Project name: AAV6_1mer_M0

Status: done

Started: 2026-10-21 19:57:07
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]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:05)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:05)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:50)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/1438fe09e077d/tmp/folded.pdb                  (00:03:50)
[INFO]       Main:     Simulation completed successfully.                                          (00:17:43)
Show buried residues

Minimal score value
-3.8685
Maximal score value
2.2334
Average score
-0.5355
Total score value
-278.4415

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 -1.0193
16 A A -1.2060
17 D A -1.9172
18 G A -1.0198
19 V A 0.4763
20 G A -0.5808
21 N A -1.5147
22 A A -1.1171
23 S A -1.1866
24 G A -1.0892
25 N A -1.1215
26 W A -0.2772
27 H A -1.1132
28 C A -1.0468
29 D A -1.8450
30 S A -0.9285
31 T A -0.4013
32 W A -0.3223
33 L A -0.1826
34 G A -1.3389
35 D A -2.6158
36 R A -2.1604
37 V A 0.0000
38 I A -0.6898
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 0.3809
45 W A 0.0000
46 A A 0.6571
47 L A 0.0000
48 P A 0.0702
49 T A -0.1966
50 Y A -0.1622
51 N A -0.5556
52 N A -0.9237
53 H A -0.1109
54 L A 0.5499
55 Y A -0.0277
56 K A -1.1323
57 Q A -0.8627
58 I A 0.1142
59 S A -0.0354
60 S A 0.0000
61 A A -0.2890
62 S A -0.3790
63 T A -0.5737
64 G A -0.9148
65 A A -1.2258
66 S A -1.7424
67 N A -2.7127
68 D A -2.7443
69 N A -2.3796
70 H A -1.8904
71 Y A -0.1943
72 F A 0.3614
73 G A 0.0000
74 Y A 0.0000
75 S A -0.2298
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 -0.5522
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 -1.0794
92 P A -1.4235
93 R A -2.5041
94 D A -1.8093
95 W A 0.0000
96 Q A -2.1246
97 R A -2.3323
98 L A 0.0000
99 I A 0.0000
100 N A 0.0000
101 N A -1.6193
102 N A 0.0000
103 W A 0.0000
104 G A 0.0000
105 F A 0.0000
106 R A -1.0647
107 P A 0.0000
108 K A -2.1990
109 R A -2.1385
110 L A 0.0000
111 N A -0.9232
112 F A 0.0000
113 K A -0.8943
114 L A 0.0000
115 F A 0.0000
116 N A -1.0101
117 I A 0.0000
118 Q A -1.0004
119 V A 0.0000
120 K A -0.6349
121 E A -0.1866
122 V A 0.3798
123 T A 0.2006
124 T A -0.5246
125 N A -1.7798
126 D A -2.1085
127 G A -0.9277
128 V A 0.4992
129 T A 0.3852
130 T A 0.6526
131 I A 0.8449
132 A A -0.1131
133 N A -1.1609
134 N A -0.6719
135 L A 0.2112
136 T A -0.0574
137 S A 0.0000
138 T A 0.0000
139 V A 0.0000
140 Q A -0.4556
141 V A 0.0000
142 F A 0.0000
143 S A -0.4462
144 D A 0.0000
145 S A -1.3161
146 E A -2.2641
147 Y A -1.3530
148 Q A -1.4257
149 L A 0.0000
150 P A 0.3972
151 Y A 0.0777
152 V A 0.3328
153 L A 0.0000
154 G A -0.3479
155 S A -0.5324
156 A A -0.7365
157 H A -1.3512
158 Q A -1.6114
159 G A -0.6859
160 C A -0.4657
161 L A 0.0000
162 P A 0.0000
163 P A -0.0851
164 F A 0.5985
165 P A 0.0277
166 A A -0.1626
167 D A -0.5777
168 V A 1.2168
169 F A 0.0000
170 M A 1.2558
171 I A 0.0000
172 P A -0.3069
173 Q A -0.3605
174 Y A 0.0000
