Project name: AAV3_1mer_M3

Status: done

Started: 2026-10-21 19:06:17
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.  (00:00:13)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:13)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:04:03)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/50981f8dd9517c/tmp/folded.pdb                 (00:04:03)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:46)
Show buried residues

Minimal score value
-3.6887
Maximal score value
2.4512
Average score
-0.5708
Total score value
-296.2277

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 -1.1237
17 D A -1.9764
18 G A -1.0669
19 V A 0.5153
20 G A -0.6542
21 N A -1.7331
22 S A -1.4940
23 S A -1.3834
24 G A -1.2049
25 N A -1.2662
26 W A -0.4302
27 H A -1.2091
28 C A -0.8427
29 D A -1.4993
30 S A -0.9644
31 Q A -0.7632
32 W A -0.3937
33 L A 0.2438
34 G A -1.1101
35 D A -2.3461
36 R A -1.4886
37 V A 0.0000
38 I A -0.6772
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 0.5768
45 W A 0.0000
46 A A 0.6628
47 L A 0.0000
48 P A 0.0581
49 T A -0.3242
50 Y A -0.3768
51 N A -1.0074
52 N A -1.2387
53 H A -0.5620
54 L A -0.3933
55 Y A -0.5522
56 K A -1.5972
57 Q A -1.0732
58 I A -0.2619
59 S A -0.4649
60 S A 0.0000
61 Q A -1.5847
62 S A -1.1194
63 G A -1.3139
64 A A -1.6062
65 S A -1.9168
66 N A -2.7161
67 D A -2.7331
68 N A -2.5105
69 H A -2.1441
70 Y A -0.3847
71 F A 0.0000
72 G A 0.0000
73 Y A 0.1749
74 S A -0.4091
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 -0.5403
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 -0.8942
91 P A -1.3776
92 R A -2.3993
93 D A 0.0000
94 W A 0.0000
95 Q A -2.1072
96 R A -2.3024
97 L A 0.0000
98 I A 0.0000
99 N A 0.0000
100 N A -1.9987
101 N A 0.0000
102 W A 0.0000
103 G A 0.0000
104 F A 0.0000
105 R A -0.8445
106 P A 0.0000
107 K A -1.9081
108 K A -2.0136
109 L A 0.0000
110 S A -0.9498
111 F A 0.0000
112 K A -1.1013
113 L A 0.0000
114 F A 0.0000
115 N A -1.3156
116 I A 0.0000
117 Q A -1.2067
118 V A 0.0000
119 K A -0.5145
120 E A -0.0935
121 V A -0.0130
122 T A -0.8522
123 Q A -2.2186
124 N A -2.9075
125 D A -2.9327
126 G A -2.0928
127 T A -1.6923
128 T A -0.9326
129 T A -0.0466
130 I A 0.7379
131 A A -0.0739
132 N A -1.1315
133 N A -0.6533
134 L A 0.2077
135 T A -0.1395
136 S A 0.0000
137 T A 0.0000
138 V A 0.0000
139 Q A -0.4796
140 V A 0.0000
141 F A 0.0000
142 T A -0.4228
143 D A 0.0000
144 S A -1.3108
145 E A -2.2571
146 Y A -1.3573
147 Q A -1.3534
148 L A 0.0000
149 P A 0.4142
150 Y A 0.1127
151 V A 0.3492
152 L A 0.0000
153 G A -0.3719
154 S A -0.5833
155 A A -0.8539
156 H A -1.6076
157 Q A -1.7487
158 G A -0.7680
159 C A -0.5165
160 L A 0.0000
161 P A 0.0000
162 P A 0.1580
163 F A 1.1021
164 P A 0.4597
165 A A 0.3982
166 D A 0.5792
167 V A 1.7376
168 F A 0.0000
169 M A 1.2717
170 V A 0.0000
171 P A -0.3221
172 Q A -0.3785
173 Y A 0.0000
174 G A -0.0377
175 Y A 0.0000
176 L A 1.9406
177 T A 1.1873
178 L A 0.2459
