Project name: AAV2_1mer_M4

Status: done

Started: 2026-10-21 18:13:52
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]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:02)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/5add818cfbc8ac/tmp/folded.pdb                 (00:02:02)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:02)
Show buried residues

Minimal score value
-3.9226
Maximal score value
2.2904
Average score
-0.6256
Total score value
-324.6736

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 -0.9611
16 A A -0.7968
17 D A -1.6531
18 G A -0.7586
19 V A 0.8144
20 G A -0.6100
21 N A -1.5849
22 S A -1.3703
23 S A -1.3615
24 G A -1.2773
25 N A -1.2115
26 W A -0.3390
27 H A -1.2710
28 C A -1.0311
29 D A -1.8987
30 S A -0.9124
31 T A -0.1839
32 W A -0.2390
33 M A 0.0665
34 G A -1.1285
35 D A -2.2335
36 R A -1.2363
37 V A 0.0000
38 I A -0.3047
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 0.4778
45 W A 0.0000
46 A A 0.7648
47 L A 0.0000
48 P A 0.0929
49 T A -0.3002
50 Y A -0.3524
51 N A -0.9775
52 N A -1.2074
53 H A -0.5296
54 L A -0.3254
55 Y A -0.5449
56 K A -1.6088
57 Q A -1.0751
58 I A -0.3025
59 S A -0.4469
60 S A 0.0000
61 Q A -1.5493
62 S A -1.1089
63 G A -1.2708
64 A A -1.5608
65 S A -1.8948
66 N A -2.6888
67 D A -2.5786
68 N A -2.4701
69 H A -2.0728
70 Y A -0.3783
71 F A 0.0000
72 G A 0.0000
73 Y A 0.1663
74 S A -0.4044
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 -0.7759
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 -1.1539
91 P A -1.3762
92 R A -2.5446
93 D A -2.0579
94 W A 0.0000
95 Q A -2.0917
96 R A -2.5204
97 L A 0.0000
98 I A 0.0000
99 N A -1.1371
100 N A -2.1844
101 N A 0.0000
102 W A -1.1104
103 G A 0.0000
104 F A 0.0000
105 R A -0.9616
106 P A 0.0000
107 K A -2.0633
108 R A -2.4741
109 L A 0.0000
110 N A -1.3563
111 F A 0.0000
112 K A -1.1578
113 L A 0.0000
114 F A 0.0000
115 N A -1.3167
116 I A 0.0000
117 Q A -1.0773
118 V A 0.0000
119 K A -0.4829
120 E A -0.1250
121 V A 0.0306
122 T A -0.6108
123 Q A -2.2162
124 N A -2.9042
125 D A -2.9268
126 G A -2.0747
127 T A -1.6928
128 T A -0.9383
129 T A -0.0852
130 I A 0.6836
131 A A -0.1094
132 N A -1.1446
133 N A -0.7469
134 L A 0.2466
135 T A -0.2774
136 S A 0.0000
137 T A 0.0000
138 V A 0.0000
139 Q A -0.4351
140 V A 0.0000
141 F A 0.0000
142 T A -0.4075
143 D A 0.0000
144 S A -1.2820
145 E A -2.2096
146 Y A -1.2758
147 Q A -1.3150
148 L A 0.0000
149 P A 0.4330
150 Y A 0.0866
151 V A 0.3305
152 L A 0.0000
153 G A -0.3881
154 S A -0.5323
155 A A -0.7333
156 H A -1.3546
157 Q A -1.6622
158 G A -0.6697
159 C A 0.0000
160 L A 0.0000
161 P A -0.0809
162 P A -0.2626
163 F A 0.3427
164 P A -0.0644
165 A A -0.2200
166 D A -0.5201
167 V A 1.3302
168 F A 1.1304
169 M A 1.4213
170 V A 0.0000
171 P A -0.2373
172 Q A -0.3486
173 Y A 0.0000
174 G A -0.0324
175 Y A 0.0000
176 L A 1.8936
177 T A 1.0868
178 L A 0.0075
179 N A -0.8102
180 N A -1.8746
