Project name: AAV2_1mer_M1

Status: done

Started: 2026-10-21 18:13:01
Settings
Chain sequence(s) GADGVGNSSGNWHCDSTWMGDRVITTSTRTWALPTYNNHLYKQISSQSGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTQNDGTTTIANNLTSTVQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMVPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLSRTNTPSGTTTQSRLQFSQAGASDIRDQSRNWLPGPCYRQQRVSKTSADNNNSEYSWTGATKYHLNGRDSLVNPGPAMASHKDDEEKFFPQSGVLIFGKQGSEKTNVDIEKVMITDEEEIRTTNPVATEQYGSVSTNLQRGNRQAATADVNTQGVLPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPSTTFSAAKFASFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYNKSVNVDFTVDTNGVYSEPRPIGTRYLTRNL 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                                          (00:00:04)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:04:15)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/c381d488a99fe4/tmp/folded.pdb                 (00:04:15)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:00)
Show buried residues

Minimal score value
-3.8541
Maximal score value
2.1593
Average score
-0.5839
Total score value
-303.0308

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 -0.7916
16 A A -0.6977
17 D A -1.1870
18 G A -0.5220
19 V A 0.6751
20 G A -0.4242
21 N A -1.4268
22 S A -1.2598
23 S A 0.0000
24 G A -1.2951
25 N A -1.2023
26 W A -0.3649
27 H A -1.2541
28 C A -1.0641
29 D A -1.8570
30 S A -0.8935
31 T A -0.2070
32 W A -0.2395
33 M A 0.1428
34 G A -1.0534
35 D A -2.1597
36 R A -1.3416
37 V A 0.0000
38 I A -0.4558
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 0.6421
45 W A 0.0000
46 A A 0.7495
47 L A 0.0000
48 P A 0.0860
49 T A -0.3071
50 Y A -0.3481
51 N A -0.9487
52 N A -1.2095
53 H A -0.5306
54 L A -0.3039
55 Y A -0.5120
56 K A -1.5123
57 Q A -1.0349
58 I A -0.2582
59 S A -0.4397
60 S A 0.0000
61 Q A -1.5769
62 S A -1.1159
63 G A -1.3112
64 A A -1.5454
65 S A -1.8310
66 N A -2.6168
67 D A -2.3387
68 N A -2.3926
69 H A -2.0685
70 Y A -0.2903
71 F A 0.0000
72 G A 0.0000
73 Y A 0.0000
74 S A -0.4295
75 T A 0.0000
76 P A 0.0000
77 W A 0.0000
78 G A 0.0000
79 Y A 0.0000
80 F A 0.0000
81 D A 0.0000
82 F A 0.0000
83 N A 0.0000
84 R A -0.7677
85 F A 0.0000
86 H A 0.0000
87 C A 0.0000
88 H A 0.0000
89 F A 0.0000
90 S A -1.0827
91 P A -1.3119
92 R A -2.5138
93 D A -2.0230
94 W A 0.0000
95 Q A -2.1243
96 R A -2.5027
97 L A 0.0000
98 I A 0.0000
99 N A -1.1423
100 N A -2.1317
101 N A 0.0000
102 W A -1.0576
103 G A 0.0000
104 F A 0.0000
105 R A -0.9262
106 P A 0.0000
107 K A -2.0225
108 R A -2.3819
109 L A 0.0000
110 N A -1.3063
111 F A 0.0000
112 K A -1.1390
113 L A 0.0000
114 F A 0.0000
115 N A -1.2873
116 I A 0.0000
117 Q A -1.1003
118 V A 0.0000
119 K A -0.5506
120 E A -0.1146
121 V A 0.0616
122 T A -0.8243
123 Q A -2.2151
124 N A -2.9061
125 D A -2.9346
126 G A -2.0867
127 T A -1.6959
128 T A -0.9398
129 T A -0.0656
130 I A 0.6771
131 A A -0.1281
132 N A -1.1602
133 N A -0.8294
134 L A 0.0596
135 T A -0.1824
136 S A 0.0000
137 T A 0.0000
138 V A 0.0000
139 Q A -0.4807
140 V A 0.0000
141 F A 0.0000
142 T A -0.3939
143 D A 0.0000
144 S A -1.3154
145 E A -2.2663
146 Y A -1.3261
147 Q A -1.4420
148 L A 0.0000
149 P A 0.4182
150 Y A 0.0499
151 V A 0.3282
152 L A 0.0000
