Project name: AAV1_1mer_M4

Status: done

Started: 2026-10-21 17:41:58
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]                                                (00:00:00)
[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                                          (00:02:26)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/842176626edeaa/tmp/folded.pdb                 (00:02:26)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:20)
Show buried residues

Minimal score value
-3.9322
Maximal score value
2.3002
Average score
-0.5421
Total score value
-280.8018

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 -2.5030
18 G A -1.3222
19 V A 0.3210
20 G A -0.6709
21 N A -1.7373
22 A A -1.3104
23 S A -1.4129
24 G A -1.1736
25 N A -1.1254
26 W A -0.2998
27 H A -1.2377
28 C A -1.0266
29 D A -1.8125
30 S A -0.8265
31 T A -0.0921
32 W A 0.0920
33 L A 0.3155
34 G A -1.0614
35 D A -2.1894
36 R A -1.1823
37 V A 0.0000
38 I A -0.2192
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 0.4224
45 W A 0.0000
46 A A 0.6894
47 L A 0.0000
48 P A 0.0846
49 T A -0.2133
50 Y A -0.1958
51 N A -0.6527
52 N A -1.0166
53 H A -0.2537
54 L A 0.2775
55 Y A -0.1275
56 K A -1.1527
57 Q A -0.7994
58 I A 0.1716
59 S A 0.0097
60 S A 0.0000
61 A A -0.2845
62 S A -0.2879
63 T A -0.5748
64 G A -0.9090
65 A A -1.1937
66 S A -1.6710
67 N A -2.6147
68 D A -2.5589
69 N A -2.3099
70 H A -1.7995
71 Y A -0.1468
72 F A 0.3700
73 G A 0.0000
74 Y A 0.3620
75 S A -0.2082
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 -0.5845
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 -1.1229
92 P A -1.4485
93 R A -2.5478
94 D A -1.8495
95 W A 0.0000
96 Q A -2.1148
97 R A -2.6177
98 L A 0.0000
99 I A 0.0000
100 N A -1.0592
101 N A -1.9993
102 N A 0.0000
103 W A -0.8867
104 G A 0.0000
105 F A 0.0000
106 R A -0.8561
107 P A 0.0000
108 K A -2.0651
109 R A -2.4450
110 L A 0.0000
111 N A -1.2973
112 F A 0.0000
113 K A -1.0101
114 L A 0.0000
115 F A 0.0000
116 N A -1.1288
117 I A 0.0000
118 Q A -1.0903
119 V A 0.0000
120 K A -0.5404
121 E A -0.2400
122 V A 0.4240
123 T A 0.1856
124 T A -0.5012
125 N A -1.7894
126 D A -2.1033
127 G A -0.9352
128 V A 0.4980
129 T A 0.3989
130 T A 0.6495
131 I A 0.8984
132 A A -0.0710
133 N A -1.1144
134 N A -0.6060
135 L A 0.3708
136 T A 0.0340
137 S A 0.0000
138 T A 0.0000
139 V A 0.0000
140 Q A -0.4673
141 V A 0.0000
142 F A 0.0000
143 S A -0.4410
144 D A 0.0000
145 S A -1.3073
146 E A -2.2491
147 Y A -1.3263
148 Q A -1.3318
149 L A 0.0000
150 P A 0.2382
151 Y A 0.0948
152 V A 0.3288
153 L A 0.0000
154 G A -0.4139
155 S A -0.5209
156 A A -0.7077
157 H A -1.2732
158 Q A -1.5601
159 G A -0.6222
160 C A -0.4333
161 L A 0.0000
162 P A -0.0107
163 P A -0.0953
164 F A 0.6142
165 P A 0.0552
166 A A -0.1408
167 D A -0.4755
168 V A 1.2604
169 F A 0.0000
170 M A 1.3541
171 I A 0.0000
172 P A -0.2660
173 Q A -0.3283
174 Y A 0.0000
175 G A -0.0238
176 Y A 0.0000
