Project name: AAV4_1mer_M3

Status: done

Started: 2026-10-21 19:29:29
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.  (00:00:04)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:04)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:37)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/d9318df873167/tmp/folded.pdb                  (00:03:37)
[INFO]       Main:     Simulation completed successfully.                                          (00:14:44)
Show buried residues

Minimal score value
-2.8197
Maximal score value
1.8623
Average score
-0.5153
Total score value
-268.4883

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 -0.5435
19 V A 0.6222
20 G A -0.4008
21 N A -1.2684
22 A A -1.0974
23 S A -1.1897
24 G A -1.4735
25 D A -1.7993
26 W A -0.8704
27 H A -1.5107
28 C A -1.1826
29 D A -1.9235
30 S A -1.0428
31 T A -0.5718
32 W A -0.6454
33 S A -1.2258
34 E A -2.3269
35 G A -1.6948
36 H A -1.5355
37 V A 0.0000
38 T A -0.7678
39 T A 0.0000
40 T A -1.0354
41 S A 0.0000
42 T A 0.0000
43 R A 0.0000
44 T A 0.1808
45 W A 0.0000
46 V A 0.9259
47 L A 0.0000
48 P A 0.1037
49 T A -0.2637
50 Y A -0.2447
51 N A -0.7072
52 N A -1.2050
53 H A -0.4003
54 L A 0.2041
55 Y A -0.1534
56 K A -1.3139
57 R A -1.1655
58 L A -0.6285
59 G A -1.1012
60 E A -1.7170
61 S A -1.2830
62 L A -0.6646
63 Q A -1.6468
64 S A -1.1651
65 N A -1.6376
66 T A 0.0000
67 Y A -0.4756
68 N A 0.0000
69 G A 0.0000
70 F A -0.0154
71 S A -0.3657
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 -0.6680
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 -1.0588
88 P A -1.2653
89 R A -2.3974
90 D A 0.0000
91 W A 0.0000
92 Q A -2.0363
93 R A -2.3661
94 L A 0.0000
95 I A 0.0000
96 N A -0.9903
97 N A -1.7783
98 N A 0.0000
99 W A -0.6705
100 G A 0.0000
101 M A 0.0000
102 R A -1.0737
103 P A 0.0000
104 K A -1.9442
105 A A -1.1777
106 M A 0.0000
107 R A -1.6571
108 V A 0.0000
109 K A -1.5887
110 I A 0.0000
111 F A 0.0000
112 N A -1.2404
113 I A 0.0000
114 Q A -1.0228
115 V A 0.0000
116 K A -0.5360
117 E A -0.1548
118 V A 0.4181
119 T A -0.0877
120 T A -0.9891
121 S A -1.6396
122 N A -2.1949
123 G A -2.0691
124 E A -2.5862
125 T A -1.0044
126 T A 0.0247
127 V A 0.9188
128 A A -0.0490
129 N A -1.1165
130 N A -0.6294
131 L A 0.3028
132 T A 0.0069
133 S A 0.0000
134 T A -0.5013
135 V A 0.0000
136 Q A -0.4543
137 I A 0.0000
138 F A 0.0000
139 A A -0.3505
140 D A 0.0000
141 S A -0.6259
142 S A -0.8965
143 Y A -1.1064
144 E A -1.7011
145 L A 0.0000
146 P A -0.0925
147 Y A -0.0467
148 V A 0.1224
149 M A 0.0000
150 D A -0.5513
151 A A -0.7640
152 G A -1.4468
153 Q A -2.3278
154 E A -2.5565
155 G A -1.2112
156 S A -0.8753
157 L A 0.0000
158 P A -0.4231
159 P A -0.4630
160 F A -0.5405
161 P A -0.7598
162 N A -1.6326
163 D A -1.6437
164 V A 0.8573
165 F A 0.0000
166 M A 1.3263
167 V A 0.0000
168 P A -0.4325
169 Q A -0.3837
170 Y A 0.0000
171 G A -0.1758
172 Y A 0.0000
173 C A 1.0048
174 G A 0.4670
175 L A -0.2180
176 V A 0.0000
177 T A -0.9582
