Project name: AAV4_1mer_M1

Status: done

Started: 2026-10-21 19:29:02
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                                          (00:00:04)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:06)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/561b0769ec0872/tmp/folded.pdb                 (00:03:06)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:04)
Show buried residues

Minimal score value
-2.8574
Maximal score value
1.7799
Average score
-0.4943
Total score value
-257.5137

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 -0.5380
19 V A 0.5972
20 G A -0.4030
21 N A -1.2645
22 A A -1.1069
23 S A -1.1787
24 G A -1.3594
25 D A -1.5655
26 W A -0.3603
27 H A -0.8996
28 C A -0.5880
29 D A -1.1302
30 S A -0.7080
31 T A -0.4443
32 W A -0.7304
33 S A -1.1938
34 E A -2.2550
35 G A -1.5567
36 H A -1.4411
37 V A 0.0000
38 T A -0.6975
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 0.2961
45 W A 0.0000
46 V A 1.0144
47 L A 0.0000
48 P A 0.1042
49 T A -0.2349
50 Y A -0.1992
51 N A -0.6432
52 N A -1.1371
53 H A -0.3052
54 L A 0.3787
55 Y A -0.0726
56 K A -1.2904
57 R A -1.0514
58 L A -0.5825
59 G A -0.9994
60 E A -1.5398
61 S A -1.0471
62 L A -0.2527
63 Q A -1.3797
64 S A -1.0437
65 N A -1.4457
66 T A 0.0000
67 Y A -0.3270
68 N A 0.0000
69 G A 0.0000
70 F A 0.0118
71 S A -0.3367
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 -0.6583
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 -0.9927
88 P A -1.2852
89 R A -2.4159
90 D A 0.0000
91 W A 0.0000
92 Q A -2.0882
93 R A -2.2538
94 L A 0.0000
95 I A 0.0000
96 N A 0.0000
97 N A -1.7202
98 N A 0.0000
99 W A -0.6990
100 G A 0.0000
101 M A 0.0000
102 R A -0.9054
103 P A 0.0000
104 K A -1.5498
105 A A -1.0169
106 M A 0.0000
107 R A -1.5442
108 V A 0.0000
109 K A -1.3250
110 I A 0.0000
111 F A 0.0000
112 N A -1.2550
113 I A 0.0000
114 Q A -1.0224
115 V A 0.0000
116 K A -0.4201
117 E A 0.0407
118 V A 0.6061
119 T A -0.0016
120 T A -0.9612
121 S A -1.6474
122 N A -2.1952
123 G A -2.0749
124 E A -2.5941
125 T A -0.9417
126 T A 0.1805
127 V A 1.2814
128 A A 0.1476
129 N A -1.0300
130 N A -0.5821
131 L A 0.2068
132 T A -0.0419
133 S A 0.0000
134 T A 0.0000
135 V A 0.0000
136 Q A -0.4681
137 I A 0.0000
138 F A 0.0000
139 A A -0.3005
140 D A 0.0000
141 S A -0.6287
142 S A -0.9035
143 Y A -1.0841
144 E A -1.7045
145 L A 0.0000
146 P A -0.0853
147 Y A -0.0316
148 V A 0.1407
149 M A 0.0000
150 D A -0.5580
151 A A -0.7431
152 G A -1.4275
153 Q A -2.3252
154 E A -2.5564
155 G A -1.1997
156 S A -0.8592
157 L A 0.0000
158 P A -0.3571
159 P A -0.4463
160 F A -0.5262
161 P A -0.7165
162 N A -1.5404
163 D A -1.4429
164 V A 1.0177
165 F A 0.9723
166 M A 1.3460
167 V A 0.0000
168 P A -0.4277
169 Q A -0.3983
170 Y A 0.0000
171 G A -0.1710
172 Y A 0.0000
173 C A 1.0685
174 G A 0.5674
175 L A -0.0229
176 V A 0.0000
177 T A -0.9244
178 G A -1.2293
179 N A -1.2598
180 T A -1.0065
181 S A -1.0429
182 Q A -1.4100
