Project name: AAV4_1mer_M2

Status: done

Started: 2026-10-21 19:29:16
Settings
Chain sequence(s) GVGNASGDWHCDSTWSEGHVTTTSTRTWVLPTYNNHLYKRLGESLQSNTYNGFSTPWGYFDFNRFHCHFSPRDWQRLINNNWGMRPKAMRVKIFNIQVKEVTTSNGETTVANNLTSTVQIFADSSYELPYVMDAGQEGSLPPFPNDVFMVPQYGYCGLVTGNTSQQQTDRNAFYCLEYFPSQMLRTGNNFEITYSFEKVPFHSMYAHSQSLDRLMNPLIDQYLWGLQSTTTGTTLNAGTATTNFTKLRPTNFSNFKKNWLPGPSIKQQGFSKTANQNYKIPATGSDSLIKYETHSTLDGRWSALTPGPPMATAGPADSKFSNSQLIFAGPKQNGNTATVPGTLIFTSEEELAATNATDTDMWGNLPGGDQSNSNLPTVDRLTALGAVPGMVWQNRDIYYQGPIWAKIPHTDGHFHPSPLIGGFGLKHPPPQIFIKNTPVPANPATTFSSTPVNSFITQYSTGQVSVQIDWEIQKERSKRWNPEVQFTSNYGQQNSLLWAPDAAGKYTEPRAIGTRYLTHHL 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]                                                (00:00:01)
[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-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:03)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:03)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:41)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/a922b84bbf214a/tmp/folded.pdb                 (00:03:41)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:29)
Show buried residues

Minimal score value
-2.9221
Maximal score value
1.741
Average score
-0.514
Total score value
-267.8107

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
18 G A -0.4384
19 V A 0.7477
20 G A -0.4009
21 N A -1.2340
22 A A -1.0694
23 S A -1.1144
24 G A -1.3652
25 D A -1.6177
26 W A -0.5249
27 H A -1.1916
28 C A -0.9655
29 D A -1.7905
30 S A -0.9920
31 T A -0.5753
32 W A -0.8128
33 S A -1.2079
34 E A -2.2711
35 G A -1.5807
36 H A -1.4833
37 V A 0.0000
38 T A -0.7420
39 T A 0.0000
40 T A 0.0000
41 S A 0.0000
42 T A 0.0000
43 R A 0.0000
44 T A 0.2456
45 W A 0.0000
46 V A 0.9766
47 L A 0.0000
48 P A 0.1097
49 T A -0.2252
50 Y A -0.1936
51 N A -0.6241
52 N A -1.1113
53 H A -0.3021
54 L A 0.4211
55 Y A 0.0725
56 K A -1.4233
57 R A -1.3334
58 L A -0.7327
59 G A -0.9842
60 E A -1.6377
61 S A -1.2226
62 L A -0.6636
63 Q A -1.5899
64 S A -1.0970
65 N A -1.5792
66 T A 0.0000
67 Y A -0.2657
68 N A 0.0000
69 G A 0.0000
70 F A -0.1226
71 S A -0.4132
72 T A 0.0000
73 P A 0.0000
74 W A 0.0000
75 G A 0.0000
76 Y A 0.0000
77 F A 0.0000
78 D A 0.0000
79 F A 0.0000
80 N A 0.0000
81 R A -0.6819
82 F A 0.0000
83 H A 0.0000
84 C A 0.0000
85 H A 0.0000
86 F A 0.0000
87 S A -1.0953
88 P A -1.2828
89 R A -2.4173
90 D A 0.0000
91 W A 0.0000
92 Q A -2.0416
93 R A -2.3824
94 L A 0.0000
95 I A 0.0000
96 N A -1.0244
