Project name: AAV1_1mer_M0

Status: done

Started: 2026-10-21 17:40:31
Settings
Chain sequence(s) DGVGNASGNWHCDSTWLGDRVITTSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTTNDGVTTIANNLTSTVQVFSDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEEVPFHSSYAHSQSLDRLMNPLIDQYLYYLNRTQNQSGSAQNKDLLFSRGSPAGMSVQPKNWLPGPCYRQQRVSKTKTDNNNSNFTWTGASKYNLNGRESIINPGTAMASHKDDEDKFFPMSGVMIFGKESAGASNTALDNVMITDEEEIKATNPVATERFGTVAVNFQSSSTDPATGDVHAMGALPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKNPPPQILIKNTPVPANPPAEFSATKFASFITQYSTGQVSVEIEWELQKENSKRWNPEVQYTSNYAKSANVDFTVDNNGLYTEPRPIGTRYLTRPL 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                                          (00:03:28)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/c82e6380622522/tmp/folded.pdb                 (00:03:28)
[INFO]       Main:     Simulation completed successfully.                                          (00:11:11)
Show buried residues

Minimal score value
-3.8957
Maximal score value
2.3843
Average score
-0.5412
Total score value
-280.3655

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
17 D A -2.3675
18 G A -1.2375
19 V A 0.3176
20 G A -0.6767
21 N A -1.7701
22 A A -1.3203
23 S A -1.4133
24 G A -1.1539
25 N A -1.1212
26 W A -0.3083
27 H A -1.2349
28 C A -1.0197
29 D A -1.8183
30 S A -0.8511
31 T A -0.1917
32 W A 0.1078
33 L A 0.3342
34 G A -0.9382
35 D A -1.8228
36 R A -1.0537
37 V A 0.0000
38 I A -0.2368
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 0.4138
45 W A 0.0000
46 A A 0.7007
47 L A 0.0000
48 P A 0.0641
49 T A -0.2958
50 Y A -0.3508
51 N A -0.9208
52 N A -1.1950
53 H A -0.4862
54 L A -0.2034
55 Y A -0.4344
56 K A -1.4214
57 Q A -0.9715
58 I A 0.1205
59 S A 0.0003
60 S A 0.0000
61 A A -0.2862
62 S A -0.2924
63 T A -0.5760
64 G A -0.9141
65 A A -1.1738
66 S A -1.6553
67 N A -2.5634
68 D A -2.4896
69 N A -2.2401
70 H A -1.7785
71 Y A -0.0288
72 F A 0.4701
73 G A 0.0000
74 Y A 0.2289
75 S A -0.3544
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 -0.5141
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 -1.1107
92 P A -1.3774
93 R A -2.3403
94 D A -1.6085
95 W A 0.0000
96 Q A -1.7377
97 R A -2.1207
98 L A 0.0000
99 I A 0.0000
100 N A -1.0218
101 N A -2.2296
102 N A 0.0000
103 W A -1.1442
104 G A 0.0000
105 F A 0.0000
106 R A -0.8085
107 P A 0.0000
108 K A -1.7836
109 R A -1.7942
110 L A 0.0000
111 N A -0.9277
112 F A 0.0000
113 K A -0.7156
114 L A 0.0000
115 F A 0.0000
116 N A -1.1686
117 I A 0.0000
118 Q A -1.1041
119 V A 0.0000
120 K A -0.5131
121 E A -0.1560
122 V A 0.4966
123 T A 0.2488
124 T A -0.4625
125 N A -1.7789
126 D A -2.0997
127 G A -0.9337
128 V A 0.4979
129 T A 0.4532
130 T A 0.7559
131 I A 1.0994
132 A A 0.0214
133 N A -1.0936
134 N A -0.6263
135 L A 0.2520
136 T A -0.0812
137 S A 0.0000
138 T A 0.0000
139 V A 0.0000
140 Q A -0.5884
141 V A 0.0000
142 F A 0.0000
143 S A -0.4260
144 D A 0.0000
145 S A -1.3137
146 E A -2.2830
147 Y A -1.5456
148 Q A -1.3412
149 L A 0.0000
150 P A 0.2330
151 Y A 0.0341
152 V A 0.2443
153 L A 0.0000
154 G A -0.4531
155 S A -0.5568
156 A A -0.6779
157 H A -1.1938