153 G A -0.3604
154 S A -0.5020
155 A A -0.6945
156 H A -1.3106
157 Q A -1.6382
158 G A -0.6486
159 C A 0.0000
160 L A 0.0000
161 P A 0.0000
162 P A 0.1215
163 F A 1.0367
164 P A 0.4299
165 A A 0.3604
166 D A 0.5410
167 V A 1.8308
168 F A 1.3700
169 M A 1.4286
170 V A 0.0000
171 P A -0.2171
172 Q A -0.3098
173 Y A 0.0000
174 G A -0.0675
175 Y A 0.0000
176 L A 1.9485
177 T A 1.2426
178 L A 0.3372
179 N A -0.7084
180 N A -1.8621
181 G A -1.8713
182 S A -1.5372
183 Q A -1.4569
184 A A -1.1146
185 V A -0.9264
186 G A -1.1121
187 R A -1.6326
188 S A -0.2539
189 S A 0.7529
190 F A 1.8496
191 Y A 1.3421
192 C A 0.9583
193 L A 0.0000
194 E A -0.1376
195 Y A 1.0923
196 F A 0.3775
197 P A -0.1622
198 S A -0.4740
199 Q A -1.0659
200 M A -0.1967
201 L A 0.0000
202 R A -1.3098
203 T A -1.0501
204 G A -1.0101
205 N A -1.3579
206 N A -1.3973
207 F A 0.0000
208 T A -0.5348
209 F A -0.1519
210 S A -0.7514
211 Y A -0.7426
212 T A -1.4847
213 F A 0.0000
214 E A -2.0759
215 D A -2.1075
216 V A 0.0000
217 P A -0.4793
218 F A -0.0380
219 H A 0.0000
220 S A -0.0764
221 S A 0.0000
222 Y A -0.3912
223 A A -0.4429
224 H A -0.9286
225 S A -0.9405
226 Q A -1.0289
227 S A -0.9505
228 L A 0.0000
229 D A -1.4001
230 R A -1.9786
231 L A -0.5761
232 M A -0.4333
233 N A -0.6367
234 P A 0.1142
235 L A 1.6148
236 I A 1.5896
237 D A -0.5619
238 Q A 0.3224
239 Y A 1.4400
240 L A 1.6587
241 Y A 2.1593
242 Y A 1.1094
243 L A 1.3059
244 S A -0.0107
245 R A -1.6215
246 T A -1.2951
247 N A -2.2980
248 T A -1.6440
249 P A -1.0737
250 S A -0.8360
251 G A -0.7222
252 T A -0.4139
253 T A -0.5279
254 T A -1.1896
255 Q A -1.5833
256 S A -1.9080
257 R A -2.3198
258 L A -0.0110
259 Q A 0.0010
260 F A 2.1473
261 S A 0.8214
262 Q A 0.1166
263 A A 0.0000
264 G A -0.7481
265 A A -0.3395
266 S A -0.8883
267 D A -1.5473
268 I A -1.6681
269 R A -2.8715
270 D A -2.3066
271 Q A 0.0000
272 S A -0.7806
273 R A -1.4130
274 N A -0.9817
275 W A 0.4447
276 L A 0.9132
277 P A 0.6188
278 G A 0.0000
279 P A 0.3461
280 C A 0.0000
281 Y A -0.5538
282 R A -1.2727
283 Q A 0.0000
284 Q A -1.3952
285 R A -1.6409
286 V A 0.0000
287 S A 0.0000
288 K A -1.7562
289 T A -1.0984
290 S A -1.1904
291 A A -1.3211
292 D A -2.1912
293 N A -2.3293
294 N A -2.6893
295 N A -2.6041
296 S A -2.1091
297 E A -2.2564
298 Y A -1.1457
299 S A -0.4595
300 W A 0.1658
301 T A -0.2330
302 G A -0.6107
303 A A -0.2310
304 T A -0.2110
305 K A 0.1620
306 Y A 0.9050
307 H A -0.5202
308 L A 0.1298
309 N A -1.4516
310 G A -1.5934
311 R A -2.0060
312 D A -1.3125
313 S A -0.2558
314 L A 0.3239
315 V A 0.0000
316 N A -0.8815
317 P A 0.0000
318 G A 0.0000
319 P A 0.0031
320 A A 0.0355
321 M A 0.0000
322 A A 0.0000
323 S A 0.0000
324 H A 0.0000
325 K A -3.1718
326 D A -3.8541
327 D A -3.7746
328 E A -3.3749
329 E A -3.7695
330 K A -2.5937
331 F A -2.1065
332 F A 0.0000
333 P A 0.0000
334 Q A -0.8982
335 S A 0.0000
336 G A 0.0000
337 V A 0.0000
338 L A 0.5896
339 I A 1.4284
340 F A 0.1992
341 G A -1.6908
342 K A -2.5603
343 Q A -2.2409
344 G A -2.1003
345 S A -2.8848
346 E A -3.5567
347 K A -2.9159
348 T A -2.1016
349 N A -2.1547
350 V A -2.1968
351 D A -2.4060
352 I A -1.0555
353 E A -2.4439
354 K A -2.8000
355 V A -1.1604