175 G A -0.0593
176 Y A 0.0000
177 L A 1.9003
178 T A 1.1348
179 L A 0.0945
180 N A -0.7527
181 N A -1.8378
182 G A -1.7683
183 S A -1.2209
184 Q A -1.4352
185 A A -0.8290
186 V A -0.5470
187 G A -0.9486
188 R A -1.5856
189 S A -0.2363
190 S A 0.6553
191 F A 1.7073
192 Y A 1.2194
193 C A 0.9702
194 L A 0.0000
195 E A -0.1252
196 Y A 1.0726
197 F A 0.2935
198 P A -0.1978
199 S A -0.4732
200 Q A -1.0425
201 M A -0.0739
202 L A 0.0000
203 R A -1.5992
204 T A -1.1440
205 G A 0.0000
206 N A -1.4092
207 N A -1.3253
208 F A 0.0000
209 T A -0.4104
210 F A -0.0718
211 S A -0.5446
212 Y A -0.5738
213 T A -1.3382
214 F A 0.0000
215 E A -2.0768
216 D A -2.1421
217 V A 0.0000
218 P A -0.4183
219 F A 0.0054
220 H A -0.0840
221 S A -0.0944
222 S A 0.0000
223 Y A -0.3019
224 A A -0.4906
225 H A -0.7468
226 S A -0.8573
227 Q A -0.9482
228 S A -0.8971
229 L A 0.0000
230 D A -1.3420
231 R A -1.3736
232 L A -0.4809
233 M A -0.4379
234 N A -0.5515
235 P A 0.1776
236 L A 1.6420
237 I A 1.5896
238 D A -0.7101
239 Q A -0.0969
240 Y A 1.2203
241 L A 1.0861
242 Y A 1.9965
243 Y A 1.4969
244 L A 1.6360
245 N A 0.2619
246 R A -1.4518
247 T A -1.4307
248 Q A -2.8124
249 N A -2.6279
250 Q A -2.4690
251 S A -1.5511
252 G A -1.3882
253 S A -1.0433
254 A A -1.6132
255 Q A -2.9084
256 N A -3.4004
257 K A -3.1289
258 D A -1.8690
259 L A 0.8812
260 L A 0.9900
261 F A 2.2334
262 S A 0.7165
263 R A -0.3278
264 G A 0.0000
265 S A -0.2437
266 P A -0.0347
267 A A 0.0027
268 G A -0.1802
269 M A -0.1100
270 S A -0.1410
271 V A 0.6609
272 Q A 0.0000
273 P A -0.3518
274 K A -1.3849
275 N A -1.3241
276 W A 0.1717
277 L A 0.5303
278 P A 0.4285
279 G A 0.0000
280 P A 0.5964
281 C A 0.0000
282 Y A 0.5289
283 R A -0.8528
284 Q A 0.0000
285 Q A -1.4072
286 R A -1.8045
287 V A -1.5293
288 S A 0.0000
289 K A -1.8018
290 T A -1.8276
291 K A -2.8001
292 T A -2.2529
293 D A -2.8748
294 N A -2.8322
295 N A -2.8139
296 N A -2.6926
297 S A -1.7884
298 N A -1.6155
299 F A -0.6752
300 T A 0.0094
301 W A 0.4382
302 T A -0.0052
303 G A -0.4162
304 A A 0.0930
305 S A -0.0215
306 K A 0.1036
307 Y A 0.4455
308 N A -1.1737
309 L A -0.5314
310 N A -1.7604
311 G A -1.6924
312 R A -2.2594
313 E A -1.5477
314 S A -0.3932
315 I A 0.3868
316 I A 0.2455
317 N A -0.7757
318 P A 0.0000
319 G A 0.0000
320 T A 0.0936
321 A A 0.1982
322 M A 0.0000
323 A A 0.0000
324 S A 0.0000
325 H A 0.0000
326 K A -3.1807
327 D A -3.8685
328 D A -3.8328
329 K A -3.5905
330 D A -3.8393
331 K A -2.5352
332 F A -1.9171
333 F A -1.0632
334 P A 0.0000
335 M A -0.4704
336 S A -0.3051
337 G A 0.0000
338 V A 0.0000
339 M A 0.0000
340 I A 1.3307
341 F A 0.2755
342 G A -1.1594
343 K A -2.2733
344 E A -2.4198
345 S A -1.7982
346 A A -1.6895
347 G A -1.2680
348 A A -0.6151
349 S A -0.9404
350 N A -1.3942
351 T A -1.0874
352 A A -0.7148
353 L A -0.8272
354 D A -1.7727
355 N A -1.6931
356 V A -0.6308
357 M A 0.0000
358 I A 0.4619
359 T A 0.0000
360 D A -1.4154
361 E A 0.0000
362 E A -2.6486
363 E A -1.9577
