Project name: AAV6_1mer_M1

Status: done

Started: 2026-10-21 19:57:18
Settings
Chain sequence(s) GADGVGNASGNWHCDSTWLGDRVITTSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTTNDGVTTIANNLTSTVQVFSDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLNRTQNQSGSAQNKDLLFSRGSPAGMSVQPKNWLPGPCYRQQRVSKTKTDNNNSNFTWTGASKYNLNGRESIINPGTAMASHKDDKDKFFPMSGVMIFGKESAGASNTALDNVMITDEEEIKATNPVATERFGTVAVNLQSSSTDPATGDVHVMGALPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPPAEFSATKFASFITQYSTGQVSVEIEWELQKENSKRWNPEVQYTSNYAKSANVDFTVDNNGLYTEPRPIGTRYLTRPL 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                                          (00:03:45)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/abe7353e503fbe/tmp/folded.pdb                 (00:03:45)
[INFO]       Main:     Simulation completed successfully.                                          (00:11:59)
Show buried residues

Minimal score value
-3.9879
Maximal score value
2.2951
Average score
-0.5294
Total score value
-275.3076

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 -1.1689
16 A A -1.3909
17 D A -2.1938
18 G A -1.1196
19 V A 0.3954
20 G A -0.5997
21 N A -1.5606
22 A A -1.2072
23 S A -1.2927
24 G A -1.2975
25 N A -1.1676
26 W A -0.3506
27 H A -1.2741
28 C A -1.0865
29 D A -1.8206
30 S A -0.7814
31 T A -0.0838
32 W A 0.1529
33 L A 0.4654
34 G A -0.8922
35 D A -1.9129
36 R A -0.9360
37 V A 0.0000
38 I A -0.1276
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 0.3736
45 W A 0.0000
46 A A 0.6679
47 L A 0.0000
48 P A 0.0623
49 T A -0.2138
50 Y A -0.1844
51 N A -0.5744
52 N A -0.9312
53 H A -0.1035
54 L A 0.6037
55 Y A 0.0230
56 K A -1.0147
57 Q A -0.7825
58 I A 0.2036
59 S A -0.0385
60 S A 0.0000
61 A A -0.2983
62 S A -0.3790
63 T A -0.5769
64 G A -0.9131
65 A A -1.2083
66 S A -1.6986
67 N A -2.6302
68 D A -2.6255
69 N A -2.3269
70 H A -1.8869
71 Y A -0.2475
72 F A 0.0000
73 G A 0.0000
74 Y A 0.2697
75 S A -0.1256
76 T A 0.0000
77 P A 0.0000
78 W A 0.0000
79 G A 0.0000
80 Y A 0.0000
81 F A 0.0000
82 D A 0.0000
83 F A 0.0000
84 N A 0.0000
85 R A -0.7132
86 F A 0.0000
87 H A 0.0000
88 C A 0.0000
89 H A 0.0000
90 F A 0.0000
91 S A -0.9900
92 P A -1.3318
93 R A -2.3721
94 D A 0.0000
95 W A 0.0000
96 Q A -1.9823
97 R A -2.3444
98 L A 0.0000
99 I A 0.0000
100 N A -0.9701
101 N A -1.8502
102 N A 0.0000
103 W A -0.8690
104 G A 0.0000
105 F A 0.0000
106 R A -0.9015
107 P A 0.0000
108 K A -1.8488
109 R A -1.6752
110 L A 0.0000
111 N A -0.9128
112 F A 0.0000
113 K A -1.5067
114 L A 0.0000
115 F A 0.0000
116 N A -1.0541
117 I A 0.0000
118 Q A -1.0990
119 V A 0.0000
120 K A -0.4367
121 E A 0.0464
122 V A 0.6371
123 T A 0.3689
124 T A -0.4383
125 N A -1.7759
126 D A -2.1081
127 G A -0.9305
128 V A 0.4958
129 T A 0.5268
130 T A 0.9669
131 I A 1.4945
132 A A 0.2123
133 N A -1.0369
134 N A -0.6659
135 L A 0.1084
136 T A -0.1328
137 S A 0.0000
138 T A -0.5899
139 V A 0.0000
140 Q A -0.4540
141 V A 0.0000
142 F A 0.0000
143 S A -0.4427
144 D A 0.0000
145 S A -1.3054
146 E A -2.2443
147 Y A -1.3269
148 Q A -1.3384
149 L A 0.0000
150 P A 0.3991
151 Y A 0.0809
152 V A 0.3342
153 L A 0.0000
154 G A -0.3291
155 S A -0.5128
156 A A -0.7077
157 H A -1.3540