178 G A -1.2699
179 N A -1.4740
180 T A -1.1919
181 S A -1.1646
182 Q A -1.5204
183 Q A -1.7845
184 Q A -1.8939
185 T A -2.0782
186 D A -2.8197
187 R A -2.6502
188 N A -1.3687
189 A A 0.2212
190 F A 1.7153
191 Y A 1.2511
192 C A 0.9353
193 L A 0.0000
194 E A -0.2881
195 Y A 0.9871
196 F A 0.1583
197 P A -0.2210
198 S A -0.4999
199 Q A -0.9559
200 M A -0.1564
201 L A 0.0000
202 R A -1.5702
203 T A -1.2321
204 G A -1.1857
205 N A -1.7231
206 N A -1.8843
207 F A 0.0000
208 E A -2.2295
209 I A -1.0607
210 T A -0.8484
211 Y A -0.4601
212 S A -1.0993
213 F A 0.0000
214 E A -2.0109
215 K A -2.1914
216 V A 0.0000
217 P A -0.5291
218 F A -0.1338
219 H A -0.0999
220 S A -0.0630
221 M A 0.0000
222 Y A -0.0127
223 A A -0.4313
224 H A -0.6338
225 S A -0.9535
226 Q A -1.1714
227 S A -0.9193
228 L A 0.0000
229 D A -1.6282
230 R A -1.3445
231 L A -0.5691
232 M A -0.3402
233 N A -0.1204
234 P A 0.2358
235 L A 1.5891
236 I A 1.5492
237 D A 0.0737
238 Q A 0.0333
239 Y A 1.3350
240 L A 0.6548
241 W A 1.1504
242 G A 0.7069
243 L A 1.2661
244 Q A -0.2850
245 S A -0.1820
246 T A -0.1165
247 T A -0.5713
248 T A -0.4095
249 G A -0.4788
250 T A -0.2060
251 T A 0.1108
252 L A 0.8780
253 N A -0.6132
254 A A -0.4597
255 G A -0.6862
256 T A -0.5261
257 A A -0.5181
258 T A -0.0742
259 T A 0.1576
260 N A 0.3548
261 F A 1.8623
262 T A 0.5441
263 K A -0.1397
264 L A 0.0000
265 R A -1.3974
266 P A -0.5807
267 T A -0.7627
268 N A -1.2668
269 F A -1.4187
270 S A -1.4009
271 N A -1.9918
272 F A 0.0000
273 K A -2.4742
274 K A -2.2607
275 N A -1.6837
276 W A -0.2285
277 L A 0.5720
278 P A 0.5786
279 G A 0.0000
280 P A 0.4584
281 S A 0.0000
282 I A 0.4910
283 K A -0.5372
284 Q A 0.0000
285 Q A -0.9180
286 G A -0.8752
287 F A -0.4361
288 S A -1.1740
289 K A -0.9950
290 T A -0.9507
291 A A -0.9835
292 N A -2.0284
293 Q A -2.0920
294 N A -1.1876
295 Y A -0.0914
296 K A -1.2641
297 I A -0.2385
298 P A -0.3097
299 A A -0.1249
300 T A -0.4010
301 G A -0.9086
302 S A -0.9696
303 D A -1.1350
304 S A 0.0000
305 L A 0.2474
306 I A 0.3658
307 K A -0.4581
308 Y A 0.0980
309 E A -0.2533
310 T A -0.1794
311 H A -0.0733
312 S A -0.0322
313 T A 0.1006
314 L A 0.3949
315 D A -1.4012
316 G A -1.1209
317 R A -0.9586
318 W A -0.2373
319 S A -0.0040
320 A A 0.0575
321 L A 0.2105
322 T A 0.1195
323 P A 0.0000
324 G A 0.0000
325 P A 0.2980
326 P A 0.2110
327 M A 0.0000
328 A A 0.0000
329 T A 0.0000
330 A A -1.2038
331 G A -1.3283
332 P A -0.9964
333 A A -0.9630
334 D A -1.8584
335 S A -1.5540
336 K A -1.6230
337 F A -0.6572
338 S A 0.0000
339 N A -0.0962
340 S A 0.0000
341 Q A 0.0000
342 L A 0.8759
343 I A 1.4752
344 F A 0.9514
345 A A -0.2870
346 G A -0.6401
347 P A -1.3095
348 K A -1.9999
349 Q A -1.6792
350 N A -2.3257
351 G A -1.7533
352 N A -1.8325
353 T A -0.8647
354 A A -0.0966
355 T A 0.6960
356 V A 1.3706
357 P A 0.6706
358 G A -0.0970
359 T A -0.3446
360 L A 0.5509
361 I A 0.5495
362 F A 0.0000
363 T A 0.0000
364 S A -0.6695
365 E A 0.0000
366 E A -2.0029
367 E A -1.1539