177 L A 1.9557
178 T A 1.1584
179 L A 0.0215
180 N A -0.8093
181 N A -1.9027
182 G A -1.7513
183 S A -1.2869
184 Q A -1.5050
185 A A -1.0061
186 V A -0.9062
187 G A -1.1230
188 R A -1.6875
189 S A -0.4592
190 S A 0.6705
191 F A 1.8527
192 Y A 1.3094
193 C A 0.9680
194 L A 0.0000
195 E A -0.2055
196 Y A 1.0176
197 F A 0.2472
198 P A -0.2385
199 S A -0.5140
200 Q A -1.1191
201 M A -0.2247
202 L A 0.0000
203 R A -1.7879
204 T A -1.3796
205 G A -1.6744
206 N A -1.9871
207 N A -1.6508
208 F A -0.5597
209 T A -0.4343
210 F A -0.1255
211 S A -0.7391
212 Y A -0.7482
213 T A -1.4859
214 F A 0.0000
215 E A -2.0940
216 E A -2.1260
217 V A 0.0000
218 P A -0.4330
219 F A 0.1080
220 H A 0.0000
221 S A 0.0121
222 S A 0.0000
223 Y A -0.2915
224 A A -0.6595
225 H A -0.7686
226 S A -0.8826
227 Q A -1.1250
228 S A -1.1217
229 L A 0.0000
230 D A -1.6363
231 R A -1.6711
232 L A -0.5495
233 M A -0.2914
234 N A -0.0843
235 P A 0.3725
236 L A 1.7945
237 I A 1.7063
238 D A -0.7210
239 Q A -0.1190
240 Y A 1.1474
241 L A 0.9868
242 Y A 1.7786
243 Y A 1.5090
244 L A 1.8211
245 N A 0.4447
246 R A -0.5507
247 T A -1.0946
248 Q A -2.7040
249 N A -2.4910
250 Q A -2.3862
251 S A -1.5281
252 G A -1.3259
253 S A -1.0171
254 A A -1.6010
255 Q A -2.9051
256 N A -3.4415
257 K A -3.2466
258 D A -1.8361
259 L A 1.0823
260 L A 1.1459
261 F A 2.3002
262 S A 0.6629
263 R A -0.6210
264 G A 0.0000
265 S A -0.2664
266 P A 0.0484
267 A A 0.0108
268 G A 0.0142
269 M A -0.1008
270 S A -0.0507
271 V A 0.9731
272 Q A 0.0000
273 P A -0.2177
274 K A -1.1657
275 N A -1.2439
276 W A 0.2308
277 L A 0.5354
278 P A 0.4341
279 G A 0.0000
280 P A 0.3097
281 C A 0.0000
282 Y A -0.0715
283 R A -1.3619
284 Q A 0.0000
285 Q A -1.5191
286 R A -1.8553
287 V A -1.5851
288 S A 0.0000
289 K A -1.8182
290 T A -1.8473
291 K A -2.8146
292 T A -2.2644
293 D A -2.9359
294 N A -2.8689
295 N A -2.8260
296 N A -2.6945
297 S A -1.8116
298 N A -1.6302
299 F A -0.7299
300 T A -0.0750
301 W A 0.2923
302 T A -0.0809
303 G A -0.4927
304 A A -0.1670
305 S A -0.1049
306 K A 0.0113
307 Y A 0.4751
308 N A -0.9894
309 L A -0.0379
310 N A -1.5098
311 G A -1.5083
312 R A -2.0355
313 E A -1.5783
314 S A -0.4082
315 I A 0.2513
316 I A 0.2119
317 N A -0.7580
318 P A 0.0000
319 G A 0.1120
320 T A 0.1323
321 A A 0.2394
322 M A 0.0000
323 A A 0.0000
324 S A 0.0000
325 H A 0.0000
326 K A -3.2293
327 D A -3.9322
328 D A -3.8171
329 E A -3.4010
330 D A -3.7900
331 K A -2.4911
332 F A -1.9225
333 F A -1.0911
334 P A 0.0000
335 M A -0.5086
336 S A 0.0000
337 G A 0.0000
338 V A 0.0000
339 M A 0.0000
340 I A 1.3824
341 F A 0.2604
342 G A -1.1380
343 K A -2.2208
344 E A -2.3943
345 S A -1.7386
346 A A -1.6562
347 G A -1.2565
348 A A -0.6184
349 S A -0.9421
350 N A -1.3968
351 T A -1.0990
352 A A -0.7345
353 L A -0.8300
354 D A -1.7627
355 N A -1.6575
356 V A -0.6057
357 M A 0.0000
358 I A 0.4502
359 T A 0.0000
360 D A -1.3349
361 E A 0.0000
362 E A -2.5065
363 E A -1.8379