183 Q A -1.7655
184 Q A -1.8738
185 T A -2.0439
186 D A -2.7969
187 R A -2.6021
188 N A -1.2972
189 A A 0.2727
190 F A 1.7799
191 Y A 1.2734
192 C A 0.9468
193 L A 0.0000
194 E A -0.2957
195 Y A 0.9856
196 F A 0.1609
197 P A -0.2158
198 S A -0.4868
199 Q A -1.1255
200 M A -0.1750
201 L A 0.0000
202 R A -1.7197
203 T A -1.2664
204 G A -1.2204
205 N A -1.7808
206 N A -1.9357
207 F A 0.0000
208 E A -1.8159
209 I A -0.8151
210 T A -0.7299
211 Y A -0.4001
212 S A -1.0199
213 F A 0.0000
214 E A -1.9991
215 K A -2.1696
216 V A 0.0000
217 P A -0.5575
218 F A -0.1551
219 H A -0.1255
220 S A -0.1150
221 M A 0.0000
222 Y A -0.0428
223 A A -0.5234
224 H A -0.7648
225 S A -1.0338
226 Q A -1.3956
227 S A -1.1094
228 L A 0.0000
229 D A -1.8308
230 R A -1.6841
231 L A -0.7188
232 M A -0.3963
233 N A -0.1053
234 P A 0.2170
235 L A 1.5745
236 I A 1.5068
237 D A 0.1272
238 Q A 0.0855
239 Y A 1.3834
240 L A 0.7524
241 W A 1.1637
242 G A 0.4931
243 L A 0.7661
244 Q A -0.6297
245 S A -0.5024
246 T A -0.3559
247 T A -0.7042
248 T A -0.6427
249 G A -0.6097
250 T A -0.2089
251 T A 0.1109
252 L A 0.9185
253 N A -0.6176
254 A A -0.4647
255 G A -0.6933
256 T A -0.5371
257 A A -0.6074
258 T A -0.2920
259 T A -0.2396
260 N A -0.4099
261 F A 1.3790
262 T A 0.3614
263 K A -0.0522
264 L A 0.0000
265 R A -1.2924
266 P A -0.5506
267 T A -0.7564
268 N A -1.2489
269 F A -1.4902
270 S A -1.4685
271 N A -2.0400
272 F A 0.0000
273 K A -2.5690
274 K A -2.5002
275 N A -1.7639
276 W A -0.2810
277 L A 0.4726
278 P A 0.5060
279 G A 0.0000
280 P A 0.4416
281 S A 0.0000
282 I A 0.5559
283 K A -0.4497
284 Q A 0.0000
285 Q A -0.8791
286 G A -0.8909
287 F A -0.3403
288 S A -1.0588
289 K A -0.8923
290 T A -0.8921
291 A A -0.9315
292 N A -1.9935
293 Q A -2.0137
294 N A -1.0849
295 Y A -0.0501
296 K A -1.2785
297 I A -0.3313
298 P A -0.3792
299 A A -0.1738
300 T A -0.4367
301 G A -0.9365
302 S A -0.9943
303 D A -1.2056
304 S A -0.4867
305 L A 0.1263
306 I A 0.2767
307 K A -0.5277
308 Y A 0.0218
309 E A -0.3277
310 T A -0.2002
311 H A -0.1555
312 S A -0.1847
313 T A -0.1513
314 L A -0.1717
315 D A -1.6337
316 G A -1.2226
317 R A -0.9889
318 W A -0.3277
319 S A -0.0969
320 A A 0.0135
321 L A 0.1765
322 T A 0.0708
323 P A 0.0000
324 G A 0.0000
325 P A 0.3062
326 P A 0.1658
327 M A 0.0000
328 A A 0.0000
329 T A 0.0000
330 A A -1.1363
331 G A -1.2281
332 P A -0.7610
333 A A -0.8432
334 D A -1.6401
335 S A -1.3960
336 K A -1.4607
337 F A -0.4753
338 S A 0.0000
339 N A -0.2316
340 S A 0.0000
341 Q A 0.0000
342 L A 0.0000
343 I A 1.4287
344 F A 0.8976
345 A A -0.3179
346 G A -0.7128
347 P A -1.4550
348 K A -2.2251
349 Q A -1.7019
350 N A -2.3420
351 G A -1.7544
352 N A -1.8325
353 T A -0.8645
354 A A -0.0932
355 T A 0.7200
356 V A 1.5488
357 P A 0.6897
358 G A -0.0796
359 T A -0.3430
360 L A 0.5298
361 I A 0.5020
362 F A 0.0000
363 T A 0.0000
364 S A 0.0000
365 E A 0.0000
366 E A -2.0176
367 E A -1.2269
368 L A 0.0000
369 A A -0.6291