356 M A 0.0000
357 I A 0.3951
358 T A 0.0000
359 D A -1.0135
360 E A 0.0000
361 E A -2.1580
362 E A -1.2763
363 I A 0.0000
364 R A -1.7106
365 T A -0.9448
366 T A 0.0000
367 N A 0.0000
368 P A 0.0000
369 V A 0.0000
370 A A 0.0000
371 T A -1.2555
372 E A -1.5295
373 Q A -1.6944
374 Y A -0.7869
375 G A -0.7122
376 S A -0.4299
377 V A 0.8196
378 S A 0.1945
379 T A -0.0823
380 N A -0.4533
381 L A -0.0427
382 Q A -2.3998
383 R A -3.2284
384 G A -2.6459
385 N A -2.8596
386 R A -2.8355
387 Q A -2.5215
388 A A -1.2742
389 A A -0.3639
390 T A -0.1769
391 A A -0.7222
392 D A -1.8713
393 V A -1.0816
394 N A -1.5429
395 T A -0.9189
396 Q A -0.3161
397 G A 0.0864
398 V A 1.2754
399 L A 1.0112
400 P A 0.4806
401 G A 0.3316
402 M A 0.0000
403 V A 1.1038
404 W A 0.2647
405 Q A -0.4059
406 D A -0.4669
407 R A 0.0000
408 D A 0.0000
409 V A 0.0000
410 Y A 0.0000
411 L A 0.0000
412 Q A 0.0000
413 G A 0.0000
414 P A -0.3575
415 I A 0.0000
416 W A 0.0000
417 A A -0.4762
418 K A -1.3168
419 I A 0.0000
420 P A -1.5345
421 H A -2.0083
422 T A -1.7916
423 D A -2.4453
424 G A -1.5211
425 H A -0.8580
426 F A 1.1929
427 H A -0.0187
428 P A -0.2002
429 S A 0.0897
430 P A 0.2995
431 L A 0.9988
432 M A 0.4272
433 G A 0.0000
434 G A -0.0033
435 F A 0.0000
436 G A -0.7517
437 L A 0.0000
438 K A -2.4218
439 H A -2.1379
440 P A 0.0000
441 P A 0.0000
442 P A 0.0000
443 Q A 0.0000
444 I A 0.0000
445 L A 0.0000
446 I A 0.0000
447 K A 0.0000
448 N A 0.0000
449 T A 0.1318
450 P A 0.1699
451 V A 0.4828
452 P A 0.2888
453 A A -0.1372
454 N A -1.3125
455 P A -0.5466
456 S A -0.2901
457 T A 0.0047
458 T A 0.6731
459 F A 1.7279
460 S A 0.5856
461 A A 0.1885
462 A A -0.2012
463 K A -1.0164
464 F A 0.5708
465 A A 0.1676
466 S A -0.0317
467 F A 0.5208
468 I A 0.7381
469 T A 0.2175
470 Q A 0.0000
471 Y A 0.2417
472 S A 0.0000
473 T A 0.1127
474 G A 0.0000
475 Q A -0.3407
476 V A 0.0000
477 S A -0.7293
478 V A 0.0000
479 E A -1.4255
480 I A 0.0000
481 E A -1.2063
482 W A 0.0000
483 E A -1.3875
484 L A 0.0000
485 Q A -2.0690
486 K A -2.8269
487 E A -2.5722
488 N A -2.7813
489 S A -2.5085
490 K A -2.5786
491 R A -2.1384
492 W A -0.2210
493 N A -0.8343
494 P A -0.3388
495 E A 0.1903
496 I A 1.5626
497 Q A 0.1245
498 Y A 0.0000
499 T A -0.2591
500 S A -0.7753
501 N A -1.2733
502 Y A -0.3772
503 N A -1.9210
504 K A -1.8848
505 S A -0.5344
506 V A 0.9631
507 N A 0.0539
508 V A 0.9359
509 D A 0.0670
510 F A 0.1441
511 T A 0.7278
512 V A 0.7442
513 D A -0.3129
514 T A -0.9202
515 N A -1.2808
516 G A -0.6066
517 V A 0.1775
518 Y A 0.4345
519 S A -0.1951
520 E A -0.7244
521 P A -0.7975
522 R A -0.8481
523 P A -0.3646
524 I A 0.0000
525 G A -0.2165
526 T A 0.0000
527 R A 0.0000
528 Y A 0.4902
529 L A 0.0000
530 T A -0.7766
531 R A -1.9856
532 N A -1.4113
533 L A 0.0350
Download PDB file
View in 3Dmol

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 -0.3167 4.3227 View CSV PDB
4.5 -0.3607 4.1429 View CSV PDB
5.0 -0.412 4.0291 View CSV PDB
5.5 -0.4626 4.0291 View CSV PDB
6.0 -0.5043 4.0291 View CSV PDB
6.5 -0.5318 4.0291 View CSV PDB
7.0 -0.5465 4.0291 View CSV PDB
7.5 -0.554 4.0291 View CSV PDB
8.0 -0.5569 4.029 View CSV PDB
8.5 -0.5542 4.0289 View CSV PDB
9.0 -0.544 4.0285 View CSV PDB