97 N A -1.7495
98 N A 0.0000
99 W A -0.7661
100 G A 0.0000
101 M A 0.0000
102 R A -0.9957
103 P A 0.0000
104 K A -1.6720
105 A A -1.1545
106 M A 0.0000
107 R A -2.1553
108 V A 0.0000
109 K A -1.6563
110 I A 0.0000
111 F A 0.0000
112 N A -1.1407
113 I A 0.0000
114 Q A -0.9216
115 V A 0.0000
116 K A -0.5362
117 E A -0.1174
118 V A 0.4077
119 T A -0.1198
120 T A -1.0113
121 S A -1.6451
122 N A -2.1905
123 G A -2.0720
124 E A -2.5917
125 T A -1.0231
126 T A -0.0124
127 V A 0.8801
128 A A -0.0495
129 N A -1.1046
130 N A -0.5547
131 L A 0.4759
132 T A 0.1635
133 S A 0.0000
134 T A 0.0000
135 V A 0.0000
136 Q A -0.5988
137 I A 0.0000
138 F A 0.0000
139 A A -0.3264
140 D A 0.0000
141 S A -0.6287
142 S A -0.9084
143 Y A -1.0884
144 E A -1.7105
145 L A 0.0000
146 P A -0.0941
147 Y A -0.0328
148 V A 0.1367
149 M A 0.0000
150 D A -0.5581
151 A A -0.7444
152 G A -1.4326
153 Q A -2.3246
154 E A -2.5563
155 G A -1.2280
156 S A -0.8887
157 L A 0.0000
158 P A -0.4007
159 P A -0.4545
160 F A -0.5236
161 P A -0.7252
162 N A -1.5620
163 D A -1.4939
164 V A 0.9291
165 F A 0.0000
166 M A 1.2833
167 V A 0.0000
168 P A -0.4391
169 Q A -0.3902
170 Y A 0.0000
171 G A -0.2102
172 Y A 0.0000
173 C A 0.8643
174 G A 0.5735
175 L A -0.0489
176 V A 0.0000
177 T A -0.8481
178 G A -1.1828
179 N A -1.3233
180 T A -1.0821
181 S A -1.0877
182 Q A -1.4159
183 Q A -1.6826
184 Q A -1.7227
185 T A -1.9858
186 D A -2.7716
187 R A -2.5850
188 N A -1.2667
189 A A 0.3012
190 F A 1.7410
191 Y A 1.3131
192 C A 1.0254
193 L A 0.0000
194 E A -0.1424
195 Y A 1.0629
196 F A 0.2109
197 P A -0.2530
198 S A -0.6127
199 Q A -1.2877
200 M A -0.5694
201 L A 0.0000
202 R A -1.2006
203 T A -0.8826
204 G A -0.8730
205 N A -1.3680
206 N A -1.7685
207 F A -1.3914
208 E A -2.2610
209 I A -1.1619
210 T A -1.0492
211 Y A -0.5614
212 S A -1.1237
213 F A 0.0000
214 E A -2.0381
215 K A -2.2034
216 V A 0.0000
217 P A -0.5477
218 F A -0.1239
219 H A -0.1035
220 S A -0.1192
221 M A 0.0000
222 Y A -0.1212
223 A A -0.5549
224 H A -0.7335
225 S A -1.0053
226 Q A -1.3512
227 S A -1.0577
228 L A 0.0000
229 D A -1.7428
230 R A -1.6388
231 L A -0.6318
232 M A -0.4624
233 N A -0.3500
234 P A 0.1165
235 L A 1.5146
236 I A 1.4782
237 D A 0.1124
238 Q A 0.0819
239 Y A 1.4003
240 L A 0.7768
241 W A 1.1432
242 G A 0.5211
243 L A 0.8135
244 Q A -0.5017
245 S A -0.3197
246 T A -0.2055
247 T A -0.5829
248 T A -0.4201
249 G A -0.6089
250 T A -0.2074
251 T A 0.1095
252 L A 0.9145
