Project name: AAV6_1mer_M2

Status: done

Started: 2026-10-21 19:57:32
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.  (00:00:04)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:04)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:36)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/3d0f1f95a80749/tmp/folded.pdb                 (00:03:36)
[INFO]       Main:     Simulation completed successfully.                                          (00:11:40)
Show buried residues

Minimal score value
-3.8265
Maximal score value
2.3802
Average score
-0.5146
Total score value
-267.5933

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 -1.0371
16 A A -1.4079
17 D A -2.2936
18 G A -1.0809
19 V A 0.4252
20 G A -0.6068
21 N A -1.5737
22 A A -1.1414
23 S A -1.2146
24 G A -1.0998
25 N A -1.1268
26 W A -0.3048
27 H A -1.2153
28 C A -1.0305
29 D A -1.8063
30 S A -0.8686
31 T A -0.4839
32 W A -0.5553
33 L A -0.6802
34 G A -1.6429
35 D A -2.9207
36 R A -2.7065
37 V A 0.0000
38 I A -0.7374
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 0.3841
45 W A 0.0000
46 A A 0.6927
47 L A 0.0000
48 P A 0.1020
49 T A -0.1831
50 Y A -0.1486
51 N A -0.5568
52 N A -0.9236
53 H A -0.1263
54 L A 0.5438
55 Y A -0.0249
56 K A -1.1342
57 Q A -0.8788
58 I A 0.0872
59 S A -0.0813
60 S A 0.0000
61 A A -0.3062
62 S A -0.3815
63 T A -0.5761
64 G A -0.9022
65 A A -1.1580
66 S A -1.6240
67 N A -2.4832
68 D A -2.4915
69 N A -2.2317
70 H A -1.7955
71 Y A -0.1518
72 F A 0.0000
73 G A 0.0000
74 Y A 0.2181
75 S A -0.1729
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 -0.6404
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 -1.0095
92 P A -1.3555
93 R A -2.4059
94 D A 0.0000
95 W A 0.0000
96 Q A -2.1151
97 R A -2.3236
98 L A 0.0000
99 I A 0.0000
100 N A 0.0000
101 N A -1.9247
102 N A 0.0000
103 W A 0.0000
104 G A 0.0000
105 F A 0.0000
106 R A -1.0912
107 P A 0.0000
108 K A -2.2819
109 R A -1.9290
110 L A 0.0000
111 N A -0.9206
112 F A 0.0000
113 K A -0.9035
114 L A 0.0000
115 F A 0.0000
116 N A -0.9387
117 I A 0.0000
118 Q A -1.0220
119 V A 0.0000
120 K A -0.5557
121 E A -0.0894
122 V A 0.4544
123 T A 0.2446
124 T A -0.5138
125 N A -1.7819
126 D A -2.1080
127 G A -0.9330
128 V A 0.4959
129 T A 0.3991
130 T A 0.6986
131 I A 0.9523
132 A A -0.0543
133 N A -1.1352
134 N A -0.6430
135 L A 0.2162
136 T A -0.0306
137 S A 0.0000
138 T A 0.0000
139 V A 0.0000
140 Q A -0.4410
141 V A 0.0000
142 F A 0.0000
143 S A -0.4414
144 D A 0.0000
145 S A -1.2946
146 E A -2.2216
147 Y A -1.2904
148 Q A -1.2816
149 L A 0.0000
150 P A 0.4106
151 Y A 0.0876
152 V A 0.3324
153 L A 0.0000
154 G A -0.3514
155 S A -0.5110
156 A A -0.7017
157 H A -1.2888
158 Q A -1.6319
159 G A -0.6491
160 C A -0.4395
161 L A 0.0000
162 P A 0.0000
163 P A -0.0883
164 F A 0.5490
165 P A 0.0146
166 A A -0.2543
167 D A -0.6737
168 V A 1.1871
169 F A 0.0000
170 M A 1.3495
171 I A 0.0000
172 P A -0.2692
173 Q A -0.3308
174 Y A 0.0000
175 G A -0.0235