370 A A -0.7832
371 T A 0.0000
372 N A 0.0000
373 A A -0.1605
374 T A -0.7360
375 D A 0.0000
376 T A -1.0868
377 D A -1.8881
378 M A -0.9908
379 W A -0.3814
380 G A -0.9622
381 N A -1.5120
382 L A -0.6272
383 P A -1.0704
384 G A -1.3643
385 G A -1.6097
386 D A -2.7564
387 Q A -2.6808
388 S A -2.1032
389 N A -1.9773
390 S A -1.3812
391 N A -1.9098
392 L A -0.0055
393 P A -0.6974
394 T A -0.2245
395 V A 0.2972
396 D A -1.9046
397 R A -2.5059
398 L A -0.9919
399 T A -0.7516
400 A A 0.0671
401 L A 0.4560
402 G A 0.0144
403 A A 0.5061
404 V A 0.6448
405 P A 0.2346
406 G A -0.0589
407 M A 0.5978
408 V A 0.9248
409 W A 0.4411
410 Q A -0.1731
411 N A -0.3512
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 -0.4454
420 I A 0.0000
421 W A 0.0000
422 A A -0.4792
423 K A -1.1823
424 I A 0.0000
425 P A -1.4739
426 H A -1.9559
427 T A -1.7775
428 D A -2.4289
429 G A -1.4682
430 H A -0.7255
431 F A 1.1590
432 H A 0.0203
433 P A -0.2648
434 S A -0.0178
435 P A 0.2388
436 L A 1.0032
437 I A 0.8425
438 G A 0.0000
439 G A 0.0288
440 F A 0.0000
441 G A -0.7630
442 L A 0.0000
443 K A -2.2288
444 H A -1.8654
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 0.1595
455 P A 0.0247
456 V A 0.3807
457 P A 0.0093
458 A A -0.3414
459 N A -1.2755
460 P A -0.5550
461 A A 0.1115
462 T A 0.1186
463 T A 0.7667
464 F A 1.7109
465 S A 0.7158
466 S A 0.2223
467 T A 0.0794
468 P A -0.0057
469 V A 0.6200
470 N A -0.7249
471 S A -0.5373
472 F A 0.1018
473 I A 0.6080
474 T A 0.1632
475 Q A 0.0000
476 Y A 0.3746
477 S A 0.0000
478 T A 0.1589
479 G A 0.0000
480 Q A -0.3195
481 V A 0.0000
482 S A -0.7488
483 V A 0.0000
484 Q A -1.0505
485 I A 0.0000
486 D A -1.1991
487 W A 0.0000
488 E A -1.1406
489 I A 0.0000
490 Q A -1.7038
491 K A -2.0562
492 E A -2.0676
493 R A -2.8574
494 S A -2.2311
495 K A -2.3737
496 R A -1.7839
497 W A -0.1133
498 N A -0.5917
499 P A -0.3410
500 E A 0.0702
501 V A 1.1768
502 Q A -0.1038
503 F A 0.0000
504 T A -0.7362
505 S A -0.9118
506 N A -1.4957
507 Y A -0.7479
508 G A -1.3504
509 Q A -1.9820
510 Q A -1.6567
511 N A -1.6985
512 S A -0.5385
513 L A 0.8113
514 L A 0.6271
515 W A 0.2729
516 A A 0.1075
517 P A -0.8257
518 D A -1.2749
519 A A -0.7838
520 A A -0.9182
521 G A -1.5121
522 K A -2.2712
523 Y A -1.2751
524 T A -0.8562
525 E A -0.2738
526 P A -0.4596
527 R A -0.5152
528 A A 0.0000
529 I A 0.0000
530 G A -0.0555
531 T A 0.0000
532 R A 0.0000
533 Y A 0.4075
534 L A 0.0000
535 T A -0.3321
536 H A -1.3222
537 H A -1.1802
538 L A -0.2365
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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 -0.085 4.3143 View CSV PDB
4.5 -0.1204 4.3147 View CSV PDB
5.0 -0.1619 4.3157 View CSV PDB
5.5 -0.2021 4.3187 View CSV PDB
6.0 -0.2332 4.3271 View CSV PDB
6.5 -0.2501 4.3458 View CSV PDB
7.0 -0.2539 4.3771 View CSV PDB
7.5 -0.2502 4.4171 View CSV PDB
8.0 -0.2424 4.4611 View CSV PDB
8.5 -0.2303 4.5065 View CSV PDB
9.0 -0.2124 4.5523 View CSV PDB