Project name: AAV1_1mer_M3

Status: done

Started: 2026-10-21 17:41:34
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.  (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:08)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/32a6838c97427f/tmp/folded.pdb                 (00:02:08)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:26)
Show buried residues

Minimal score value
-4.0528
Maximal score value
2.2809
Average score
-0.5291
Total score value
-274.0566

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 -2.4743
18 G A -1.3167
19 V A 0.3138
20 G A -0.6664
21 N A -1.7187
22 A A -1.2752
23 S A -1.3509
24 G A -1.1462
25 N A -1.0937
26 W A -0.2343
27 H A -1.1653
28 C A -0.9107
29 D A -1.7746
30 S A -0.8440
31 T A -0.1864
32 W A 0.0315
33 L A 0.2360
34 G A -1.1053
35 D A -2.2319
36 R A -1.1535
37 V A 0.0000
38 I A -0.2375
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 0.4391
45 W A 0.0000
46 A A 0.6925
47 L A 0.0000
48 P A 0.0851
49 T A -0.2187
50 Y A -0.2024
51 N A -0.6780
52 N A -0.9553
53 H A -0.2602
54 L A 0.2565
55 Y A -0.1471
56 K A -1.2082
57 Q A -0.8549
58 I A 0.2092
59 S A 0.0060
60 S A 0.0000
61 A A -0.2922
62 S A -0.2804
63 T A -0.5832
64 G A -0.9194
65 A A -1.2531
66 S A -1.7645
67 N A -2.7653
68 D A -2.8810
69 N A -2.4615
70 H A -1.9515
71 Y A -0.1746
72 F A 0.4236
73 G A 0.0000
74 Y A 0.2851
75 S A -0.2071
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 -0.5389
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 -1.0689
92 P A -1.3562
93 R A -2.3230
94 D A -1.6064
95 W A 0.0000
96 Q A -1.6433
97 R A -1.9904
98 L A 0.0000
99 I A 0.0000
100 N A -0.8066
101 N A -1.7144
102 N A 0.0000
103 W A -0.9306
104 G A 0.0000
105 F A 0.0000
106 R A -0.7939
107 P A 0.0000
108 K A -1.7454
109 R A -1.7548
110 L A 0.0000
111 N A -0.9837
112 F A 0.0000
113 K A -0.9555
114 L A 0.0000
115 F A 0.0000
116 N A -1.0803
117 I A 0.0000
118 Q A -1.0792
119 V A 0.0000
120 K A -0.4872
121 E A -0.0910
122 V A 0.4682
123 T A 0.2057
124 T A -0.5086
125 N A -1.7856
126 D A -2.1007
127 G A -0.9325
128 V A 0.4965
129 T A 0.3953
130 T A 0.6662
131 I A 0.9368
132 A A -0.0274
133 N A -1.0872
134 N A -0.5942
135 L A 0.2935
136 T A -0.0258
137 S A 0.0000
138 T A 0.0000
139 V A 0.0000
140 Q A -0.4990
141 V A 0.0000
142 F A 0.0000
143 S A -0.4180
144 D A 0.0000
145 S A -1.3431
146 E A -2.2906
147 Y A -1.3886
148 Q A -1.3985
149 L A 0.0000
150 P A 0.2321
151 Y A 0.0755
152 V A 0.3165
153 L A 0.0000
154 G A -0.3731
155 S A -0.5390
156 A A -0.7472
157 H A -1.3934
158 Q A -1.6322
159 G A -0.6645
160 C A -0.4539
161 L A 0.0000
162 P A 0.0003
163 P A -0.0831
164 F A 0.6288
165 P A 0.0731
166 A A -0.1381
167 D A -0.4815
168 V A 1.2628
169 F A 0.0000
170 M A 1.3509
171 I A 0.0000
172 P A -0.2831
173 Q A -0.3236
174 Y A 0.0000
175 G A 0.0026
176 Y A 0.0000
177 L A 1.9816
178 T A 1.2355
179 L A 0.3428