176 Y A 0.0000
177 L A 1.9006
178 T A 1.1399
179 L A 0.1424
180 N A -0.7396
181 N A -1.8136
182 G A -1.6905
183 S A -1.2100
184 Q A -1.4540
185 A A -0.8653
186 V A -0.5926
187 G A -0.9626
188 R A -1.5966
189 S A -0.2755
190 S A 0.6191
191 F A 1.6128
192 Y A 1.1831
193 C A 0.9067
194 L A 0.0000
195 E A -0.1660
196 Y A 1.0538
197 F A 0.3105
198 P A -0.1958
199 S A -0.4729
200 Q A -1.0049
201 M A -0.0262
202 L A 0.0000
203 R A -1.4993
204 T A -1.1411
205 G A 0.0000
206 N A -1.4273
207 N A -1.2300
208 F A 0.0000
209 T A -0.4415
210 F A -0.0665
211 S A -0.4959
212 Y A -0.5113
213 T A -1.2766
214 F A 0.0000
215 E A -2.0717
216 D A -2.1845
217 V A 0.0000
218 P A -0.3901
219 F A 0.0453
220 H A 0.0000
221 S A -0.0082
222 S A 0.0000
223 Y A -0.3330
224 A A -0.5337
225 H A -0.7665
226 S A -0.8564
227 Q A -0.9757
228 S A -0.9870
229 L A 0.0000
230 D A -1.5520
231 R A -1.3871
232 L A -0.5259
233 M A -0.2638
234 N A -0.0268
235 P A 0.4161
236 L A 1.7928
237 I A 1.7025
238 D A -0.5922
239 Q A 0.0306
240 Y A 1.3029
241 L A 1.1922
242 Y A 2.1188
243 Y A 1.6166
244 L A 1.7719
245 N A 0.2472
246 R A -0.5449
247 T A -0.8353
248 Q A -2.4978
249 N A -2.3422
250 Q A -2.5395
251 S A -1.6155
252 G A -1.3715
253 S A -1.0883
254 A A -1.6872
255 Q A -2.9366
256 N A -3.4232
257 K A -3.0695
258 D A -1.5471
259 L A 1.1561
260 L A 1.2867
261 F A 2.3802
262 S A 1.0769
263 R A 0.1457
264 G A 0.0000
265 S A -0.0286
266 P A 0.2457
267 A A 0.0499
268 G A 0.0111
269 M A -0.2781
270 S A 0.0463
271 V A 1.0481
272 Q A 0.0000
273 P A -0.1867
274 K A -1.3346
275 N A -1.4090
276 W A 0.0055
277 L A 0.4509
278 P A 0.3986
279 G A 0.0000
280 P A 0.6042
281 C A 0.0000
282 Y A 0.5216
283 R A -0.6949
284 Q A 0.0000
285 Q A -1.2491
286 R A -1.5953
287 V A -1.4805
288 S A 0.0000
289 K A -1.7828
290 T A -1.8569
291 K A -2.8376
292 T A -2.3372
293 D A -3.0501
294 N A -2.8979
295 N A -2.8585
296 N A -2.7168
297 S A -1.7940
298 N A -1.6119
299 F A -0.6672
300 T A 0.0237
301 W A 0.4724
302 T A 0.0189
303 G A -0.3760
304 A A 0.1128
305 S A -0.0211
306 K A 0.0833
307 Y A 0.4213
308 N A -1.1438
309 L A -0.4673
310 N A -1.7181
311 G A -1.6215
312 R A -2.1166
313 E A -1.4585
314 S A -0.3692
315 I A 0.3379
316 I A 0.2067
317 N A -0.7865
318 P A 0.0000
319 G A 0.0000
320 T A 0.1028
321 A A 0.2134
322 M A 0.0000
323 A A 0.0000
324 S A 0.0000
325 H A 0.0000
326 K A -3.0833
327 D A -3.8174
328 D A -3.7842
329 K A -3.5315
330 D A -3.8265
331 K A -2.5360
332 F A -1.9648
333 F A -1.0262
334 P A 0.0000
335 M A -0.4299
336 S A -0.2957
337 G A 0.0000
338 V A 0.0000
339 M A 0.0000
340 I A 1.3294
341 F A 0.2396
342 G A -1.1812
343 K A -2.2886
344 E A -2.4153
345 S A -1.7951
346 A A -1.6861
347 G A -1.2678
348 A A -0.6164
349 S A -0.9422
350 N A -1.3939
351 T A -1.0872
352 A A -0.7119
353 L A -0.8156
354 D A -1.7659
355 N A -1.6555
356 V A -0.6539
357 M A 0.0000
358 I A 0.3898
359 T A 0.0000
360 D A -1.4920
361 E A 0.0000
362 E A -2.8733
363 E A -2.1683
364 I A 0.0000
