Project name: AAV2_1mer_M3

Status: done

Started: 2026-10-21 18:13:38
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.  (00:00:04)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:04)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:04:01)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/4f80092aeb0dd6/tmp/folded.pdb                 (00:04:01)
[INFO]       Main:     Simulation completed successfully.                                          (00:11:46)
Show buried residues

Minimal score value
-3.9699
Maximal score value
2.1935
Average score
-0.6222
Total score value
-322.9018

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 -0.9020
16 A A -0.9029
17 D A -1.5279
18 G A -0.6492
19 V A 0.8153
20 G A -0.5726
21 N A -1.5492
22 S A -1.2964
23 S A -1.3846
24 G A -1.3301
25 N A -1.1769
26 W A -0.2615
27 H A -1.1310
28 C A -0.8697
29 D A -1.7933
30 S A -0.8044
31 T A -0.1048
32 W A -0.1377
33 M A 0.3036
34 G A -1.1273
35 D A -2.4184
36 R A -1.3097
37 V A 0.0000
38 I A -0.2323
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 0.4658
45 W A 0.0000
46 A A 0.7520
47 L A 0.0000
48 P A 0.0745
49 T A -0.3143
50 Y A -0.3655
51 N A -1.0130
52 N A -1.2312
53 H A -0.5570
54 L A -0.3428
55 Y A -0.5765
56 K A -1.6546
57 Q A -1.0869
58 I A -0.2847
59 S A -0.4707
60 S A 0.0000
61 Q A -1.5939
62 S A -1.1232
63 G A -1.3158
64 A A -1.5761
65 S A -1.8678
66 N A -2.6600
67 D A -2.4110
68 N A -2.4430
69 H A -2.1195
70 Y A -0.3698
71 F A 0.0000
72 G A 0.0000
73 Y A 0.1527
74 S A -0.4290
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 -0.7644
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 -1.1014
91 P A -1.4085
92 R A -2.5062
93 D A -1.9515
94 W A 0.0000
95 Q A -2.2157
96 R A -2.5228
97 L A 0.0000
98 I A 0.0000
99 N A -1.4538
100 N A -2.3694
101 N A 0.0000
102 W A -1.1269
103 G A 0.0000
104 F A 0.0000
105 R A -0.8782
106 P A 0.0000
107 K A -1.8086
108 R A -2.0405
109 L A 0.0000
110 N A -1.2781
111 F A 0.0000
112 K A -1.1266
113 L A 0.0000
114 F A 0.0000
115 N A -1.2793
116 I A 0.0000
117 Q A -1.0801
118 V A 0.0000
119 K A -0.4871
120 E A -0.1079
121 V A 0.0537
122 T A -0.8237
123 Q A -2.2129
124 N A -2.9029
125 D A -2.9321
126 G A -2.0818
127 T A -1.6910
128 T A -0.9328
129 T A -0.0527
130 I A 0.7014
131 A A -0.1045
132 N A -1.1516
133 N A -0.7428
134 L A 0.1811
135 T A -0.2701
136 S A 0.0000
137 T A 0.0000
138 V A 0.0000
139 Q A -0.4277
140 V A 0.0000
141 F A 0.0000
142 T A -0.4160
143 D A 0.0000
144 S A -1.2987
145 E A -2.2347
146 Y A -1.3205
147 Q A -1.3294
148 L A 0.0000
149 P A 0.4269
150 Y A 0.0962
151 V A 0.3477
152 L A 0.0000
153 G A -0.3276
154 S A -0.5014
155 A A -0.7016
156 H A -1.3310
157 Q A -1.6357
158 G A -0.6298
159 C A -0.4288
160 L A 0.0000
161 P A -0.0800
162 P A -0.2529
163 F A 0.3096
164 P A -0.0624
165 A A -0.2559
166 D A -0.6004
167 V A 1.2906
168 F A 1.1140
169 M A 1.4275
170 V A 0.0000
171 P A -0.2282
172 Q A -0.3542
173 Y A 0.0000
174 G A -0.0563