158 Q A -1.6436
159 G A -0.6673
160 C A -0.4544
161 L A 0.0000
162 P A -0.0604
163 P A -0.1221
164 F A 0.5281
165 P A -0.0119
166 A A -0.2228
167 D A -0.6868
168 V A 1.1720
169 F A 0.0000
170 M A 1.3126
171 I A 0.0000
172 P A -0.2832
173 Q A -0.3500
174 Y A 0.0000
175 G A 0.0012
176 Y A 0.0000
177 L A 1.8816
178 T A 1.0914
179 L A 0.0559
180 N A -0.7927
181 N A -1.8506
182 G A -1.7550
183 S A -1.2448
184 Q A -1.4704
185 A A -0.8785
186 V A -0.5769
187 G A -0.9545
188 R A -1.6025
189 S A -0.2925
190 S A 0.6151
191 F A 1.6041
192 Y A 1.1656
193 C A 0.8744
194 L A 0.0000
195 E A -0.0871
196 Y A 1.0781
197 F A 0.3177
198 P A -0.1787
199 S A -0.4530
200 Q A -1.0688
201 M A -0.1323
202 L A 0.0000
203 R A -1.8507
204 T A -1.3318
205 G A 0.0000
206 N A -1.6183
207 N A -1.6274
208 F A 0.0000
209 T A -0.7117
210 F A -0.1963
211 S A -0.5301
212 Y A -0.4468
213 T A -1.1613
214 F A 0.0000
215 E A -2.0431
216 D A -2.1609
217 V A 0.0000
218 P A -0.4833
219 F A -0.0513
220 H A -0.0975
221 S A -0.1288
222 S A 0.0000
223 Y A -0.2858
224 A A -0.4914
225 H A -0.7848
226 S A -0.8709
227 Q A -1.1601
228 S A -1.1200
229 L A 0.0000
230 D A -1.6695
231 R A -1.6652
232 L A -0.7340
233 M A -0.5271
234 N A -0.5513
235 P A 0.1680
236 L A 1.6592
237 I A 1.6289
238 D A -0.5895
239 Q A -0.0491
240 Y A 1.2436
241 L A 1.0652
242 Y A 1.8948
243 Y A 1.5015
244 L A 1.7445
245 N A 0.2458
246 R A -0.7057
247 T A -1.0207
248 Q A -2.8307
249 N A -2.8139
250 Q A -2.9580
251 S A -1.8226
252 G A -1.3616
253 S A -1.1315
254 A A -1.8599
255 Q A -3.2130
256 N A -3.6678
257 K A -3.2692
258 D A -1.7673
259 L A 1.0244
260 L A 1.1449
261 F A 2.2951
262 S A 0.9105
263 R A -0.1291
264 G A 0.0000
265 S A -0.1251
266 P A 0.1809
267 A A 0.0575
268 G A -0.0364
269 M A -0.2153
270 S A -0.0327
271 V A 0.9412
272 Q A 0.0000
273 P A -0.2893
274 K A -1.4121
275 N A -1.4765
276 W A -0.1523
277 L A 0.4249
278 P A 0.3808
279 G A 0.0000
280 P A 0.6215
281 C A 0.0000
282 Y A 0.5253
283 R A -0.7546
284 Q A 0.0000
285 Q A -1.3537
286 R A -1.6607
287 V A -1.4845
288 S A 0.0000
289 K A -1.9774
290 T A -1.8285
291 K A -2.8225
292 T A -2.2775
293 D A -2.9182
294 N A -2.8320
295 N A -2.8204
296 N A -2.6964
297 S A -1.7942
298 N A -1.6208
299 F A -0.6983
300 T A -0.0103
301 W A 0.4268
302 T A -0.0391
303 G A -0.4324
304 A A -0.0686
305 S A -0.0321
306 K A 0.1100
307 Y A 0.4743
308 N A -1.0671
309 L A -0.3053
310 N A -1.6395
311 G A -1.5848
312 R A -2.0934
313 E A -1.4627
314 S A -0.3491
315 I A 0.3702
316 I A 0.2404
317 N A -0.7682
318 P A 0.0000
319 G A 0.0000
320 T A 0.0971
321 A A 0.1925
322 M A 0.0000
323 A A 0.0000
324 S A 0.0000
325 H A 0.0000
326 K A -3.3843
327 D A -3.9879
328 D A -3.8480
329 K A -3.5970
330 D A -3.8498
331 K A -2.4487
332 F A -1.9624
333 F A -1.1419
334 P A 0.0000
335 M A -0.3881
336 S A -0.3053
337 G A 0.0000
338 V A 0.0000
339 M A 0.0000
340 I A 1.3000
341 F A 0.2452
342 G A -1.1604
343 K A -2.2367
344 E A -2.3849
345 S A -1.7697
346 A A -1.6612
347 G A -1.2569
348 A A -0.6167
349 S A -0.9423
350 N A -1.3992
351 T A -1.0901
352 A A -0.7240
353 L A -0.8694
354 D A -1.8397
355 N A -1.6196
356 V A -0.6425
357 M A 0.0000
358 I A 0.3825
359 T A 0.0000
360 D A -1.4224