365 K A -1.9392
366 A A -1.2138
367 T A 0.0000
368 N A 0.0000
369 P A -0.6395
370 V A 0.0000
371 A A 0.0000
372 T A -1.3320
373 E A -1.9908
374 R A -1.9683
375 F A -0.5487
376 G A -0.6510
377 T A -0.3091
378 V A 1.0250
379 A A 1.0369
380 V A 1.6463
381 N A 0.4199
382 L A 0.6238
383 Q A -1.2841
384 S A -1.1513
385 S A -1.2219
386 S A -1.0405
387 T A -1.4120
388 D A -2.3049
389 P A -1.1863
390 A A -0.0808
391 T A 0.2896
392 G A -0.3027
393 D A -1.6547
394 V A -0.6477
395 H A -0.6179
396 V A 1.1869
397 M A 0.7626
398 G A 0.3155
399 A A 0.4958
400 L A 0.7738
401 P A 0.2746
402 G A 0.0860
403 M A 0.6479
404 V A 1.0204
405 W A 0.4166
406 Q A 0.0000
407 D A -0.3297
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 -0.3414
416 I A 0.0000
417 W A 0.0000
418 A A -0.4854
419 K A -1.2970
420 I A 0.0000
421 P A -1.5583
422 H A -2.0316
423 T A -1.8146
424 D A -2.4659
425 G A -1.5670
426 H A -0.9667
427 F A 1.0243
428 H A -0.0976
429 P A -0.2696
430 S A -0.0104
431 P A 0.2731
432 L A 0.9750
433 M A 0.3704
434 G A 0.0000
435 G A 0.0108
436 F A 0.0000
437 G A -0.7832
438 L A 0.0000
439 K A -2.4947
440 H A -2.1888
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 0.1510
451 P A -0.0193
452 V A 0.2475
453 P A 0.0648
454 A A -0.2808
455 N A -1.3204
456 P A -0.8496
457 P A -0.8229
458 A A -0.7300
459 E A -0.9995
460 F A 0.9285
461 S A 0.1503
462 A A 0.0996
463 T A -0.4346
464 K A -1.3351
465 F A -0.0380
466 A A -0.0930
467 S A -0.2526
468 F A 0.2971
469 I A 0.6666
470 T A 0.3108
471 Q A 0.0000
472 Y A 0.3337
473 S A 0.0000
474 T A 0.0204
475 G A 0.0000
476 Q A -0.3202
477 V A 0.0000
478 S A 0.0000
479 V A 0.0000
480 E A -1.1626
481 I A 0.0000
482 E A -1.6332
483 W A 0.0000
484 E A -1.9885
485 L A 0.0000
486 Q A -1.8625
487 K A -2.4251
488 E A -2.3038
489 N A -2.5257
490 S A -2.0210
491 K A -2.2398
492 R A -1.4626
493 W A 0.1229
494 N A -0.1967
495 P A -0.1449
496 E A 0.2159
497 V A 1.2678
498 Q A -0.0490
499 Y A -0.2946
500 T A -0.2885
501 S A -0.4990
502 N A -0.9102
503 Y A 0.2326
504 A A -0.6213
505 K A -1.6090
506 S A -1.0891
507 A A -0.7766
508 N A -0.9988
509 V A 0.4759
510 D A -0.3367
511 F A -0.0434
512 T A 0.4176
513 V A 0.1996
514 D A -1.2320
515 N A -2.1677
516 N A -1.9285
517 G A -1.2167
518 L A -0.3672
519 Y A -0.1384
520 T A -0.3299
521 E A -0.8522
522 P A -0.8597
523 R A -0.9698
524 P A -0.3626
525 I A 0.0000
526 G A -0.2699
527 T A 0.0000
528 R A 0.0000
529 Y A 0.2965
530 L A 0.0000
531 T A -0.3197
532 R A -1.2062
533 P A -0.3942
534 L A 0.4128
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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 -0.1257 4.6023 View CSV PDB
4.5 -0.1738 4.586 View CSV PDB
5.0 -0.2294 4.5676 View CSV PDB
5.5 -0.2848 4.5484 View CSV PDB
6.0 -0.3319 4.5289 View CSV PDB
6.5 -0.3656 4.5094 View CSV PDB
7.0 -0.3861 4.49 View CSV PDB
7.5 -0.398 4.4708 View CSV PDB
8.0 -0.4041 4.4526 View CSV PDB
8.5 -0.4027 4.4365 View CSV PDB
9.0 -0.391 4.4246 View CSV PDB