Project name: AAV3_1mer_M2

Status: done

Started: 2026-10-21 19:06:03
Settings
Chain sequence(s) ADGVGNSSGNWHCDSQWLGDRVITTSTRTWALPTYNNHLYKQISSQSGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKKLSFKLFNIQVKEVTQNDGTTTIANNLTSTVQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMVPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFQFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLNRTQGTTSGTTNQSRLLFSQAGPQSMSLQARNWLPGPCYRQQRLSKTANDNNNSNFPWTAASKYHLNGRDSLVNPGPAMASHKDDEEKFFPMHGNLIFGKEGTTASNAELDNVMITDEEEIRTTNPVATEQYGTVANNLQSSNTAPTTRTVNDQGALPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQIMIKNTPVPANPPTTFSPAKFASFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYNKSVNVDFTVDTNGVYSEPRPIGTRYLTRNL 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                                          (00:00:03)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:04:11)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/3709b4a4d4ede8/tmp/folded.pdb                 (00:04:11)
[INFO]       Main:     Simulation completed successfully.                                          (00:13:02)
Show buried residues

Minimal score value
-3.8216
Maximal score value
2.5238
Average score
-0.5558
Total score value
-288.4737

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
16 A A -1.0108
17 D A -1.6113
18 G A -0.8581
19 V A 0.6225
20 G A -0.5761
21 N A -1.5758
22 S A -1.4273
23 S A 0.0000
24 G A -1.3565
25 N A -1.2064
26 W A -0.2869
27 H A -1.0566
28 C A -0.7347
29 D A -1.3972
30 S A -0.9074
31 Q A -0.8197
32 W A -0.5065
33 L A -0.2637
34 G A -1.5031
35 D A -2.6782
36 R A -1.9212
37 V A 0.0000
38 I A -0.6958
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 0.5972
45 W A 0.0000
46 A A 0.6985
47 L A 0.0000
48 P A 0.0653
49 T A -0.2896
50 Y A -0.3265
51 N A -0.9347
52 N A -1.1941
53 H A -0.4846
54 L A -0.2496
55 Y A -0.4429
56 K A -1.5004
57 Q A -1.0271
58 I A -0.2451
59 S A -0.4411
60 S A 0.0000
61 Q A -1.5469
62 S A -1.1084
63 G A -1.2945
64 A A -1.5854
65 S A -1.9657
66 N A -2.8246
67 D A -2.8584
68 N A -2.5838
69 H A -2.1578
70 Y A -0.3300
71 F A 0.0000
72 G A 0.0000
73 Y A 0.2105
74 S A -0.3669
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 -0.5318
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 -0.9240
91 P A -1.3448
92 R A -2.4142
93 D A 0.0000
94 W A 0.0000
95 Q A -2.1243
96 R A -2.4579
97 L A 0.0000
98 I A 0.0000
99 N A -1.3856
100 N A -2.3630
101 N A 0.0000
102 W A 0.0000
103 G A 0.0000
104 F A 0.0000
105 R A -0.9369
106 P A 0.0000
107 K A -1.9362
108 K A -2.1332
109 L A 0.0000
110 S A -1.0631
111 F A 0.0000
112 K A -1.4528
113 L A 0.0000
114 F A 0.0000
115 N A -1.2307
116 I A 0.0000
117 Q A -1.1545
118 V A 0.0000
119 K A -0.4774
120 E A -0.0409
121 V A 0.0588
122 T A -0.6397
123 Q A -2.2169
124 N A -2.8975
125 D A -2.9310
126 G A -2.0947
127 T A -1.6892
128 T A -0.9144
129 T A -0.0217
130 I A 0.7844
131 A A -0.0351
132 N A -1.0976
133 N A -0.6023
134 L A 0.3469
135 T A -0.2405
136 S A 0.0000
137 T A -0.3711
138 V A 0.0000
139 Q A -0.4228
140 V A 0.0000
141 F A 0.0000
142 T A -0.5363
143 D A 0.0000
144 S A -1.3226
145 E A -2.3082
146 Y A -1.5363
147 Q A -1.5919
148 L A 0.0000
149 P A 0.3585
150 Y A 0.0534
