Project name: AAV3_1mer_M1

Status: done

Started: 2026-10-21 19:05:47
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.  (00:00:04)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:04)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:45)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/2ba2d05db0154a/tmp/folded.pdb                 (00:03:45)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:34)
Show buried residues

Minimal score value
-3.8209
Maximal score value
2.6162
Average score
-0.5935
Total score value
-308.0267

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 -0.9179
17 D A -1.5746
18 G A -0.7853
19 V A 0.6014
20 G A -0.5531
21 N A -1.5500
22 S A -1.4094
23 S A -1.3152
24 G A -1.3534
25 N A -1.2338
26 W A -0.3532
27 H A -1.1901
28 C A -0.8383
29 D A -1.5892
30 S A -1.1026
31 Q A -1.0036
32 W A -0.4323
33 L A 0.0535
34 G A -0.9642
35 D A -1.8460
36 R A -1.2924
37 V A 0.0000
38 I A -0.6841
39 T A 0.0000
40 T A -0.9593
41 S A 0.0000
42 T A 0.0000
43 R A 0.0000
44 T A 0.3869
45 W A 0.0000
46 A A 0.6880
47 L A 0.0000
48 P A 0.0391
49 T A -0.3062
50 Y A -0.3318
51 N A -0.9529
52 N A -1.1908
53 H A -0.4974
54 L A -0.2463
55 Y A -0.5133
56 K A -1.6311
57 Q A -1.1046
58 I A -0.3058
59 S A -0.4632
60 S A 0.0000
61 Q A -1.5467
62 S A -1.1058
63 G A -1.2676
64 A A -1.6380
65 S A -2.0537
66 N A -2.9493
67 D A -3.1269
68 N A -2.7242
69 H A -2.2536
70 Y A -0.4632
71 F A 0.0000
72 G A 0.0000
73 Y A 0.0000
74 S A -0.4740
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 -0.6275
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 -1.0569
91 P A -1.4273
92 R A -2.4991
93 D A -1.9985
94 W A 0.0000
95 Q A -2.1516
96 R A -2.5601
97 L A 0.0000
98 I A 0.0000
99 N A -1.2709
100 N A -2.0454
101 N A 0.0000
102 W A 0.0000
103 G A 0.0000
104 F A 0.0000
105 R A -0.8147
106 P A 0.0000
107 K A -1.8571
108 K A -2.0175
109 L A 0.0000
110 S A -0.9613
111 F A 0.0000
112 K A -1.2246
113 L A 0.0000
114 F A 0.0000
115 N A -1.1734
116 I A 0.0000
117 Q A -1.2275
118 V A 0.0000
119 K A -0.5059
120 E A -0.1601
121 V A 0.0231
122 T A -0.6427
123 Q A -2.2072
124 N A -2.9011
125 D A -2.9285
126 G A -2.0947
127 T A -1.6910
128 T A -0.9290
129 T A -0.0219
130 I A 0.8003
131 A A -0.0433
132 N A -1.1224
133 N A -0.6799
134 L A 0.1490
135 T A -0.1704
136 S A 0.0000
137 T A 0.0000
138 V A 0.0000
139 Q A -0.5128
140 V A 0.0000
141 F A 0.0000
142 T A -0.4123
143 D A 0.0000
144 S A -1.3327
145 E A -2.3010
146 Y A -1.5594
147 Q A -1.4906
148 L A 0.0000
149 P A 0.4030
150 Y A 0.0615
151 V A 0.3404
152 L A 0.0000
153 G A -0.3888
154 S A -0.5010
155 A A -0.6806
156 H A -1.3035
157 Q A -1.5636
158 G A -0.6565
159 C A -0.4441
160 L A 0.0000
161 P A -0.0964
162 P A -0.2125
163 F A 0.3988
164 P A -0.0315
165 A A -0.2258
166 D A -0.6379
167 V A 1.1921
168 F A 0.0000
169 M A 1.3333
170 V A 0.0000
171 P A -0.2447
172 Q A -0.3360
173 Y A 0.0000
174 G A -0.0938
175 Y A 0.0000
176 L A 1.8730
177 T A 1.0977
178 L A 0.0671
179 N A -0.8044
180 N A -1.8834
181 G A -1.9365
182 S A -1.5282
183 Q A -1.4732
184 A A -1.1634
185 V A -0.9761
186 G A -1.1413
187 R A -1.6947
188 S A -0.3516
189 S A 0.6797
190 F A 1.8104
191 Y A 1.3240
192 C A 0.9346
193 L A 0.0000
194 E A -0.2488
195 Y A 1.0298
196 F A 0.2991
197 P A -0.2044
198 S A -0.5033
199 Q A -1.0949
200 M A -0.1319
201 L A 0.0000
202 R A -1.6407
203 T A -1.2169
204 G A 0.0000
205 N A -1.5599
206 N A -1.8792
207 F A 0.0000
208 Q A -1.3012