158 Q A -1.5122
159 G A -0.6025
160 C A -0.4075
161 L A 0.0000
162 P A -0.0878
163 P A -0.2352
164 F A 0.3626
165 P A -0.0815
166 A A -0.2223
167 D A -0.6086
168 V A 1.2092
169 F A 0.0000
170 M A 1.3539
171 I A 0.0000
172 P A -0.2585
173 Q A -0.3495
174 Y A 0.0000
175 G A -0.0557
176 Y A 0.0000
177 L A 1.9961
178 T A 1.2811
179 L A 0.4121
180 N A -0.6107
181 N A -1.8350
182 G A -1.7064
183 S A -1.1905
184 Q A -1.4623
185 A A -0.9311
186 V A -0.8893
187 G A -1.1048
188 R A -1.6657
189 S A -0.4262
190 S A 0.5303
191 F A 1.4097
192 Y A 1.0654
193 C A 0.8338
194 L A 0.0000
195 E A -0.3584
196 Y A 0.9613
197 F A 0.2313
198 P A -0.2720
199 S A -0.5818
200 Q A -1.2340
201 M A -0.4732
202 L A 0.0000
203 R A -1.7347
204 T A -1.4177
205 G A -1.6811
206 N A -2.0988
207 N A -1.6977
208 F A -0.5318
209 T A -0.2981
210 F A -0.0251
211 S A -0.5251
212 Y A -0.5443
213 T A -1.2760
214 F A 0.0000
215 E A -2.1209
216 E A -2.1390
217 V A 0.0000
218 P A -0.4554
219 F A 0.0594
220 H A 0.0000
221 S A -0.0044
222 S A 0.0000
223 Y A -0.3515
224 A A -0.6062
225 H A -0.7195
226 S A -0.8878
227 Q A -1.0286
228 S A -0.8836
229 L A 0.0000
230 D A -1.5803
231 R A -1.3125
232 L A -0.3802
233 M A -0.1876
234 N A 0.0585
235 P A 0.4640
236 L A 1.8210
237 I A 1.7300
238 D A -0.6569
239 Q A -0.0304
240 Y A 1.2339
241 L A 1.1248
242 Y A 1.9411
243 Y A 1.5609
244 L A 1.8204
245 N A 0.3450
246 R A -0.5883
247 T A -1.0561
248 Q A -2.7574
249 N A -2.6990
250 Q A -2.4638
251 S A -1.6742
252 G A -1.2085
253 S A -1.0622
254 A A -1.7127
255 Q A -2.9456
256 N A -3.4277
257 K A -3.2414
258 D A -1.6966
259 L A 1.1376
260 L A 1.1836
261 F A 2.3843
262 S A 0.7640
263 R A -0.3897
264 G A 0.0000
265 S A -0.1925
266 P A 0.0699
267 A A 0.0042
268 G A 0.0266
269 M A -0.0761
270 S A -0.0807
271 V A 0.8479
272 Q A 0.0000
273 P A -0.3849
274 K A -1.3182
275 N A -1.3602
276 W A 0.1000
277 L A 0.4630
278 P A 0.4332
279 G A 0.0000
280 P A 0.3118
281 C A 0.0000
282 Y A 0.0293
283 R A -1.1271
284 Q A 0.0000
285 Q A -1.3216
286 R A -1.6511
287 V A -1.5543
288 S A 0.0000
289 K A -1.8080
290 T A -1.8157
291 K A -2.7611
292 T A -2.2390
293 D A -2.9022
294 N A -2.8102
295 N A -2.8190
296 N A -2.6936
297 S A -1.8210
298 N A -1.6421
299 F A -0.7467
300 T A -0.0711
301 W A 0.3264
302 T A -0.0761
303 G A -0.4420
304 A A -0.1304
305 S A -0.0705
306 K A 0.0240
307 Y A 0.3135
308 N A -1.2519
309 L A -0.6540
310 N A -1.8164
311 G A -1.6987
312 R A -2.2302
313 E A -1.5416
314 S A -0.4308
315 I A 0.2383
316 I A 0.1815
317 N A -0.7971
318 P A 0.0000
319 G A 0.0791
320 T A 0.1223
321 A A 0.2268
322 M A 0.0000
323 A A 0.0000
324 S A 0.0000
325 H A 0.0000
326 K A -3.1032
327 D A -3.8827
328 D A -3.8525
329 E A -3.5164
330 D A -3.8957
331 K A -2.6672
332 F A -2.0283
333 F A 0.0000
334 P A 0.0000
335 M A -0.4959
336 S A -0.3513
337 G A 0.0000
338 V A 0.0000
339 M A 0.0000
340 I A 1.3434
341 F A 0.2450
342 G A -1.1161
343 K A -2.2005
344 E A -2.3520
345 S A -1.7667
346 A A -1.6403
347 G A -1.2575
348 A A -0.6166
349 S A -0.9423
350 N A -1.3790
351 T A -1.0633
352 A A -0.6841
353 L A -0.6728
354 D A -1.6839
355 N A -1.5737