181 G A -1.8643
182 S A -1.5407
183 Q A -1.4723
184 A A -1.1498
185 V A -0.9194
186 G A -1.1189
187 R A -1.6956
188 S A -0.3732
189 S A 0.6303
190 F A 1.7332
191 Y A 1.2299
192 C A 0.9418
193 L A 0.0000
194 E A -0.1422
195 Y A 1.0502
196 F A 0.3993
197 P A -0.2080
198 S A -0.4859
199 Q A -1.1184
200 M A -0.1367
201 L A 0.0000
202 R A -1.5769
203 T A -1.2505
204 G A -1.4535
205 N A -1.9523
206 N A -1.5275
207 F A 0.0000
208 T A -0.5705
209 F A -0.1631
210 S A -0.7912
211 Y A -0.8126
212 T A -1.5646
213 F A 0.0000
214 E A -2.1654
215 D A -2.1830
216 V A 0.0000
217 P A -0.5061
218 F A -0.1553
219 H A -0.1751
220 S A -0.1422
221 S A 0.0000
222 Y A -0.4105
223 A A -0.4482
224 H A -0.8928
225 S A -0.9878
226 Q A -1.3335
227 S A -1.4621
228 L A 0.0000
229 D A -2.9387
230 R A -2.8426
231 L A -1.3096
232 M A -0.7946
233 N A -0.5722
234 P A 0.1467
235 L A 1.6902
236 I A 1.6517
237 D A -0.5396
238 Q A 0.3428
239 Y A 1.4441
240 L A 1.6357
241 Y A 2.2904
242 Y A 1.3531
243 L A 1.4123
244 S A 0.1172
245 R A -1.7149
246 T A -1.3756
247 N A -2.3908
248 T A -1.6710
249 P A -1.0466
250 S A -0.7854
251 G A -0.6946
252 T A -0.4111
253 T A -0.4889
254 T A -1.1305
255 Q A -1.4475
256 S A -1.8974
257 R A -2.3671
258 L A -0.1127
259 Q A -0.1945
260 F A 2.0733
261 S A 0.7824
262 Q A 0.3467
263 A A 0.0000
264 G A -0.5853
265 A A -0.2526
266 S A -0.7953
267 D A -1.2587
268 I A -1.7242
269 R A -2.6724
270 D A -1.2201
271 Q A 0.0000
272 S A -0.6673
273 R A -1.5690
274 N A -1.3041
275 W A -0.0612
276 L A 0.6344
277 P A 0.4662
278 G A 0.0000
279 P A 0.3748
280 C A 0.0000
281 Y A -0.5599
282 R A -1.3127
283 Q A 0.0000
284 Q A -1.4839
285 R A -1.7567
286 V A 0.0000
287 S A 0.0000
288 K A -1.8168
289 T A -1.1515
290 S A -1.2249
291 A A -1.3746
292 D A -2.2989
293 N A -2.3983
294 N A -2.7160
295 N A -2.6167
296 S A -2.1103
297 E A -2.2526
298 Y A -1.1405
299 S A -0.5393
300 W A 0.1891
301 T A -0.2151
302 G A -0.5956
303 A A -0.1923
304 T A -0.1503
305 K A 0.1772
306 Y A 0.7940
307 H A -0.7983
308 L A -0.4995
309 N A -1.7402
310 G A -1.7398
311 R A -2.1005
312 D A -1.4420
313 S A -0.3057
314 L A 0.4052
315 V A 0.0000
316 N A -0.6930
317 P A 0.0000
318 G A 0.0000
319 P A -0.0243
320 A A 0.0553
321 M A 0.0000
322 A A 0.0000
323 S A 0.0000
324 H A 0.0000
325 K A -2.8217
326 D A -3.6902
327 D A -3.7077
328 E A -3.3317
329 E A -3.8070
330 K A -2.6637
331 F A -2.1291
332 F A 0.0000
333 P A 0.0000
334 Q A -0.8858
335 S A 0.0000
336 G A 0.0000
337 V A 0.0000
338 L A 0.5855
339 I A 1.3156
340 F A 0.2076
341 G A -1.6792
342 K A -2.5476
343 Q A -2.2478
344 G A -2.0947
345 S A -2.8890
346 E A -3.5627
347 K A -2.9211
348 T A -2.1072
349 N A -2.1549
350 V A -2.1975
351 D A -2.3706
352 I A -1.1143
353 E A -2.4072
354 K A -2.7687
355 V A -1.1170
356 M A 0.0000
357 I A 0.3804
358 T A 0.0000
359 D A -1.2744
360 E A 0.0000
361 E A -2.3137
362 E A -1.4199
363 I A 0.0000
364 R A -1.2611
365 T A -1.0036
366 T A 0.0000