368 L A 0.0000
369 A A -0.5906
370 A A -0.6477
371 T A 0.0000
372 N A 0.0000
373 A A -0.1793
374 T A -0.7658
375 D A 0.0000
376 T A -1.1219
377 D A -1.9662
378 M A -1.1850
379 W A -0.4941
380 G A -1.1247
381 N A -1.7564
382 L A -0.6441
383 P A -1.0914
384 G A -1.3270
385 G A -1.6903
386 D A -2.8133
387 Q A -2.7871
388 S A -2.1652
389 N A -2.0275
390 S A -1.4431
391 N A -2.0480
392 L A -0.5699
393 P A -0.8585
394 T A -0.3633
395 V A -0.0525
396 D A -2.2270
397 R A -2.7569
398 L A -1.2467
399 T A -0.9337
400 A A 0.1687
401 L A 0.3987
402 G A 0.0009
403 A A 0.4967
404 V A 0.6093
405 P A 0.1979
406 G A -0.0848
407 M A 0.6250
408 V A 1.0394
409 W A 0.6190
410 Q A 0.0000
411 N A -0.1953
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 -0.4687
420 I A 0.0000
421 W A 0.0000
422 A A -0.4754
423 K A -1.1566
424 I A -1.2374
425 P A -1.4146
426 H A -1.9527
427 T A -1.7410
428 D A -2.4334
429 G A -1.4835
430 H A -0.7085
431 F A 1.1504
432 H A 0.0385
433 P A -0.2501
434 S A 0.0332
435 P A 0.2634
436 L A 0.9543
437 I A 0.7662
438 G A 0.0000
439 G A 0.0167
440 F A 0.0000
441 G A -0.7354
442 L A 0.0000
443 K A -2.4759
444 H A -1.9733
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 0.1712
455 P A -0.0883
456 V A 0.4271
457 P A 0.0546
458 A A -0.3217
459 N A -1.2635
460 P A -0.5504
461 A A 0.1084
462 T A 0.1314
463 T A 0.7658
464 F A 1.7110
465 S A 0.7097
466 S A 0.2164
467 T A 0.0713
468 P A -0.0190
469 V A 0.6018
470 N A -0.7587
471 S A -0.5220
472 F A 0.1296
473 I A 0.6008
474 T A 0.1464
475 Q A 0.0000
476 Y A 0.3157
477 S A 0.0000
478 T A 0.1138
479 G A 0.0000
480 Q A -0.4033
481 V A 0.0000
482 S A -0.9660
483 V A 0.0000
484 Q A -1.1134
485 I A 0.0000
486 D A -1.2047
487 W A 0.0000
488 E A -1.3354
489 I A 0.0000
490 Q A -1.7540
491 K A -2.1266
492 E A -2.0271
493 R A -2.8128
494 S A -2.1305
495 K A -2.3023
496 R A -1.6628
497 W A -0.0569
498 N A -0.5629
499 P A -0.2956
500 E A 0.1468
501 V A 1.2459
502 Q A 0.0116
503 F A 0.0000
504 T A -0.7065
505 S A -0.8941
506 N A -1.5421
507 Y A -0.8434
508 G A -1.3911
509 Q A -1.9904
510 Q A -1.6456
511 N A -1.7019
512 S A -0.5815
513 L A 0.7668
514 L A 0.5929
515 W A 0.2456
516 A A 0.0596
517 P A -0.9237
518 D A -1.4691
519 A A -0.7260
520 A A -0.9863
521 G A -1.5894
522 K A -2.3578
523 Y A -1.3619
524 T A -0.8436
525 E A -0.1965
526 P A -0.3603
527 R A -0.3282
528 A A 0.0159
529 I A 0.0000
530 G A -0.0354
531 T A 0.0000
532 R A 0.0000
533 Y A 0.4967
534 L A 0.0000
535 T A -0.2399
536 H A -1.2110
537 H A -1.0024
538 L A 0.1297
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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 -0.1141 4.7941 View CSV PDB
4.5 -0.1504 4.7945 View CSV PDB
5.0 -0.1936 4.7959 View CSV PDB
5.5 -0.2352 4.7998 View CSV PDB
6.0 -0.267 4.8103 View CSV PDB
6.5 -0.2837 4.8332 View CSV PDB
7.0 -0.287 4.8701 View CSV PDB
7.5 -0.283 4.9161 View CSV PDB
8.0 -0.2751 4.9661 View CSV PDB
8.5 -0.2632 5.0175 View CSV PDB
9.0 -0.2456 5.0691 View CSV PDB