0.3426
190 R A -2.0518
191 D A -1.6056
192 M A -0.2605
193 H A -0.6348
194 Q A -0.8638
195 K A -1.1684
196 V A 0.0000
197 E A 0.0000
198 H A -0.3815
199 V A 0.0000
200 R A -1.9609
201 R A -2.4240
202 G A 0.0000
203 D A 0.0000
204 V A 0.0000
205 F A 0.0000
206 A A 0.0000
207 N A 0.0000
208 T A 0.0106
209 P A -0.2589
210 G A -0.0100
211 S A 0.0000
212 A A 0.0000
213 H A 0.0000
214 W A 0.3497
215 I A 0.0000
216 Y A -0.0049
217 N A 0.0000
218 S A -1.0372
219 G A -1.8676
220 E A -2.8503
221 Q A -2.5105
222 P A -1.4885
223 L A 0.0000
224 V A -0.4692
225 I A 0.0000
226 I A 0.0000
227 A A 0.0000
228 L A 0.0000
229 L A 0.0000
230 D A 0.0000
231 I A 0.0000
232 A A -0.2729
233 N A 0.0000
234 Y A 0.9837
235 Q A 0.2470
236 N A 0.0000
237 Q A -0.4421
238 L A 0.4723
239 D A -0.7149
240 R A -1.4329
241 N A -1.1605
242 P A 0.0000
243 R A -0.7474
244 V A 0.1094
245 F A 0.5656
246 H A 0.0000
247 L A 0.7589
248 A A 0.2757
249 G A 0.0000
250 N A 0.0000
251 N A 0.0000
252 Q A -3.5143
253 Q A -3.0300
254 G A 0.0000
255 G A -1.9666
256 F A -1.1358
257 G A -1.3502
258 G A -1.5570
259 S A -1.6276
260 Q A -3.0344
261 Q A -3.2931
262 Q A -3.6110
263 Q A -3.9676
264 E A -4.1198
265 Q A -2.5997
266 K A -1.9122
267 N A 0.0000
268 L A 0.7926
269 W A 0.2332
270 S A -0.4500
271 G A 0.0000
272 F A 0.9423
273 D A -0.6958
274 A A -0.7123
275 Q A -0.6405
276 V A 0.8191
277 I A 0.0000
278 A A 0.0000
279 Q A -1.0857
280 A A -0.1757
281 L A -0.1621
282 K A -1.4459
283 I A -0.8450
284 D A -1.4431
285 V A -0.8668
286 Q A -1.2794
287 L A -0.3093
288 A A 0.0000
289 Q A -1.5380
290 Q A -1.5734
291 L A -0.3153
292 Q A 0.0000
293 N A -1.8359
294 Q A -2.3178
295 Q A -2.3909
296 D A -2.0440
297 S A -1.8619
298 R A -2.1804
299 G A 0.0000
300 N A 0.0000
301 I A 0.0000
302 V A 0.0000
303 R A -1.4692
304 V A -0.9779
305 K A -1.8830
306 G A -1.4231
307 P A -0.8740
308 F A -0.3576
309 Q A -1.0462
310 V A -0.2114
311 V A -0.5769
312 R A -0.8152
313 P A -0.5190
314 P A -0.4265
315 L A 0.0051
316 R A -2.0255
317 Q A -1.9092
318 P A -0.9756
319 Y A -0.6511
320 E A -2.6365
321 S A -2.4620
322 E A -3.0122
323 E A -3.1205
324 W A -1.6055
325 R A -2.8352
326 H A -2.4047
327 P A -2.0231
328 R A -2.9364
329 S A -1.9724
330 P A -1.7248
331 Q A -2.1674
332 G A -1.9313
333 N A -2.2506
334 G A -1.2860
335 L A -0.0425
336 E A -2.0778
337 E A -2.2720
338 T A -0.4921
339 I A 1.4327
340 C A 0.0427
341 S A -0.9012
342 M A -0.4574
343 R A -1.5366
344 S A 0.0000
345 H A -0.7247
346 E A 0.0000
347 N A -1.0424
348 I A 0.0000
349 D A 0.0000
350 D A -1.3181
351 P A -0.7849
352 A A -0.7136
353 R A -1.3147
354 A A -0.9493
355 D A -1.4680
356 V A -0.0412
357 Y A 0.6874
358 K A 0.0599
359 P A -0.3319
360 S A -0.8412
361 L A 0.0000
362 G A 0.0000
363 R A 0.0000
364 V A -0.0649
365 T A 0.0000
366 S A -0.5851
367 V A 0.0000
368 N A -0.5023
369 S A -0.4051
370 Y A 0.8298