180 N A -0.6777
181 N A -1.8589
182 G A -1.7816
183 S A -1.3131
184 Q A -1.4784
185 A A -0.9338
186 V A -0.8411
187 G A -1.0867
188 R A -1.6670
189 S A -0.4363
190 S A 0.5226
191 F A 1.4112
192 Y A 1.0839
193 C A 0.8688
194 L A 0.0000
195 E A -0.2708
196 Y A 1.0039
197 F A 0.2484
198 P A -0.2350
199 S A -0.5118
200 Q A -1.1061
201 M A -0.2219
202 L A 0.0000
203 R A -1.8488
204 T A -1.3837
205 G A -1.6315
206 N A -1.8845
207 N A -1.5652
208 F A -0.5175
209 T A -0.3920
210 F A -0.0793
211 S A -0.5512
212 Y A -0.5440
213 T A -1.2773
214 F A 0.0000
215 E A -2.2428
216 E A -2.2317
217 V A 0.0000
218 P A -0.4799
219 F A 0.0565
220 H A 0.0000
221 S A -0.0178
222 S A 0.0000
223 Y A -0.3326
224 A A -0.6206
225 H A -0.7234
226 S A -0.9006
227 Q A -1.1022
228 S A -0.9684
229 L A 0.0000
230 D A -1.5813
231 R A -1.5184
232 L A -0.4866
233 M A -0.1940
234 N A 0.0296
235 P A 0.5019
236 L A 1.9455
237 I A 2.0367
238 D A -0.0464
239 Q A 0.1677
240 Y A 1.2883
241 L A 1.0765
242 Y A 1.7917
243 Y A 1.4482
244 L A 1.7235
245 N A 0.3011
246 R A -0.6263
247 T A -1.0204
248 Q A -2.6014
249 N A -2.5675
250 Q A -2.2848
251 S A -1.6995
252 G A -1.3970
253 S A -1.0920
254 A A -1.7046
255 Q A -2.9076
256 N A -3.3968
257 K A -3.0048
258 D A -1.5706
259 L A 1.1873
260 L A 1.1830
261 F A 2.2809
262 S A 0.6018
263 R A -0.5259
264 G A 0.0000
265 S A -0.0045
266 P A 0.1975
267 A A 0.0832
268 G A -0.0379
269 M A -0.1187
270 S A -0.1362
271 V A 0.7319
272 Q A 0.0000
273 P A -0.2667
274 K A -1.1776
275 N A -1.2516
276 W A 0.2215
277 L A 0.5670
278 P A 0.5064
279 G A 0.0000
280 P A 0.3266
281 C A 0.0000
282 Y A 0.0190
283 R A -1.1289
284 Q A 0.0000
285 Q A -1.2090
286 R A -1.4597
287 V A -1.4522
288 S A 0.0000
289 K A -2.0427
290 T A -1.8738
291 K A -2.7203
292 T A -2.0639
293 D A -2.5325
294 N A -2.6171
295 N A -2.7211
296 N A -2.6380
297 S A -1.8149
298 N A -1.6382
299 F A -0.7352
300 T A -0.0816
301 W A 0.2860
302 T A -0.0828
303 G A -0.4379
304 A A -0.1358
305 S A -0.1115
306 K A -0.0385
307 Y A 0.2720
308 N A -1.3144
309 L A -0.6106
310 N A -1.8089
311 G A -1.7491
312 R A -2.4009
313 E A -1.8320
314 S A -0.6026
315 I A 0.1605
316 I A 0.1199
317 N A -0.8188
318 P A 0.0000
319 G A 0.0483
320 T A 0.1051
321 A A 0.1747
322 M A 0.0000
323 A A 0.0000
324 S A 0.0000
325 H A 0.0000
326 K A -3.2143
327 D A -3.9254
328 D A -3.9239
329 E A -3.6493
330 D A -4.0528
331 K A -2.8183
332 F A 0.0000
333 F A -1.1934
334 P A 0.0000
335 M A -0.4516
336 S A -0.2889
337 G A 0.0000
338 V A 0.0000
339 M A 0.6058
340 I A 1.5025
341 F A 0.2299
342 G A -1.1956
343 K A -2.3462
344 E A -2.4050
345 S A -1.7549
346 A A -1.6568
347 G A -1.2585
348 A A -0.6165
349 S A -0.9424
350 N A -1.3957
351 T A -1.0961
352 A A -0.7304
353 L A -0.8452
354 D A -1.7521
355 N A -1.6537
356 V A -0.6774
357 M A 0.0000
358 I A 0.4098
359 T A 0.0000
360 D A -1.3873
361 E A 0.0000
362 E A -2.4216