253 N A -0.6128
254 A A -0.4620
255 G A -0.6888
256 T A -0.5278
257 A A -0.5230
258 T A -0.0831
259 T A 0.0511
260 N A 0.2007
261 F A 1.6749
262 T A 0.4688
263 K A -0.1024
264 L A 0.0000
265 R A -1.3188
266 P A -0.5952
267 T A -0.7444
268 N A -1.2355
269 F A -1.4635
270 S A -1.4544
271 N A -2.0603
272 F A 0.0000
273 K A -2.5336
274 K A -2.4514
275 N A -1.6739
276 W A -0.1072
277 L A 0.5456
278 P A 0.5100
279 G A 0.0000
280 P A 0.4249
281 S A 0.0000
282 I A 0.5305
283 K A -0.4806
284 Q A 0.0000
285 Q A -0.8990
286 G A -0.9637
287 F A -0.4769
288 S A -1.1714
289 K A -0.9589
290 T A -0.9485
291 A A -0.9975
292 N A -2.0467
293 Q A -2.1141
294 N A -1.2628
295 Y A -0.1206
296 K A -1.2794
297 I A -0.3059
298 P A -0.3688
299 A A -0.1667
300 T A -0.4552
301 G A -0.9845
302 S A -1.0812
303 D A -1.3708
304 S A -0.5230
305 L A 0.1806
306 I A 0.3136
307 K A -0.5419
308 Y A 0.0421
309 E A -0.2500
310 T A -0.1529
311 H A -0.0745
312 S A 0.1514
313 T A 0.1374
314 L A 0.4285
315 D A -1.3479
316 G A -1.0685
317 R A -0.8927
318 W A -0.2139
319 S A -0.0079
320 A A 0.0475
321 L A 0.1293
322 T A 0.0944
323 P A 0.0000
324 G A 0.0000
325 P A 0.3114
326 P A 0.1556
327 M A 0.0000
328 A A 0.0000
329 T A 0.0000
330 A A -1.1346
331 G A -1.2226
332 P A -0.8509
333 A A -0.8373
334 D A -1.6559
335 S A -1.4326
336 K A -1.5325
337 F A -0.6287
338 S A 0.0000
339 N A -0.1633
340 S A 0.0000
341 Q A 0.0000
342 L A 0.0000
343 I A 1.3973
344 F A 0.8588
345 A A -0.3330
346 G A -0.7385
347 P A -1.4064
348 K A -2.1871
349 Q A -1.6887
350 N A -2.3317
351 G A -1.7549
352 N A -1.8341
353 T A -0.8705
354 A A -0.1025
355 T A 0.6951
356 V A 1.5418
357 P A 0.6713
358 G A -0.0956
359 T A -0.3486
360 L A 0.4994
361 I A 0.4340
362 F A 0.0000
363 T A 0.0000
364 S A 0.0000
365 E A 0.0000
366 E A -1.9981
367 E A -1.2320
368 L A 0.0000
369 A A -0.6280
370 A A -0.7706
371 T A 0.0000
372 N A 0.0000
373 A A -0.1905
374 T A -0.7534
375 D A 0.0000
376 T A -1.1220
377 D A -1.9451
378 M A -1.1483
379 W A -0.5021
380 G A -1.1285
381 N A -1.7777
382 L A -0.7173
383 P A -1.1752
384 G A -1.3882
385 G A -1.7565
386 D A -2.8252
387 Q A -2.7488
388 S A -2.1289
389 N A -1.9900
390 S A -1.4002
391 N A -1.9551
392 L A -0.1444
393 P A -0.8297
394 T A -0.3704
395 V A 0.0818
396 D A -2.2451
397 R A -2.7501
398 L A -1.2335
399 T A -0.8925
400 A A 0.0129
401 L A 0.4144
402 G A 0.0132
403 A A 0.4723
404 V A 0.6458
405 P A 0.2639
406 G A 0.0105
407 M A 0.6274
408 V A 0.8827
409 W A 0.3554