175 Y A 0.0000
176 L A 1.9466
177 T A 1.2123
178 L A 0.2695
179 N A -0.7506
180 N A -1.8826
181 G A -1.9052
182 S A -1.5796
183 Q A -1.4862
184 A A -1.0156
185 V A -0.9154
186 G A -1.1092
187 R A -1.6512
188 S A -0.2895
189 S A 0.6891
190 F A 1.7562
191 Y A 1.2464
192 C A 0.9559
193 L A 0.0000
194 E A -0.1126
195 Y A 1.0659
196 F A 0.4117
197 P A -0.2022
198 S A -0.4818
199 Q A -1.0879
200 M A -0.0737
201 L A 0.0000
202 R A -1.4947
203 T A -1.1003
204 G A -1.3801
205 N A -1.7927
206 N A -1.3983
207 F A 0.0000
208 T A -0.5445
209 F A -0.1717
210 S A -0.7089
211 Y A -0.6629
212 T A -1.3491
213 F A 0.0000
214 E A -2.0333
215 D A -2.1031
216 V A 0.0000
217 P A -0.4686
218 F A -0.0727
219 H A -0.1323
220 S A -0.1043
221 S A 0.0000
222 Y A -0.3777
223 A A -0.4420
224 H A -0.9186
225 S A -0.9710
226 Q A -1.1401
227 S A -1.0582
228 L A 0.0000
229 D A -1.5155
230 R A -2.1494
231 L A -0.9486
232 M A -0.5634
233 N A -0.6616
234 P A 0.0918
235 L A 1.6439
236 I A 1.6219
237 D A -0.5107
238 Q A 0.3739
239 Y A 1.4769
240 L A 1.6959
241 Y A 2.1842
242 Y A 1.1084
243 L A 1.3124
244 S A -0.0350
245 R A -1.5468
246 T A -1.2683
247 N A -2.3074
248 T A -1.6987
249 P A -1.1523
250 S A -0.9348
251 G A -0.7662
252 T A -0.4108
253 T A -0.6124
254 T A -1.3482
255 Q A -1.9527
256 S A -2.0413
257 R A -2.3424
258 L A 0.0190
259 Q A 0.0953
260 F A 2.1935
261 S A 0.8609
262 Q A 0.1919
263 A A 0.0000
264 G A 0.0000
265 A A -0.3388
266 S A -0.9045
267 D A -1.5999
268 I A -1.7380
269 R A -2.9490
270 D A -2.4694
271 Q A 0.0000
272 S A -0.7916
273 R A -1.4891
274 N A -1.1853
275 W A 0.0709
276 L A 0.7187
277 P A 0.5535
278 G A 0.0000
279 P A 0.3725
280 C A 0.0000
281 Y A -0.5651
282 R A -1.3075
283 Q A 0.0000
284 Q A -1.3787
285 R A -1.8873
286 V A 0.0000
287 S A 0.0000
288 K A -1.8382
289 T A -1.1169
290 S A -1.1962
291 A A -1.2735
292 D A -2.0776
293 N A -2.3443
294 N A -2.6723
295 N A -2.5897
296 S A -2.1075
297 E A -2.2412
298 Y A -1.0943
299 S A -0.5027
300 W A 0.1935
301 T A -0.2108
302 G A -0.5759
303 A A -0.2096
304 T A -0.1776
305 K A 0.1440
306 Y A 0.8962
307 H A -0.5214
308 L A 0.1312
309 N A -1.4458
310 G A -1.5843
311 R A -1.9997
312 D A -1.3145
313 S A -0.2689
314 L A 0.3284
315 V A 0.0000
316 N A -0.8901
317 P A 0.0000
318 G A 0.0000
319 P A -0.0017
320 A A 0.1175
321 M A 0.0000
322 A A 0.0000
323 S A 0.0000
324 H A 0.0000
325 K A -3.2662
326 D A -3.8716
327 D A -3.7632
328 E A -3.3315
329 E A -3.7747
330 K A -2.6054
331 F A -2.1861
332 F A 0.0000
333 P A 0.0000
334 Q A -0.9254
335 S A 0.0000
336 G A 0.0000
337 V A 0.0000
338 L A 0.6064
339 I A 1.3410
340 F A 0.1979
341 G A -1.7292
342 K A -2.6206
343 Q A -2.2731
344 G A -2.1084
345 S A -2.9159
346 E A -3.5664
347 K A -2.9117
348 T A -2.0913
349 N A -2.1616
350 V A -2.2192
351 D A -2.4727
352 I A -1.3149
353 E A -2.5410
354 K A -2.8946
355 V A -1.2065
356 M A 0.0000
357 I A 0.3833
358 T A 0.0000
359 D A -1.0438
360 E A 0.0000
361 E A -2.1923
362 E A -1.3485