179 N A -0.7770
180 N A -1.8894
181 G A -1.9305
182 S A -1.5736
183 Q A -1.4926
184 A A -1.1621
185 V A -0.9581
186 G A -1.1269
187 R A -1.6745
188 S A -0.3293
189 S A 0.6326
190 F A 1.6619
191 Y A 1.2073
192 C A 0.9121
193 L A 0.0000
194 E A -0.2665
195 Y A 0.9963
196 F A 0.2480
197 P A -0.2354
198 S A -0.5145
199 Q A -1.0831
200 M A -0.1471
201 L A 0.0000
202 R A -1.4678
203 T A -1.2349
204 G A 0.0000
205 N A -1.5857
206 N A -1.6763
207 F A 0.0000
208 Q A -1.2304
209 F A -0.3947
210 S A -0.6502
211 Y A -0.4882
212 T A -1.2593
213 F A 0.0000
214 E A -2.0176
215 D A -2.0912
216 V A 0.0000
217 P A -0.3857
218 F A 0.1485
219 H A 0.0000
220 S A -0.0209
221 S A 0.0000
222 Y A -0.3641
223 A A -0.7054
224 H A -1.0106
225 S A -1.0854
226 Q A -1.0869
227 S A -0.8736
228 L A 0.0000
229 D A -1.3126
230 R A -1.3093
231 L A -0.3354
232 M A -0.2916
233 N A -0.3948
234 P A 0.0545
235 L A 1.6562
236 I A 1.6175
237 D A -0.5163
238 Q A 0.2173
239 Y A 1.5113
240 L A 1.7295
241 Y A 2.4427
242 Y A 1.8073
243 L A 1.8655
244 N A 0.3604
245 R A -1.4985
246 T A -1.2622
247 Q A -2.7423
248 G A -2.0309
249 T A -1.4178
250 T A -1.2009
251 S A -0.9269
252 G A -0.9833
253 T A -0.7876
254 T A -1.2576
255 N A -2.6062
256 Q A -2.7094
257 S A -2.3082
258 R A -2.1910
259 L A 0.4184
260 L A 0.9872
261 F A 2.4512
262 S A 1.3675
263 Q A 0.5799
264 A A 0.0000
265 G A 0.0000
266 P A -0.4441
267 Q A -1.3671
268 S A -0.6384
269 M A -0.4878
270 S A -0.1973
271 L A 0.9153
272 Q A 0.0000
273 A A -0.1082
274 R A -1.4808
275 N A -1.5131
276 W A -0.0244
277 L A 0.5923
278 P A 0.5206
279 G A 0.0000
280 P A -0.2084
281 C A 0.0000
282 Y A -1.1437
283 R A -1.6795
284 Q A 0.0000
285 Q A -1.4058
286 R A -1.6108
287 L A -1.2940
288 S A 0.0000
289 K A -1.8679
290 T A -1.3570
291 A A -1.5461
292 N A -2.5239
293 D A -2.6755
294 N A -2.6418
295 N A -2.7831
296 N A -2.6635
297 S A -1.8345
298 N A -1.5966
299 F A -0.5977
300 P A 0.0183
301 W A 0.6828
302 T A 0.1933
303 A A -0.1655
304 A A -0.0989
305 S A -0.2521
306 K A -0.1542
307 Y A 0.4475
308 H A -0.9788
309 L A -0.5876
310 N A -1.7553
311 G A -1.7491
312 R A -2.1641
313 D A -1.5122
314 S A -0.5622
315 L A -0.0042
316 V A 0.0000
317 N A -1.0240
318 P A 0.0000
319 G A 0.0000
320 P A 0.0007
321 A A 0.1493
322 M A 0.0000
323 A A 0.0000
324 S A 0.0000
325 H A 0.0000
326 K A -2.7181
327 D A -3.6160
328 D A -3.6409
329 E A -3.1872
330 E A -3.6887
331 K A -2.5901
332 F A -1.9552
333 F A 0.0000
334 P A 0.0000
335 M A 0.0000
336 H A -0.5969
337 G A 0.0000
338 N A 0.0000
339 L A 0.6491
340 I A 1.4614
341 F A 0.3007
342 G A -1.3181
343 K A -2.3322
344 E A -2.3810
345 G A -1.5776
346 T A -1.8609
347 T A -1.1434
348 A A -0.4646
349 S A -1.0370
350 N A -1.7131
351 A A -1.8632
352 E A -2.4396
353 L A -1.2195
354 D A -2.3422
355 N A -2.2399
356 V A -0.8721
357 M A 0.0000
358 I A 0.5149
359 T A 0.0000
360 D A -1.0184
361 E A 0.0000
362 E A -2.0818
363 E A -1.3499
364 I A 0.0000
365 R A -1.2259