361 E A 0.0000
362 E A -2.8243
363 E A -1.9851
364 I A 0.0000
365 K A -1.8769
366 A A -1.2319
367 T A 0.0000
368 N A 0.0000
369 P A -0.6123
370 V A -0.9018
371 A A 0.0000
372 T A 0.0000
373 E A -2.1933
374 R A -2.1362
375 F A -0.5925
376 G A -0.6903
377 T A -0.2775
378 V A 1.0769
379 A A 1.0547
380 V A 1.6530
381 N A 0.3915
382 L A 0.6088
383 Q A -1.2879
384 S A -1.1512
385 S A -1.2251
386 S A -1.0405
387 T A -1.4125
388 D A -2.3061
389 P A -1.1921
390 A A -0.0874
391 T A 0.3240
392 G A -0.2381
393 D A -1.5712
394 V A -0.6716
395 H A -0.7377
396 V A 1.1565
397 M A 0.7321
398 G A 0.3161
399 A A 0.4888
400 L A 0.7359
401 P A 0.2474
402 G A 0.0421
403 M A 0.6085
404 V A 0.9433
405 W A 0.3353
406 Q A -0.3981
407 D A -0.4881
408 R A 0.0000
409 D A 0.0000
410 V A 0.0000
411 Y A 0.0000
412 L A 0.0000
413 Q A 0.0000
414 G A 0.0000
415 P A 0.0000
416 I A 0.0000
417 W A 0.0000
418 A A -0.4299
419 K A -1.1915
420 I A -1.3155
421 P A -1.4759
422 H A -2.0042
423 T A -1.8003
424 D A -2.4792
425 G A -1.6587
426 H A -0.9838
427 F A 1.0043
428 H A -0.1662
429 P A -0.2416
430 S A -0.0183
431 P A 0.3107
432 L A 0.9824
433 M A 0.3721
434 G A 0.0000
435 G A -0.0380
436 F A 0.0000
437 G A -0.7401
438 L A 0.0000
439 K A -2.5354
440 H A -2.2077
441 P A 0.0000
442 P A 0.0000
443 P A 0.0000
444 Q A 0.0000
445 I A 0.0000
446 L A 0.0000
447 I A 0.0000
448 K A 0.0000
449 N A 0.0000
450 T A 0.1497
451 P A -0.0291
452 V A 0.2301
453 P A 0.0458
454 A A -0.3138
455 N A -1.3344
456 P A -0.8427
457 P A -0.8218
458 A A -0.7312
459 E A -1.0001
460 F A 0.9291
461 S A 0.1512
462 A A 0.1019
463 T A -0.4310
464 K A -1.3199
465 F A -0.0078
466 A A -0.0730
467 S A -0.2664
468 F A 0.2467
469 I A 0.5617
470 T A 0.3049
471 Q A 0.0000
472 Y A 0.3107
473 S A 0.0000
474 T A 0.0044
475 G A 0.0000
476 Q A -0.4463
477 V A 0.0000
478 S A 0.0000
479 V A 0.0000
480 E A -1.1868
481 I A 0.0000
482 E A -1.0551
483 W A 0.0000
484 E A -1.2140
485 L A 0.0000
486 Q A -1.6219
487 K A -2.5016
488 E A -2.3865
489 N A -2.5647
490 S A -2.0588
491 K A -2.2553
492 R A -1.4461
493 W A 0.1087
494 N A -0.2062
495 P A -0.1288
496 E A 0.2171
497 V A 1.3106
498 Q A 0.1097
499 Y A -0.2499
500 T A -0.2365
501 S A -0.5883
502 N A -1.0011
503 Y A 0.2331
504 A A -0.6193
505 K A -1.6047
506 S A -1.1643
507 A A -0.8454
508 N A -1.1417
509 V A 0.1797
510 D A -0.9704
511 F A -0.3681
512 T A 0.2841
513 V A 0.2986
514 D A -1.2158
515 N A -2.1292
516 N A -1.8836
517 G A -1.1333
518 L A -0.2632
519 Y A -0.1347
520 T A -0.4105
521 E A -0.9847
522 P A -1.0537
523 R A -1.0509
524 P A -0.3491
525 I A 0.0000
526 G A -0.2459
527 T A 0.0000
528 R A 0.0000
529 Y A 0.3279
530 L A 0.0000
531 T A -0.2862
532 R A -1.1086
533 P A -0.6634
534 L A 0.0664
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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 -0.1442 4.3366 View CSV PDB
4.5 -0.1926 4.3013 View CSV PDB
5.0 -0.2479 4.2824 View CSV PDB
5.5 -0.3026 4.2627 View CSV PDB
6.0 -0.3489 4.2427 View CSV PDB
6.5 -0.3809 4.2228 View CSV PDB
7.0 -0.3993 4.2029 View CSV PDB
7.5 -0.4089 4.1833 View CSV PDB
8.0 -0.4124 4.1647 View CSV PDB
8.5 -0.408 4.1485 View CSV PDB
9.0 -0.393 4.1367 View CSV PDB