Project name: AAV2_1mer_M2

Status: done

Started: 2026-10-21 18:13:17
Settings
Chain sequence(s) GADGVGNSSGNWHCDSTWMGDRVITTSTRTWALPTYNNHLYKQISSQSGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTQNDGTTTIANNLTSTVQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMVPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLSRTNTPSGTTTQSRLQFSQAGASDIRDQSRNWLPGPCYRQQRVSKTSADNNNSEYSWTGATKYHLNGRDSLVNPGPAMASHKDDEEKFFPQSGVLIFGKQGSEKTNVDIEKVMITDEEEIRTTNPVATEQYGSVSTNLQRGNRQAATADVNTQGVLPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPSTTFSAAKFASFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYNKSVNVDFTVDTNGVYSEPRPIGTRYLTRNL input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
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-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:04)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:04)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:04:35)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/b1d712a7cc93e7/tmp/folded.pdb                 (00:04:35)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:14)
Show buried residues

Minimal score value
-4.0369
Maximal score value
2.2562
Average score
-0.6166
Total score value
-319.9938

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
15 G A -1.2150
16 A A -1.2077
17 D A -2.1497
18 G A -1.0902
19 V A 0.5888
20 G A -0.6840
21 N A -1.7088
22 S A -1.2641
23 S A -1.4920
24 G A -1.3157
25 N A -1.2140
26 W A -0.3702
27 H A -1.2535
28 C A -1.0629
29 D A -1.8549
30 S A -0.8693
31 T A -0.1591
32 W A -0.0681
33 M A 0.3240
34 G A -0.7705
35 D A -1.5718
36 R A -0.8959
37 V A 0.0000
38 I A -0.3007
39 T A 0.0000
40 T A -0.9356
41 S A 0.0000
42 T A 0.0000
43 R A 0.0000
44 T A 0.4488
45 W A 0.0000
46 A A 0.7421
47 L A 0.0000
48 P A 0.0695
49 T A -0.2952
50 Y A -0.3141
51 N A -0.8343
52 N A -1.1509
53 H A -0.4003
54 L A 0.0464
55 Y A -0.2919
56 K A -1.2670
57 Q A -0.9106
58 I A -0.1820
59 S A -0.3883
60 S A 0.0000
61 Q A -1.5432
62 S A -1.1079
63 G A -1.3058
64 A A -1.5702
65 S A -1.9010
66 N A -2.6880
67 D A -2.5915
68 N A -2.4734
69 H A -2.0777
70 Y A -0.3097
71 F A 0.0000
72 G A 0.0000
73 Y A 0.2573
74 S A -0.2670
75 T A 0.0000
76 P A 0.0000
77 W A 0.0000
78 G A 0.0000
79 Y A 0.0000
80 F A 0.0000
81 D A 0.0000
82 F A 0.0000
83 N A 0.0000
84 R A -0.7628
85 F A 0.0000
86 H A 0.0000
87 C A 0.0000
88 H A 0.0000
89 F A 0.0000
90 S A -1.0437
91 P A -1.1824
92 R A -2.1376
93 D A -1.8262
94 W A 0.0000
95 Q A -1.9592
96 R A -2.2690
97 L A 0.0000
98 I A 0.0000
99 N A 0.0000
100 N A -2.2431
101 N A 0.0000
102 W A -1.2023
103 G A 0.0000
104 F A 0.0000
105 R A -0.9240
106 P A 0.0000
107 K A -1.9074
108 R A -2.4603
109 L A 0.0000
110 N A -1.6490
111 F A 0.0000
112 K A -1.2000
113 L A 0.0000
114 F A 0.0000
115 N A -1.3668
116 I A 0.0000
117 Q A -1.2092
118 V A 0.0000
119 K A -0.5702
120 E A -0.2008
121 V A -0.0001
122 T A -0.8665
123 Q A -2.2203
124 N A -2.9038
125 D A -2.9331
126 G A -2.0860
127 T A -1.6954
128 T A -0.9468
129 T A -0.1093
130 I A 0.6438
131 A A -0.1373
132 N A -1.1941
133 N A -0.7832
134 L A 0.0472
135 T A -0.3084
136 S A 0.0000
137 T A -0.3633
138 V A 0.0000
139 Q A -0.4018
140 V A 0.0000
141 F A 0.0000
142 T A -0.4194
143 D A 0.0000
144 S A -1.2882
145 E A -2.2132
146 Y A -1.2949
147 Q A -1.2763
148 L A 0.0000