363 E A -1.5778
364 I A 0.0000
365 K A -1.4631
366 A A -0.9012
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 -1.2484
373 E A -1.7842
374 R A -2.1078
375 F A -0.7949
376 G A -0.8074
377 T A -0.3263
378 V A 0.9945
379 A A 1.0881
380 V A 1.7234
381 N A 0.6086
382 F A 1.0175
383 Q A -1.0923
384 S A -1.0440
385 S A -1.1694
386 S A -1.0421
387 T A -1.3380
388 D A -2.2406
389 P A -1.0665
390 A A -0.0217
391 T A 0.2790
392 G A -0.3146
393 D A -1.8277
394 V A -1.1072
395 H A -1.4279
396 A A -0.4766
397 M A -0.0653
398 G A -0.0927
399 A A 0.4030
400 L A 0.5919
401 P A 0.1963
402 G A 0.0871
403 M A 0.6225
404 V A 0.9570
405 W A 0.3828
406 Q A -0.3368
407 D A -0.4745
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 -0.4966
419 K A -1.3040
420 I A 0.0000
421 P A -1.4636
422 H A -1.9471
423 T A -1.7302
424 D A -2.3832
425 G A -1.4372
426 H A -0.5567
427 F A 1.2461
428 H A -0.0015
429 P A -0.1586
430 S A -0.0173
431 P A 0.2390
432 L A 0.9048
433 M A 0.3589
434 G A 0.0000
435 G A -0.0005
436 F A 0.0000
437 G A -0.7939
438 L A 0.0000
439 K A -2.4179
440 N A -2.3688
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 0.1670
451 P A 0.0345
452 V A 0.3896
453 P A 0.1660
454 A A -0.2534
455 N A -1.3083
456 P A -0.8452
457 P A -0.8283
458 A A -0.7458
459 E A -1.0200
460 F A 0.8889
461 S A 0.0523
462 A A 0.0472
463 T A -0.4637
464 K A -1.3368
465 F A -0.0171
466 A A -0.0732
467 S A -0.2208
468 F A 0.3332
469 I A 0.5353
470 T A 0.1818
471 Q A 0.0000
472 Y A 0.3385
473 S A 0.0000
474 T A 0.0214
475 G A 0.0000
476 Q A -0.3214
477 V A 0.0000
478 S A -0.6288
479 V A 0.0000
480 E A -1.0950
481 I A 0.0000
482 E A -0.9135
483 W A 0.0000
484 E A -1.2833
485 L A 0.0000
486 Q A -1.8871
487 K A -2.3998
488 E A -2.4015
489 N A -2.5917
490 S A -2.1255
491 K A -2.3271
492 R A -1.5420
493 W A 0.1138
494 N A -0.1915
495 P A -0.1328
496 E A 0.1954
497 V A 1.2898
498 Q A 0.0024
499 Y A -0.1551
500 T A -0.1747
501 S A -0.4205
502 N A -0.8676
503 Y A 0.3129
504 A A -0.3913
505 K A -1.6167
506 S A -1.1143
507 A A -0.8197
508 N A -1.0672
509 V A 0.3524
510 D A -0.7845
511 F A -0.3247
512 T A 0.3621
513 V A 0.3137
514 D A -1.2342
515 N A -2.1511
516 N A -1.9152
517 G A -0.9964
518 L A -0.3150
519 Y A -0.1087
520 T A -0.4762
521 E A -1.2227
522 P A -1.2911
523 R A -1.7104
524 P A -0.7327
525 I A 0.0000
526 G A -0.3234
527 T A 0.0000
528 R A 0.0000
529 Y A 0.3205
530 L A 0.0000
531 T A -0.5344
532 R A -1.4799
533 P A -0.6938
534 L A 0.3226
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 -0.1182 4.2688 View CSV PDB
4.5 -0.1655 4.1679 View CSV PDB
5.0 -0.2203 4.0961 View CSV PDB
5.5 -0.2752 4.0779 View CSV PDB
6.0 -0.3229 4.0594 View CSV PDB
6.5 -0.3573 4.041 View CSV PDB
7.0 -0.378 4.0226 View CSV PDB
7.5 -0.3893 4.0047 View CSV PDB
8.0 -0.394 3.9878 View CSV PDB
8.5 -0.3911 3.9736 View CSV PDB
9.0 -0.3786 3.9636 View CSV PDB