371 T A 0.2610
372 L A 0.0000
373 P A -0.6090
374 I A 0.0000
375 L A 0.0000
376 E A -1.7654
377 Y A -0.4094
378 V A 0.0000
379 R A -1.4044
380 L A 0.0000
381 S A 0.0000
382 A A 0.0000
383 T A 0.0000
384 R A 0.0000
385 G A 0.0000
386 V A 0.0000
387 L A 0.0000
388 Q A -2.2118
389 G A -2.3935
390 N A -2.7111
391 A A 0.0000
392 M A -1.0821
393 V A 0.0000
394 L A 0.0000
395 P A 0.1678
396 K A 0.0000
397 Y A 0.4954
398 N A 0.0000
399 M A 0.5110
400 N A -0.1738
401 A A 0.0000
402 N A -0.7125
403 E A 0.0000
404 I A 0.0000
405 L A 0.0000
406 Y A 0.0000
407 C A 0.0000
408 T A 0.0000
409 G A -1.3365
410 G A -1.9876
411 Q A -2.4503
412 G A 0.0000
413 R A -2.4665
414 I A 0.0000
415 Q A -1.3058
416 V A 0.0000
417 V A -1.4454
418 N A 0.0000
419 D A -3.1808
420 N A -3.1133
421 G A -2.2288
422 Q A -2.8115
423 N A -2.5012
424 V A 0.0000
425 L A 0.0000
426 D A -2.1630
427 Q A -2.5031
428 Q A -2.4341
429 V A 0.0000
430 Q A -2.6822
431 K A -2.4994
432 G A -1.5497
433 Q A -1.5457
434 L A 0.0000
435 V A 0.0000
436 V A 0.0000
437 I A 0.0000
438 P A 0.0000
439 Q A -1.1789
440 G A -1.0248
441 F A 0.0000
442 A A -0.2348
443 Y A 0.0000
444 V A -0.0547
445 V A 0.0000
446 Q A -1.6988
447 S A 0.0000
448 H A -2.6768
449 G A -2.2644
450 N A -2.5711
451 K A -2.2726
452 F A 0.0000
453 E A -1.0291
454 W A 0.0000
455 I A 0.0000
456 S A 0.0000
457 F A 0.0000
458 K A 0.0000
459 T A -0.6472
460 N A -1.0125
461 E A -1.1873
462 N A -0.5390
463 A A 0.1245
464 M A 1.1499
465 I A 1.2432
466 S A 1.0085
467 T A 0.0000
468 L A 0.6417
469 A A 0.2880
470 G A 0.0000
471 R A -1.1518
472 T A -0.5486
473 S A 0.0000
474 L A 0.8855
475 L A 0.9179
476 R A -0.3232
477 A A 0.0713
478 L A 0.5500
479 P A -0.1337
480 L A -1.1129
481 E A -1.6097
482 V A 0.2002
483 I A 0.0000
484 S A -1.3255
485 N A -1.4634
486 G A -0.5045
487 F A 0.3270
488 Q A -1.0662
489 I A -1.0423
490 S A -1.7219
491 P A -2.2718
492 E A -3.1639
493 E A -2.5063
494 A A 0.0000
495 R A -3.2709
496 K A -2.8316
497 I A -0.6787
498 K A -0.7520
499 F A -0.3008
500 N A -1.0730
501 T A -0.0609
502 L A 0.7294
503 E A -0.4454
504 T A -0.4379
505 T A 0.0303
506 L A 0.0000
507 T A -1.0463
508 R A -2.3686
509 A A -1.7992
510 A A -1.5690
511 G A -2.2484
512 R A -2.8945
513 Q A -2.7321
514 Q A -2.1103
515 Q A -2.3151
516 Q A -2.3312
517 L A -0.4972
518 I A 0.1503
519 E A -1.7915
520 E A -1.4775
521 I A 1.3738
522 V A 1.0571
523 E A -1.1407
524 A A -0.1877
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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 -0.2692 7.0174 View CSV PDB
4.5 -0.3223 7.0174 View CSV PDB
5.0 -0.3901 7.0174 View CSV PDB
5.5 -0.4619 7.0174 View CSV PDB
6.0 -0.5258 7.0174 View CSV PDB
6.5 -0.5721 7.0174 View CSV PDB
7.0 -0.597 7.0174 View CSV PDB
7.5 -0.6052 7.0174 View CSV PDB
8.0 -0.6028 7.0174 View CSV PDB
8.5 -0.593 7.0174 View CSV PDB
9.0 -0.5771 7.0174 View CSV PDB