410 Q A -0.2392
411 N A -0.3304
412 R A 0.0000
413 D A 0.0000
414 I A 0.0000
415 Y A 0.0000
416 Y A 0.0000
417 Q A 0.0000
418 G A 0.0000
419 P A -0.4585
420 I A 0.0000
421 W A 0.0000
422 A A -0.4762
423 K A -1.1736
424 I A 0.0000
425 P A -1.4738
426 H A -1.9590
427 T A -1.7783
428 D A -2.4304
429 G A -1.4742
430 H A -0.7113
431 F A 1.1974
432 H A 0.1123
433 P A -0.2234
434 S A 0.0114
435 P A 0.2471
436 L A 0.9555
437 I A 0.8090
438 G A 0.0000
439 G A -0.0274
440 F A 0.0000
441 G A -0.7438
442 L A 0.0000
443 K A -2.2481
444 H A -1.8811
445 P A 0.0000
446 P A 0.0000
447 P A 0.0000
448 Q A 0.0000
449 I A 0.0000
450 F A 0.0000
451 I A 0.0000
452 K A 0.0000
453 N A 0.0000
454 T A 0.0950
455 P A -0.0739
456 V A 0.3827
457 P A 0.0317
458 A A -0.3521
459 N A -1.2742
460 P A -0.5545
461 A A 0.1059
462 T A 0.1322
463 T A 0.7625
464 F A 1.7106
465 S A 0.7073
466 S A 0.2146
467 T A 0.0653
468 P A -0.0294
469 V A 0.5746
470 N A -0.7447
471 S A -0.5488
472 F A 0.0791
473 I A 0.5260
474 T A 0.1220
475 Q A 0.0000
476 Y A 0.3103
477 S A 0.0000
478 T A 0.1353
479 G A 0.0000
480 Q A -0.3549
481 V A 0.0000
482 S A -0.9363
483 V A 0.0000
484 Q A -1.1940
485 I A 0.0000
486 D A -1.2062
487 W A 0.0000
488 E A -1.2423
489 I A 0.0000
490 Q A -1.7045
491 K A -2.1815
492 E A -2.2233
493 R A -2.9221
494 S A -2.2653
495 K A -2.3365
496 R A -1.6535
497 W A -0.0483
498 N A -0.5456
499 P A -0.2869
500 E A 0.1225
501 V A 1.1968
502 Q A -0.0207
503 F A 0.0000
504 T A -0.6815
505 S A -0.8563
506 N A -1.4875
507 Y A -0.7347
508 G A -1.3521
509 Q A -1.9926
510 Q A -1.6793
511 N A -1.6995
512 S A -0.5243
513 L A 0.8208
514 L A 0.6016
515 W A 0.2242
516 A A 0.1404
517 P A -0.7719
518 D A -1.1829
519 A A -0.5847
520 A A -0.8870
521 G A -1.4783
522 K A -2.2256
523 Y A -1.2225
524 T A -0.8386
525 E A -0.3406
526 P A -0.5873
527 R A -0.8263
528 A A 0.0000
529 I A 0.0000
530 G A -0.1405
531 T A 0.0000
532 R A 0.0662
533 Y A 0.3288
534 L A 0.0000
535 T A -0.3425
536 H A -1.2854
537 H A -1.0890
538 L A -0.0732
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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 -0.1094 4.5845 View CSV PDB
4.5 -0.1446 4.5849 View CSV PDB
5.0 -0.1867 4.5863 View CSV PDB
5.5 -0.2275 4.5904 View CSV PDB
6.0 -0.2591 4.6011 View CSV PDB
6.5 -0.2767 4.6238 View CSV PDB
7.0 -0.2813 4.6593 View CSV PDB
7.5 -0.2782 4.7028 View CSV PDB
8.0 -0.2711 4.7496 View CSV PDB
8.5 -0.2599 4.7976 View CSV PDB
9.0 -0.2432 4.8458 View CSV PDB