149 P A 0.4209
150 Y A 0.0910
151 V A 0.3486
152 L A 0.0000
153 G A -0.3739
154 S A -0.5163
155 A A -0.7133
156 H A -1.3182
157 Q A -1.6434
158 G A -0.6518
159 C A 0.0000
160 L A 0.0000
161 P A -0.0866
162 P A -0.2628
163 F A 0.2947
164 P A -0.0574
165 A A -0.2460
166 D A -0.5822
167 V A 1.2955
168 F A 1.1125
169 M A 1.4236
170 V A 0.0000
171 P A -0.2287
172 Q A -0.3353
173 Y A 0.0000
174 G A -0.0142
175 Y A 0.0000
176 L A 1.9380
177 T A 1.2200
178 L A 0.3140
179 N A -0.6594
180 N A -1.7647
181 G A -1.8503
182 S A -1.5262
183 Q A -1.3681
184 A A -0.9391
185 V A -0.5111
186 G A -0.9149
187 R A -1.5533
188 S A -0.2237
189 S A 0.6362
190 F A 1.5468
191 Y A 1.1200
192 C A 0.8262
193 L A 0.0000
194 E A -0.1991
195 Y A 1.0116
196 F A 0.2599
197 P A -0.2128
198 S A -0.4808
199 Q A -1.0327
200 M A 0.0405
201 L A 0.0000
202 R A -1.4803
203 T A -1.2557
204 G A -1.7519
205 N A -1.7744
206 N A -1.6055
207 F A 0.0000
208 T A -0.6399
209 F A -0.3013
210 S A -0.9295
211 Y A -0.9702
212 T A -1.5466
213 F A 0.0000
214 E A -2.0972
215 D A -2.1053
216 V A 0.0000
217 P A -0.4898
218 F A -0.1394
219 H A -0.1676
220 S A -0.1367
221 S A 0.0000
222 Y A -0.3931
223 A A -0.4318
224 H A -0.8666
225 S A -0.9735
226 Q A -1.2225
227 S A -1.1795
228 L A 0.0000
229 D A -2.3024
230 R A -2.3066
231 L A -0.6348
232 M A -0.2684
233 N A -0.0792
234 P A 0.3944
235 L A 1.7933
236 I A 1.7555
237 D A -0.4224
238 Q A 0.4347
239 Y A 1.4562
240 L A 1.6242
241 Y A 2.2562
242 Y A 1.3247
243 L A 1.3753
244 S A 0.0688
245 R A -1.7752
246 T A -1.5275
247 N A -2.7041
248 T A -1.9073
249 P A -1.2218
250 S A -0.9781
251 G A -0.7668
252 T A -0.4117
253 T A -0.6113
254 T A -1.4470
255 Q A -2.0596
256 S A -2.2220
257 R A -2.5617
258 L A -0.2298
259 Q A -0.2656
260 F A 1.8970
261 S A 0.9021
262 Q A 0.3392
263 A A 0.0000
264 G A 0.0000
265 A A -0.0779
266 S A -0.7007
267 D A -1.0938
268 I A -1.3466
269 R A -2.4442
270 D A -1.1174
271 Q A 0.0000
272 S A -0.6265
273 R A -1.4982
274 N A -1.1268
275 W A 0.2532
276 L A 0.8064
277 P A 0.5879
278 G A 0.0000
279 P A 0.3570
280 C A 0.0000
281 Y A -0.5961
282 R A -1.3701
283 Q A 0.0000
284 Q A -1.4943
285 R A -1.7814
286 V A 0.0000
287 S A 0.0000
288 K A -1.8011
289 T A -1.1136
290 S A -1.1995
291 A A -1.3145
292 D A -2.1664
293 N A -2.3252
294 N A -2.6792
295 N A -2.5971
296 S A -2.1085
297 E A -2.2548
298 Y A -1.1494
299 S A -0.4626
300 W A 0.1717
301 T A -0.2345
302 G A -0.6282
303 A A 0.0000
304 T A -0.1880
305 K A 0.1335
306 Y A 0.7809
307 H A -0.7996
308 L A -0.4972
309 N A -1.7317
310 G A -1.7191
311 R A -2.0654
312 D A -1.4412
313 S A -0.3203
314 L A 0.3543
315 V A 0.0000
316 N A -0.7259
317 P A 0.0000
318 G A 0.0000
319 P A -0.0267
320 A A 0.0637
321 M A 0.0000
322 A A 0.0000
323 S A 0.0000
324 H A 0.0000
325 K A -2.7381
326 D A -3.6193
327 D A -3.6457
328 E A -3.1923
329 E A -3.7241
330 K A -2.5802
331 F A -2.0994
332 F A 0.0000
333 P A 0.0000
334 Q A -0.9206
335 S A 0.0000
336 G A 0.0000
337 V A 0.0000
338 L A 0.5404
339 I A 1.2396
340 F A 0.1480
341 G A -1.7401
342 K A -2.6272
343 Q A -2.2754
344 G A -2.1201
345 S A -2.9363
346 E A -3.5791
347 K A -2.9111
348 T A -2.0912
349 N A -2.1437
350 V A -2.1929
351 D A -2.4076
352 I A -1.1603
353 E A -2.4954
354 K A -2.9304
355 V A -1.2319
356 M A 0.0000
357 I A 0.2997
358 T A 0.0000