364 I A 0.0000
365 K A -1.7825
366 A A -1.1527
367 T A 0.0000
368 N A 0.0000
369 P A -0.5703
370 V A -0.8196
371 A A 0.0000
372 T A 0.0000
373 E A -2.2055
374 R A -2.3609
375 F A -0.9113
376 G A -0.8352
377 T A -0.2251
378 V A 1.0755
379 A A 1.1251
380 V A 1.7559
381 N A 0.6065
382 F A 1.0181
383 Q A -1.0940
384 S A -1.0494
385 S A -1.1713
386 S A -1.0428
387 T A -1.3347
388 D A -2.2405
389 P A -1.0719
390 A A -0.0273
391 T A 0.3446
392 G A -0.1638
393 D A -1.5883
394 V A -1.0937
395 H A -1.5867
396 A A -0.5429
397 M A -0.1228
398 G A -0.0890
399 A A 0.4104
400 L A 0.6103
401 P A 0.2009
402 G A 0.0836
403 M A 0.6108
404 V A 0.9354
405 W A 0.3288
406 Q A -0.3959
407 D A -0.4031
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 -0.4306
419 K A -1.1509
420 I A 0.0000
421 P A -1.5241
422 H A -2.0241
423 T A -1.8377
424 D A -2.4811
425 G A -1.6586
426 H A -1.0036
427 F A 1.0291
428 H A -0.1044
429 P A -0.2658
430 S A 0.0009
431 P A 0.3339
432 L A 1.0616
433 M A 0.4718
434 G A 0.0000
435 G A 0.0291
436 F A 0.0000
437 G A -0.7398
438 L A 0.0000
439 K A -2.4277
440 N A -2.1433
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 0.1697
451 P A 0.0171
452 V A 0.3943
453 P A 0.1024
454 A A -0.3018
455 N A -1.3291
456 P A -0.8672
457 P A -0.8232
458 A A -0.7370
459 E A -1.0065
460 F A 0.9071
461 S A 0.0974
462 A A 0.0713
463 T A -0.4587
464 K A -1.3633
465 F A -0.0886
466 A A -0.1216
467 S A -0.2684
468 F A 0.2636
469 I A 0.5809
470 T A 0.1292
471 Q A 0.0000
472 Y A 0.3064
473 S A 0.0000
474 T A 0.0101
475 G A 0.0000
476 Q A -0.3684
477 V A 0.0000
478 S A -0.6988
479 V A 0.0000
480 E A -1.3178
481 I A 0.0000
482 E A -1.1679
483 W A 0.0000
484 E A -1.3357
485 L A 0.0000
486 Q A -1.8817
487 K A -2.4197
488 E A -2.3954
489 N A -2.5796
490 S A -2.0870
491 K A -2.3544
492 R A -1.6232
493 W A -0.0670
494 N A -0.5529
495 P A -0.2979
496 E A 0.1337
497 V A 1.2870
498 Q A -0.0441
499 Y A -0.2605
500 T A -0.4295
501 S A -0.6747
502 N A -0.8842
503 Y A 0.2881
504 A A -0.4009
505 K A -1.6153
506 S A -1.0865
507 A A -0.7938
508 N A -1.0052
509 V A 0.4540
510 D A -0.4684
511 F A -0.1037
512 T A 0.5705
513 V A 0.3681
514 D A -1.1607
515 N A -2.1222
516 N A -1.8899
517 G A -0.9649
518 L A -0.2743
519 Y A -0.0677
520 T A -0.3158
521 E A -0.9089
522 P A -0.7714
523 R A -0.8315
524 P A -0.3520
525 I A 0.0000
526 G A -0.2425
527 T A 0.0000
528 R A 0.0000
529 Y A 0.3353
530 L A 0.0000
531 T A -0.4541
532 R A -1.3423
533 P A -0.6686
534 L A 0.1965
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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 -0.1242 4.3803 View CSV PDB
4.5 -0.1716 4.2628 View CSV PDB
5.0 -0.227 4.2262 View CSV PDB
5.5 -0.2828 4.2015 View CSV PDB
6.0 -0.3312 4.1762 View CSV PDB
6.5 -0.3664 4.1509 View CSV PDB
7.0 -0.388 4.1255 View CSV PDB
7.5 -0.4004 4.1004 View CSV PDB
8.0 -0.4065 4.0761 View CSV PDB
8.5 -0.4057 4.0539 View CSV PDB
9.0 -0.3954 4.0363 View CSV PDB