366 T A -0.7958
367 T A 0.0000
368 N A 0.0000
369 P A -0.3640
370 V A -0.5654
371 A A 0.0000
372 T A 0.0000
373 E A -1.4800
374 Q A -1.5120
375 Y A -0.8030
376 G A -0.6521
377 T A -0.4073
378 V A 0.1690
379 A A -0.6012
380 N A -1.6840
381 N A -0.9383
382 L A 0.3246
383 Q A -1.2054
384 S A -1.0477
385 S A -1.1940
386 N A -1.6765
387 T A -1.0252
388 A A -0.6970
389 P A -0.8962
390 T A -0.9253
391 T A -1.2078
392 R A -1.9472
393 T A -1.2342
394 V A -1.1903
395 N A -2.0549
396 D A -2.3517
397 Q A -1.3089
398 G A -0.7189
399 A A 0.3931
400 L A 0.7160
401 P A 0.2822
402 G A -0.0178
403 M A 0.0000
404 V A 0.9339
405 W A 0.3818
406 Q A -0.3012
407 D A -0.4091
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 -0.3820
416 I A 0.0000
417 W A 0.0000
418 A A -0.3986
419 K A -1.1147
420 I A 0.0000
421 P A -1.5123
422 H A -2.1111
423 T A -1.8329
424 D A -2.4798
425 G A -1.5911
426 H A -1.0032
427 F A 1.0062
428 H A -0.0832
429 P A -0.2500
430 S A 0.0718
431 P A 0.2630
432 L A 0.8619
433 M A 0.3779
434 G A 0.0000
435 G A 0.0163
436 F A 0.0000
437 G A -0.7223
438 L A 0.0000
439 K A -2.3575
440 H A -2.2069
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 0.1824
451 P A 0.1831
452 V A 0.5805
453 P A 0.2691
454 A A -0.1878
455 N A -1.3133
456 P A -0.5863
457 P A -0.3332
458 T A -0.0102
459 T A 0.6723
460 F A 1.6662
461 S A 0.4261
462 P A -0.1384
463 A A -0.4041
464 K A -1.2163
465 F A 0.2851
466 A A 0.0300
467 S A -0.1176
468 F A 0.4409
469 I A 0.6593
470 T A 0.1530
471 Q A 0.0000
472 Y A 0.3216
473 S A 0.0000
474 T A 0.0282
475 G A 0.0000
476 Q A -0.3570
477 V A 0.0000
478 S A -0.6978
479 V A 0.0000
480 E A -1.3696
481 I A 0.0000
482 E A -1.4769
483 W A 0.0000
484 E A -1.4253
485 L A 0.0000
486 Q A -2.0866
487 K A -2.9056
488 E A -2.3594
489 N A -2.6315
490 S A -2.2244
491 K A -2.3734
492 R A -1.7833
493 W A -0.0995
494 N A -0.7846
495 P A -0.2982
496 E A 0.2299
497 I A 1.5252
498 Q A 0.0084
499 Y A -0.2655
500 T A -0.2953
501 S A -0.7167
502 N A -1.3247
503 Y A -0.3809
504 N A -1.9274
505 K A -1.8684
506 S A -0.5670
507 V A 0.9237
508 N A -0.0251
509 V A 0.7925
510 D A -0.2567
511 F A 0.0063
512 T A 0.6493
513 V A 0.7506
514 D A -0.3026
515 T A -0.8940
516 N A -1.2352
517 G A -0.4752
518 V A 0.2688
519 Y A 0.3959
520 S A -0.3482
521 E A -0.8889
522 P A -0.8983
523 R A -0.7900
524 P A -0.2908
525 I A 0.0000
526 G A -0.1893
527 T A 0.0000
528 R A 0.0000
529 Y A 0.4585
530 L A 0.0000
531 T A -0.6148
532 R A -1.9149
533 N A -1.5676
534 L A -0.3237
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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 -0.2097 4.9191 View CSV PDB
4.5 -0.252 4.9191 View CSV PDB
5.0 -0.3009 4.9191 View CSV PDB
5.5 -0.349 4.9191 View CSV PDB
6.0 -0.3885 4.9191 View CSV PDB
6.5 -0.4149 4.9191 View CSV PDB
7.0 -0.4297 4.9191 View CSV PDB
7.5 -0.4377 4.9191 View CSV PDB
8.0 -0.4411 4.9191 View CSV PDB
8.5 -0.4386 4.9191 View CSV PDB
9.0 -0.4281 4.9191 View CSV PDB