367 N A 0.0000
368 P A -0.4214
369 V A -0.6552
370 A A 0.0000
371 T A 0.0000
372 E A -1.8376
373 Q A -1.9248
374 Y A -0.8671
375 G A -0.7449
376 S A -0.3239
377 V A 1.0338
378 S A 0.2345
379 T A -0.1549
380 N A -0.8220
381 L A -0.3136
382 Q A -2.7308
383 R A -3.3176
384 G A -2.8078
385 N A -3.3018
386 R A -3.9226
387 Q A -3.0605
388 A A -1.5692
389 A A -0.5717
390 T A -0.1436
391 A A -0.6806
392 D A -1.8822
393 V A -1.0954
394 N A -1.6310
395 T A -0.9189
396 Q A -0.3156
397 G A 0.1007
398 V A 1.2911
399 L A 0.9526
400 P A 0.3528
401 G A 0.0564
402 M A 0.0000
403 V A 1.1022
404 W A 0.3791
405 Q A -0.3474
406 D A -0.5361
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 -0.3868
415 I A 0.0000
416 W A 0.0000
417 A A -0.4810
418 K A -1.2439
419 I A 0.0000
420 P A -1.4572
421 H A -1.9440
422 T A -1.7251
423 D A -2.3778
424 G A -1.3554
425 H A -0.5333
426 F A 1.3383
427 H A 0.0127
428 P A -0.1257
429 S A -0.0361
430 P A 0.2200
431 L A 0.9135
432 M A 0.0000
433 G A 0.0000
434 G A -0.0736
435 F A 0.0000
436 G A -0.7499
437 L A 0.0000
438 K A -2.2990
439 H A -2.0885
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 0.1612
450 P A 0.1689
451 V A 0.4659
452 P A 0.2655
453 A A -0.1560
454 N A -1.3134
455 P A -0.5503
456 S A -0.2885
457 T A 0.0085
458 T A 0.6768
459 F A 1.7300
460 S A 0.5864
461 A A 0.1866
462 A A -0.2001
463 K A -1.0233
464 F A 0.5524
465 A A 0.1544
466 S A -0.0577
467 F A 0.4732
468 I A 0.6836
469 T A 0.1878
470 Q A 0.0000
471 Y A 0.4015
472 S A 0.0000
473 T A 0.1342
474 G A 0.0000
475 Q A -0.3178
476 V A 0.0000
477 S A -0.7304
478 V A 0.0000
479 E A -1.3877
480 I A 0.0000
481 E A 0.0000
482 W A 0.0000
483 E A -1.3761
484 L A 0.0000
485 Q A -2.1646
486 K A -3.0349
487 E A -2.6296
488 N A -2.7593
489 S A -2.2997
490 K A -2.4812
491 R A -1.9926
492 W A -0.3791
493 N A -1.3624
494 P A -0.5802
495 E A 0.0860
496 I A 1.5944
497 Q A 0.2129
498 Y A -0.1617
499 T A -0.3933
500 S A -0.8334
501 N A -1.3077
502 Y A -0.3821
503 N A -1.9302
504 K A -1.8770
505 S A -0.5431
506 V A 0.9500
507 N A -0.0162
508 V A 0.8085
509 D A -0.1741
510 F A -0.1114
511 T A 0.5140
512 V A 0.5252
513 D A -0.3949
514 T A -0.9435
515 N A -1.2959
516 G A -0.7371
517 V A 0.0011
518 Y A 0.0649
519 S A -0.3570
520 E A -0.8554
521 P A -0.8370
522 R A -0.8375
523 P A -0.3597
524 I A 0.0000
525 G A -0.2132
526 T A 0.0000
527 R A 0.0000
528 Y A 0.4577
529 L A 0.0000
530 T A -0.5891
531 R A -1.8553
532 N A -1.3870
533 L A 0.0257
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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 -0.3468 4.1779 View CSV PDB
4.5 -0.3943 4.0186 View CSV PDB
5.0 -0.4493 4.0186 View CSV PDB
5.5 -0.5038 4.0186 View CSV PDB
6.0 -0.5497 4.0186 View CSV PDB
6.5 -0.5821 4.0186 View CSV PDB
7.0 -0.6016 4.0186 View CSV PDB
7.5 -0.6131 4.0186 View CSV PDB
8.0 -0.6196 4.0186 View CSV PDB
8.5 -0.6199 4.0186 View CSV PDB
9.0 -0.6116 4.0186 View CSV PDB