151 V A 0.3570
152 L A 0.0000
153 G A -0.3079
154 S A -0.4947
155 A A -0.6972
156 H A -1.2479
157 Q A -1.5650
158 G A -0.6441
159 C A -0.4301
160 L A 0.0000
161 P A 0.0000
162 P A 0.1740
163 F A 1.0888
164 P A 0.4476
165 A A 0.3892
166 D A 0.5326
167 V A 1.7475
168 F A 0.0000
169 M A 1.3430
170 V A 0.0000
171 P A -0.2519
172 Q A -0.3461
173 Y A 0.0000
174 G A -0.0427
175 Y A 0.0000
176 L A 1.9721
177 T A 1.2876
178 L A 0.4439
179 N A -0.6377
180 N A -1.8046
181 G A -1.9162
182 S A -1.5275
183 Q A -1.4234
184 A A -1.0407
185 V A -0.7719
186 G A -1.0352
187 R A -1.5934
188 S A -0.2242
189 S A 0.7104
190 F A 1.7248
191 Y A 1.3137
192 C A 1.0104
193 L A 0.0000
194 E A -0.1043
195 Y A 1.1038
196 F A 0.3358
197 P A -0.1727
198 S A -0.4606
199 Q A -1.0336
200 M A -0.0474
201 L A 0.0000
202 R A -1.2897
203 T A -1.0813
204 G A 0.0000
205 N A -1.3282
206 N A -1.7335
207 F A 0.0000
208 Q A -1.5681
209 F A -0.5589
210 S A -0.7714
211 Y A -0.5545
212 T A -1.2996
213 F A 0.0000
214 E A -2.0798
215 D A -2.1891
216 V A 0.0000
217 P A -0.5308
218 F A -0.0807
219 H A -0.1293
220 S A -0.1123
221 S A 0.0000
222 Y A -0.3156
223 A A 0.0000
224 H A -0.9311
225 S A -0.9859
226 Q A -1.2024
227 S A -1.2669
228 L A 0.0000
229 D A -2.0763
230 R A -2.1889
231 L A -0.5485
232 M A -0.3245
233 N A -0.1200
234 P A 0.1176
235 L A 1.7511
236 I A 1.7094
237 D A -0.5970
238 Q A 0.2390
239 Y A 1.4932
240 L A 1.6890
241 Y A 2.5238
242 Y A 1.7479
243 L A 1.8162
244 N A 0.2500
245 R A -1.0080
246 T A -1.1632
247 Q A -2.5802
248 G A 0.0000
249 T A -1.2911
250 T A -0.9819
251 S A -0.6702
252 G A -0.7962
253 T A -0.8850
254 T A -1.2868
255 N A -2.5982
256 Q A -2.6026
257 S A -2.2119
258 R A -2.0597
259 L A 0.5173
260 L A 1.0252
261 F A 2.3941
262 S A 1.3072
263 Q A 0.4984
264 A A 0.0000
265 G A 0.0000
266 P A -0.4770
267 Q A -1.3677
268 S A 0.0000
269 M A -0.6303
270 S A -0.3096
271 L A 0.9417
272 Q A 0.0000
273 A A 0.0911
274 R A -1.0924
275 N A -1.1995
276 W A 0.3009
277 L A 0.7346
278 P A 0.4941
279 G A 0.0000
280 P A -0.2183
281 C A 0.0000
282 Y A -1.2036
283 R A -1.7284
284 Q A 0.0000
285 Q A -1.1568
286 R A -1.4973
287 L A -1.3003
288 S A 0.0000
289 K A -1.8687
290 T A -1.3645
291 A A -1.5637
292 N A -2.5514
293 D A -2.7302
294 N A -2.6565
295 N A -2.7972
296 N A -2.6708
297 S A -1.8345
298 N A -1.5928
299 F A -0.5770
300 P A 0.0803
301 W A 0.6954
302 T A 0.2029
303 A A -0.1031
304 A A 0.0766
305 S A -0.2329
306 K A -0.1502
307 Y A 0.4214
308 H A -0.8005
309 L A -0.0041
310 N A -1.4872
311 G A -1.6465
312 R A -2.2004
313 D A -1.5495
314 S A -0.5813
315 L A -0.0076
316 V A 0.0000
317 N A -0.8884
318 P A 0.0000
319 G A 0.0000
320 P A -0.0334
321 A A 0.0213
322 M A 0.0000
323 A A 0.0000
324 S A 0.0000
325 H A 0.0000
326 K A -3.1193
327 D A -3.8127
328 D A -3.7644
329 E A -3.3223
330 E A -3.8216
331 K A -2.5604
332 F A 0.0000
333 F A 0.0000
334 P A 0.0000
335 M A 0.0000
336 H A -0.4959
337 G A 0.0000
338 N A 0.0000
339 L A 0.6134
340 I A 1.4564
341 F A 0.2899
342 G A -1.1774
343 K A -2.4167
344 E A -2.4766
345 G A -1.6190
346 T A -1.8927
347 T A -1.1570
348 A A -0.4628
349 S A -1.0365
350 N A -1.7157
351 A A -1.8641
352 E A -2.3947
353 L A -1.2399