359 D A -1.3378
360 E A 0.0000
361 E A -2.1960
362 E A -1.4149
363 I A 0.0000
364 R A -1.2352
365 T A -0.9071
366 T A 0.0000
367 N A 0.0000
368 P A -0.4445
369 V A -0.6637
370 A A 0.0000
371 T A -1.4079
372 E A -1.9282
373 Q A -2.0180
374 Y A -0.9096
375 G A -0.7756
376 S A -0.3200
377 V A 1.0726
378 S A 0.2589
379 T A -0.1342
380 N A -0.8326
381 L A -0.3786
382 Q A -2.8788
383 R A -3.6400
384 G A -2.9623
385 N A -3.4098
386 R A -4.0369
387 Q A -3.1165
388 A A -1.6216
389 A A -0.5594
390 T A -0.1299
391 A A -0.6805
392 D A -1.9032
393 V A -1.1229
394 N A -1.6774
395 T A -0.9423
396 Q A -0.3299
397 G A 0.0965
398 V A 1.2980
399 L A 1.0168
400 P A 0.4708
401 G A 0.3011
402 M A 0.0000
403 V A 1.0997
404 W A 0.3560
405 Q A -0.3516
406 D A -0.5222
407 R A 0.0000
408 D A 0.0000
409 V A 0.0000
410 Y A 0.0000
411 L A 0.0000
412 Q A 0.0000
413 G A 0.0000
414 P A -0.3779
415 I A 0.0000
416 W A 0.0000
417 A A -0.5231
418 K A -1.3407
419 I A 0.0000
420 P A -1.5814
421 H A -2.0567
422 T A -1.8180
423 D A -2.4644
424 G A -1.5605
425 H A -0.9381
426 F A 1.1510
427 H A -0.0621
428 P A -0.2564
429 S A 0.0215
430 P A 0.2217
431 L A 0.9044
432 M A 0.0000
433 G A 0.0000
434 G A -0.0687
435 F A 0.0000
436 G A -0.8047
437 L A 0.0000
438 K A -2.6206
439 H A -2.2282
440 P A 0.0000
441 P A 0.0000
442 P A 0.0000
443 Q A 0.0000
444 I A 0.0000
445 L A 0.0000
446 I A 0.0000
447 K A 0.0000
448 N A 0.0000
449 T A 0.1900
450 P A 0.1482
451 V A 0.5410
452 P A 0.2333
453 A A -0.2251
454 N A -1.3219
455 P A -0.6047
456 S A -0.2889
457 T A 0.0077
458 T A 0.6737
459 F A 1.7289
460 S A 0.5611
461 A A 0.1600
462 A A -0.2639
463 K A -1.1502
464 F A 0.3043
465 A A 0.0392
466 S A -0.1776
467 F A 0.3232
468 I A 0.5840
469 T A 0.1282
470 Q A 0.0000
471 Y A 0.3328
472 S A 0.0000
473 T A 0.0968
474 G A 0.0000
475 Q A -0.3578
476 V A 0.0000
477 S A -0.7691
478 V A 0.0000
479 E A -1.4954
480 I A 0.0000
481 E A 0.0000
482 W A 0.0000
483 E A -1.1677
484 L A 0.0000
485 Q A -2.1645
486 K A -3.0865
487 E A -2.7591
488 N A -2.8137
489 S A -2.2916
490 K A -2.3701
491 R A -1.7358
492 W A -0.0997
493 N A -0.8777
494 P A -0.3419
495 E A 0.2380
496 I A 1.6282
497 Q A 0.2430
498 Y A -0.1249
499 T A -0.1896
500 S A -0.7256
501 N A -1.2432
502 Y A -0.3781
503 N A -1.9277
504 K A -1.8064
505 S A -0.3352
506 V A 1.2506
507 N A 0.5725
508 V A 1.1782
509 D A 0.1990
510 F A 0.0000
511 T A 0.5433
512 V A 0.4202
513 D A -0.3796
514 T A -0.9253
515 N A -1.3487
516 G A -0.8285
517 V A -0.0919
518 Y A -0.0403
519 S A -0.4050
520 E A -0.8664
521 P A -0.8219
522 R A -0.8587
523 P A -0.3948
524 I A 0.0000
525 G A -0.2374
526 T A 0.0000
527 R A 0.0000
528 Y A 0.5405
529 L A 0.0000
530 T A -0.5604
531 R A -1.7975
532 N A -1.2322
533 L A 0.3114
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Calculations for various pH values

This page contains details and comparisons for all models calculated at different pH points.

pH
Average A3D Score
Max A3D Score
4.0 -0.3412 4.4053 View CSV PDB
4.5 -0.3867 4.2206 View CSV PDB
5.0 -0.4393 4.0225 View CSV PDB
5.5 -0.4911 4.0225 View CSV PDB
6.0 -0.5346 4.0225 View CSV PDB
6.5 -0.5645 4.0225 View CSV PDB
7.0 -0.5819 4.0225 View CSV PDB
7.5 -0.5918 4.0225 View CSV PDB
8.0 -0.5971 4.0225 View CSV PDB
8.5 -0.5967 4.0225 View CSV PDB
9.0 -0.5883 4.0225 View CSV PDB