356 V A -0.5672
357 M A 0.0000
358 I A 0.4088
359 T A 0.0000
360 D A -1.2272
361 E A 0.0000
362 E A -2.3236
363 E A -1.5379
364 I A 0.0000
365 K A -1.4426
366 A A -0.8926
367 T A 0.0000
368 N A 0.0000
369 P A -0.3856
370 V A -0.6226
371 A A 0.0000
372 T A -1.2820
373 E A -1.7995
374 R A -2.0387
375 F A -0.7587
376 G A -0.7835
377 T A -0.2807
378 V A 1.0147
379 A A 1.1008
380 V A 1.7370
381 N A 0.6251
382 F A 1.0229
383 Q A -1.0911
384 S A -1.0492
385 S A -1.1785
386 S A -1.0439
387 T A -1.3363
388 D A -2.2410
389 P A -1.0710
390 A A -0.0231
391 T A 0.2987
392 G A -0.2627
393 D A -1.7192
394 V A -1.0536
395 H A -1.3924
396 A A -0.4580
397 M A -0.0583
398 G A -0.0895
399 A A 0.4024
400 L A 0.5828
401 P A 0.1801
402 G A 0.0395
403 M A 0.5776
404 V A 0.9188
405 W A 0.3828
406 Q A -0.3140
407 D A -0.4113
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 -0.3442
416 I A 0.0000
417 W A 0.0000
418 A A -0.6093
419 K A -1.4330
420 I A 0.0000
421 P A -1.5867
422 H A -2.0656
423 T A -1.8227
424 D A -2.4740
425 G A -1.6588
426 H A -1.0012
427 F A 1.0299
428 H A -0.1040
429 P A -0.3136
430 S A -0.0348
431 P A 0.2533
432 L A 0.9657
433 M A 0.4288
434 G A 0.0000
435 G A 0.0374
436 F A 0.0000
437 G A -0.8692
438 L A 0.0000
439 K A -2.7291
440 N A -2.5276
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 0.1354
451 P A 0.0909
452 V A 0.3383
453 P A 0.1064
454 A A -0.3055
455 N A -1.3292
456 P A -0.8764
457 P A -0.8335
458 A A -0.7441
459 E A -1.0145
460 F A 0.8993
461 S A 0.0661
462 A A 0.0499
463 T A -0.4767
464 K A -1.3762
465 F A -0.1231
466 A A -0.1757
467 S A -0.2854
468 F A 0.2395
469 I A 0.5541
470 T A 0.1183
471 Q A 0.0000
472 Y A 0.3207
473 S A 0.0000
474 T A 0.0137
475 G A 0.0000
476 Q A -0.3366
477 V A 0.0000
478 S A -0.5699
479 V A 0.0000
480 E A -1.0922
481 I A 0.0000
482 E A -0.9338
483 W A 0.0000
484 E A -1.2124
485 L A 0.0000
486 Q A -2.0399
487 K A -2.8758
488 E A -2.7167
489 N A -2.7496
490 S A -2.1976
491 K A -2.3622
492 R A -1.6197
493 W A 0.0837
494 N A -0.1785
495 P A -0.1395
496 E A 0.1795
497 V A 1.2614
498 Q A -0.1453
499 Y A -0.2144
500 T A -0.4274
501 S A -0.5100
502 N A -0.9022
503 Y A 0.2894
504 A A -0.4086
505 K A -1.6207
506 S A -1.1098
507 A A -0.8095
508 N A -1.0615
509 V A 0.3596
510 D A -0.6417
511 F A -0.2623
512 T A 0.3532
513 V A 0.3110
514 D A -1.1446
515 N A -2.1060
516 N A -1.8574
517 G A -1.0816
518 L A -0.1721
519 Y A -0.0168
520 T A -0.3152
521 E A -0.9698
522 P A -0.8154
523 R A -0.8760
524 P A -0.3547
525 I A 0.0000
526 G A -0.1978
527 T A 0.0000
528 R A 0.0000
529 Y A 0.2911
530 L A 0.0000
531 T A -0.5201
532 R A -1.4523
533 P A -0.6475
534 L A 0.4634
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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 -0.1199 4.4331 View CSV PDB
4.5 -0.1672 4.4153 View CSV PDB
5.0 -0.2218 4.3957 View CSV PDB
5.5 -0.2755 4.3754 View CSV PDB
6.0 -0.3209 4.355 View CSV PDB
6.5 -0.3527 4.3344 View CSV PDB
7.0 -0.3715 4.314 View CSV PDB
7.5 -0.3815 4.294 View CSV PDB
8.0 -0.3852 4.2751 View CSV PDB
8.5 -0.3818 4.2589 View CSV PDB
9.0 -0.3687 4.2475 View CSV PDB