363 I A 0.0000
364 R A -1.7151
365 T A -0.9512
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 -1.4115
372 E A -1.7811
373 Q A -1.7518
374 Y A -0.7986
375 G A -0.6808
376 S A -0.2894
377 V A 1.0478
378 S A 0.2308
379 T A -0.1701
380 N A -0.8773
381 L A -0.3573
382 Q A -2.8000
383 R A -3.4407
384 G A -2.8570
385 N A -3.3399
386 R A -3.9699
387 Q A -3.0859
388 A A -1.5927
389 A A -0.5756
390 T A -0.1442
391 A A -0.6606
392 D A -1.8208
393 V A -1.0298
394 N A -1.5548
395 T A -0.8971
396 Q A -0.2930
397 G A 0.1084
398 V A 1.2957
399 L A 0.9714
400 P A 0.3502
401 G A 0.0247
402 M A 0.0000
403 V A 1.0904
404 W A 0.3352
405 Q A -0.3886
406 D A -0.4937
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 -0.3646
415 I A 0.0000
416 W A 0.0000
417 A A -0.4144
418 K A -1.1604
419 I A -1.3051
420 P A -1.4577
421 H A -1.9908
422 T A -1.7784
423 D A -2.4583
424 G A -1.5483
425 H A -0.8883
426 F A 1.1651
427 H A -0.0426
428 P A -0.1836
429 S A 0.1395
430 P A 0.3312
431 L A 0.9774
432 M A 0.4177
433 G A 0.0000
434 G A -0.0359
435 F A 0.0000
436 G A -0.7114
437 L A 0.0000
438 K A -2.5271
439 H A -2.1919
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 0.1567
450 P A 0.1304
451 V A 0.4374
452 P A 0.1937
453 A A -0.2033
454 N A -1.3151
455 P A -0.5986
456 S A -0.2869
457 T A 0.0124
458 T A 0.6737
459 F A 1.7303
460 S A 0.5488
461 A A 0.1482
462 A A -0.2744
463 K A -1.1643
464 F A 0.2632
465 A A 0.0086
466 S A -0.1527
467 F A 0.3950
468 I A 0.7034
469 T A 0.1973
470 Q A 0.0000
471 Y A 0.3787
472 S A 0.0000
473 T A 0.1227
474 G A 0.0000
475 Q A -0.2906
476 V A 0.0000
477 S A -0.6790
478 V A 0.0000
479 E A -1.2704
480 I A 0.0000
481 E A -1.0184
482 W A 0.0000
483 E A -1.3944
484 L A 0.0000
485 Q A -2.2067
486 K A -3.2641
487 E A -2.6214
488 N A -2.7550
489 S A -2.3023
490 K A -2.4350
491 R A -1.9127
492 W A -0.1533
493 N A -0.8189
494 P A -0.3870
495 E A 0.0913
496 I A 1.2670
497 Q A -0.5202
498 Y A 0.0000
499 T A -0.4526
500 S A -0.9079
501 N A -1.2938
502 Y A -0.3723
503 N A -1.9274
504 K A -1.7996
505 S A -0.3428
506 V A 1.2452
507 N A 0.5662
508 V A 1.1019
509 D A 0.0020
510 F A 0.0000
511 T A 0.5208
512 V A 0.4720
513 D A -0.4086
514 T A -0.9296
515 N A -1.3461
516 G A -0.8043
517 V A -0.0493
518 Y A -0.0209
519 S A -0.4355
520 E A -0.9292
521 P A -0.8945
522 R A -0.8901
523 P A -0.3622
524 I A 0.0000
525 G A -0.2095
526 T A 0.0000
527 R A 0.0000
528 Y A 0.2717
529 L A 0.0000
530 T A -0.5294
531 R A -1.7623
532 N A -1.3911
533 L A -0.0491
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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 -0.3638 4.342 View CSV PDB
4.5 -0.4102 4.1642 View CSV PDB
5.0 -0.4638 4.0173 View CSV PDB
5.5 -0.5162 4.0173 View CSV PDB
6.0 -0.5591 4.0173 View CSV PDB
6.5 -0.5873 4.0173 View CSV PDB
7.0 -0.6027 4.0173 View CSV PDB
7.5 -0.6106 4.0173 View CSV PDB
8.0 -0.6136 4.0173 View CSV PDB
8.5 -0.6104 4.0173 View CSV PDB
9.0 -0.5988 4.0173 View CSV PDB