354 D A -2.3452
355 N A -2.2394
356 V A -0.8970
357 M A 0.0000
358 I A 0.4290
359 T A 0.0000
360 D A -1.4064
361 E A 0.0000
362 E A -2.3358
363 E A -1.5816
364 I A 0.0000
365 R A -1.6193
366 T A -1.0994
367 T A 0.0000
368 N A 0.0000
369 P A 0.0000
370 V A 0.0000
371 A A 0.0000
372 T A -1.2008
373 E A -1.3598
374 Q A -1.5652
375 Y A -0.8836
376 G A -0.7114
377 T A -0.4743
378 V A 0.1043
379 A A -0.6027
380 N A -1.6782
381 N A -0.9388
382 L A 0.3246
383 Q A -1.2038
384 S A -1.0409
385 S A -1.1877
386 N A -1.6726
387 T A -1.0224
388 A A -0.6952
389 P A -0.8962
390 T A -0.9122
391 T A -1.2036
392 R A -1.9000
393 T A -1.2949
394 V A 0.0000
395 N A -2.1260
396 D A -2.4338
397 Q A -1.3713
398 G A -0.7312
399 A A 0.3845
400 L A 0.7073
401 P A 0.3399
402 G A 0.2165
403 M A 0.0000
404 V A 1.0184
405 W A 0.3504
406 Q A -0.3855
407 D A -0.5102
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 -0.3661
416 I A 0.0000
417 W A 0.0000
418 A A -0.2699
419 K A -0.8208
420 I A -0.9481
421 P A -1.2699
422 H A -1.8193
423 T A -1.7448
424 D A -2.4236
425 G A -1.4587
426 H A -0.7108
427 F A 1.1157
428 H A -0.0818
429 P A -0.1325
430 S A 0.0154
431 P A 0.2417
432 L A 0.8547
433 M A 0.0000
434 G A 0.0000
435 G A -0.0702
436 F A 0.0000
437 G A -0.5596
438 L A 0.0000
439 K A -1.6330
440 H A -1.6353
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 M A 0.0000
447 I A 0.0000
448 K A 0.0000
449 N A 0.0000
450 T A 0.1965
451 P A 0.1485
452 V A 0.5262
453 P A 0.1960
454 A A -0.2407
455 N A -1.3224
456 P A -0.6125
457 P A -0.3335
458 T A -0.0053
459 T A 0.6738
460 F A 1.6651
461 S A 0.4003
462 P A -0.1635
463 A A -0.4513
464 K A -1.2983
465 F A 0.1097
466 A A -0.0563
467 S A -0.2101
468 F A 0.3222
469 I A 0.5942
470 T A 0.1548
471 Q A 0.0000
472 Y A 0.3450
473 S A 0.0000
474 T A 0.0471
475 G A 0.0000
476 Q A -0.3724
477 V A 0.0000
478 S A 0.0000
479 V A 0.0000
480 E A -1.3705
481 I A 0.0000
482 E A -1.3000
483 W A 0.0000
484 E A -1.6564
485 L A 0.0000
486 Q A -2.3061
487 K A -3.3187
488 E A -2.6064
489 N A -2.7189
490 S A -2.2318
491 K A -2.3572
492 R A -1.7607
493 W A -0.1225
494 N A -0.8631
495 P A -0.3419
496 E A 0.1761
497 I A 1.3887
498 Q A -0.3016
499 Y A -0.4401
500 T A -0.3535
501 S A -0.8471
502 N A -1.2863
503 Y A -0.3813
504 N A -1.9251
505 K A -1.8814
506 S A -0.5359
507 V A 0.9615
508 N A 0.0413
509 V A 0.9223
510 D A 0.0148
511 F A 0.1022
512 T A 0.7309
513 V A 0.7945
514 D A -0.2640
515 T A -0.8856
516 N A -1.2198
517 G A -0.5184
518 V A 0.3088
519 Y A 0.4162
520 S A -0.3447
521 E A -0.8945
522 P A -0.9071
523 R A -0.8703
524 P A -0.3995
525 I A 0.0000
526 G A -0.2480
527 T A 0.0000
528 R A 0.0000
529 Y A 0.2806
530 L A 0.0000
531 T A -0.5131
532 R A -1.7023
533 N A -1.3130
534 L A -0.0110
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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 -0.1813 4.8866 View CSV PDB
4.5 -0.2225 4.8866 View CSV PDB
5.0 -0.2704 4.8866 View CSV PDB
5.5 -0.3172 4.8866 View CSV PDB
6.0 -0.3555 4.8866 View CSV PDB
6.5 -0.3809 4.8866 View CSV PDB
7.0 -0.3949 4.8866 View CSV PDB
7.5 -0.4025 4.8866 View CSV PDB
8.0 -0.406 4.8866 View CSV PDB
8.5 -0.4045 4.8866 View CSV PDB
9.0 -0.3958 4.8866 View CSV PDB