364 I A 0.0000
365 K A -1.8220
366 A A 0.0000
367 T A 0.0000
368 N A 0.0000
369 P A -0.6480
370 V A -0.9042
371 A A 0.0000
372 T A -1.5546
373 E A -2.4049
374 R A -2.2745
375 F A -0.6766
376 G A -0.7574
377 T A -0.3394
378 V A 1.0198
379 A A 1.0309
380 V A 1.6356
381 N A 0.3906
382 L A 0.6125
383 Q A -1.2892
384 S A -1.1505
385 S A -1.2139
386 S A -1.0384
387 T A -1.4124
388 D A -2.3063
389 P A -1.1916
390 A A -0.0855
391 T A 0.2838
392 G A -0.3091
393 D A -1.7355
394 V A -0.7337
395 H A -0.7308
396 V A 1.1840
397 M A 0.7589
398 G A 0.3291
399 A A 0.4851
400 L A 0.7876
401 P A 0.3014
402 G A 0.1568
403 M A 0.6603
404 V A 0.9405
405 W A 0.2903
406 Q A -0.4034
407 D A -0.4648
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 -0.3639
416 I A 0.0000
417 W A 0.0000
418 A A -0.4591
419 K A -1.2333
420 I A -1.3054
421 P A -1.4405
422 H A -1.9622
423 T A -1.7143
424 D A -2.4094
425 G A -1.4309
426 H A -0.6872
427 F A 1.1194
428 H A -0.1096
429 P A -0.2400
430 S A -0.0320
431 P A 0.2727
432 L A 0.9490
433 M A 0.3607
434 G A 0.0000
435 G A -0.0307
436 F A 0.0000
437 G A -0.7740
438 L A 0.0000
439 K A -2.5516
440 H A -2.2076
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 0.1793
451 P A 0.0380
452 V A 0.3487
453 P A 0.0717
454 A A -0.2999
455 N A -1.3253
456 P A -0.9188
457 P A -0.8472
458 A A -0.7472
459 E A -1.0144
460 F A 0.9060
461 S A 0.0830
462 A A 0.0508
463 T A -0.5079
464 K A -1.4549
465 F A -0.2814
466 A A -0.2008
467 S A -0.2867
468 F A 0.3039
469 I A 0.6428
470 T A 0.2738
471 Q A 0.0000
472 Y A 0.2870
473 S A 0.0000
474 T A 0.0181
475 G A 0.0000
476 Q A -0.3502
477 V A 0.0000
478 S A -0.5851
479 V A 0.0000
480 E A -1.1863
481 I A 0.0000
482 E A -1.5596
483 W A 0.0000
484 E A -1.7979
485 L A 0.0000
486 Q A -1.8138
487 K A -2.2180
488 E A -2.2308
489 N A -2.5161
490 S A -2.0856
491 K A -2.3598
492 R A -1.6495
493 W A -0.0856
494 N A -0.5673
495 P A -0.3203
496 E A 0.1252
497 V A 1.2688
498 Q A 0.0761
499 Y A -0.2616
500 T A -0.2681
501 S A -0.5060
502 N A -0.9218
503 Y A 0.2352
504 A A -0.6201
505 K A -1.6144
506 S A -1.1010
507 A A -0.7884
508 N A -0.9993
509 V A 0.4596
510 D A -0.3757
511 F A -0.0448
512 T A 0.4845
513 V A 0.4176
514 D A -1.1644
515 N A -2.1321
516 N A -1.8905
517 G A -1.1222
518 L A -0.2448
519 Y A -0.0127
520 T A -0.2629
521 E A -0.7889
522 P A -0.8013
523 R A -0.8024
524 P A -0.2251
525 I A 0.0000
526 G A -0.2490
527 T A 0.0000
528 R A 0.0000
529 Y A 0.3818
530 L A 0.0000
531 T A -0.3624
532 R A -1.2742
533 P A -0.5882
534 L A 0.4445
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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 -0.173 4.3411 View CSV PDB
4.5 -0.2223 4.2077 View CSV PDB
5.0 -0.2787 4.0172 View CSV PDB
5.5 -0.3343 3.8549 View CSV PDB
6.0 -0.3812 3.8087 View CSV PDB
6.5 -0.4133 3.788 View CSV PDB
7.0 -0.4312 3.7673 View CSV PDB
7.5 -0.4403 3.747 View CSV PDB
8.0 -0.4436 3.7278 View CSV PDB
8.5 -0.4398 3.7114 View CSV PDB
9.0 -0.4258 3.6997 View CSV PDB