209 F A -0.3891
210 S A -0.6658
211 Y A -0.5007
212 T A -1.2521
213 F A 0.0000
214 E A -2.0202
215 D A -2.0966
216 V A 0.0000
217 P A -0.4004
218 F A 0.1341
219 H A 0.0000
220 S A -0.0334
221 S A 0.0000
222 Y A -0.2869
223 A A -0.6190
224 H A -0.9840
225 S A -1.0663
226 Q A -1.4969
227 S A -1.4827
228 L A 0.0000
229 D A -2.1905
230 R A -2.3523
231 L A -0.8137
232 M A -0.3721
233 N A -0.1336
234 P A 0.0993
235 L A 1.7587
236 I A 1.7222
237 D A -0.5744
238 Q A 0.2788
239 Y A 1.5198
240 L A 1.7254
241 Y A 2.6162
242 Y A 1.8196
243 L A 1.9083
244 N A 0.5315
245 R A -1.2163
246 T A -1.2535
247 Q A -2.6340
248 G A -1.9323
249 T A -1.4095
250 T A -1.0273
251 S A -0.6526
252 G A -0.8462
253 T A -0.7815
254 T A -1.3156
255 N A -2.6014
256 Q A -2.6148
257 S A -2.2312
258 R A -2.1022
259 L A 0.5310
260 L A 1.1338
261 F A 2.5219
262 S A 1.4193
263 Q A 0.6039
264 A A 0.0000
265 G A 0.0000
266 P A -0.4814
267 Q A -1.3869
268 S A -0.6101
269 M A -0.6469
270 S A -0.3154
271 L A 1.0140
272 Q A 0.0000
273 A A 0.1926
274 R A -0.9265
275 N A -1.1002
276 W A 0.3716
277 L A 0.7859
278 P A 0.4796
279 G A 0.0000
280 P A -0.0590
281 C A 0.0000
282 Y A -0.8954
283 R A -1.6655
284 Q A 0.0000
285 Q A -1.4938
286 R A -1.7364
287 L A -1.4279
288 S A 0.0000
289 K A -2.0145
290 T A -1.4861
291 A A -1.6368
292 N A -2.6557
293 D A -2.9577
294 N A -2.7922
295 N A -2.8342
296 N A -2.6849
297 S A -1.8181
298 N A -1.5632
299 F A -0.5345
300 P A 0.0437
301 W A 0.6670
302 T A 0.1932
303 A A -0.1858
304 A A -0.2097
305 S A -0.3806
306 K A -0.4135
307 Y A 0.1234
308 H A -0.9588
309 L A -0.0901
310 N A -1.5068
311 G A -1.6749
312 R A -2.3230
313 D A -1.7034
314 S A -0.7730
315 L A -0.1874
316 V A 0.0000
317 N A -1.0646
318 P A 0.0000
319 G A 0.0000
320 P A 0.0683
321 A A 0.1860
322 M A 0.0000
323 A A 0.0000
324 S A 0.0000
325 H A 0.0000
326 K A -2.9155
327 D A -3.7435
328 D A -3.7378
329 E A -3.3686
330 E A -3.8209
331 K A -2.7852
332 F A -2.1367
333 F A 0.0000
334 P A 0.0000
335 M A 0.0000
336 H A -0.6695
337 G A 0.0000
338 N A 0.0000
339 L A 0.0000
340 I A 1.3422
341 F A 0.1768
342 G A -1.3873
343 K A -2.4224
344 E A -2.5033
345 G A -1.6215
346 T A -1.8853
347 T A -1.1579
348 A A -0.4624
349 S A -1.0348
350 N A -1.7075
351 A A -1.8377
352 E A -2.4084
353 L A -1.2059
354 D A -2.3135
355 N A -2.1916
356 V A -0.9298
357 M A 0.0000
358 I A 0.3840
359 T A 0.0000
360 D A -0.9456
361 E A 0.0000
362 E A -2.0026
363 E A -1.0129
364 I A 0.0000
365 R A -1.5393
366 T A -1.1142
367 T A 0.0000
368 N A 0.0000
369 P A -0.4677
370 V A -0.6685
371 A A 0.0000
372 T A 0.0000
373 E A -1.5734
374 Q A -1.6516
375 Y A -0.8891
376 G A -0.7222
377 T A -0.3979
378 V A 0.2087
379 A A -0.5204
380 N A -1.5741
381 N A -0.8767
382 L A 0.3375
383 Q A -1.1970
384 S A -1.0428
385 S A -1.1923
386 N A -1.6748
387 T A -1.0192
388 A A -0.6917
389 P A -0.8871
390 T A -0.8414
391 T A -1.0578
392 R A -1.6431
393 T A -1.2027
394 V A 0.0000
395 N A -2.1645
396 D A -2.2976
397 Q A -1.2094
398 G A -0.4775
399 A A 0.4956
400 L A 0.7668
401 P A 0.3518
402 G A 0.2671
403 M A 0.0000
404 V A 1.0760
405 W A 0.3643
406 Q A -0.3058
407 D A -0.4689
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 -0.3396
416 I A 0.0000
417 W A 0.0000
418 A A -0.4282
419 K A -1.1383
420 I A 0.0000
421 P A -1.4973
422 H A -2.0919
423 T A -1.8211
424 D A -2.4747
425 G A -1.5874
426 H A -1.0022
427 F A 1.0149
428 H A -0.0809
429 P A -0.2513
430 S A 0.0573
431 P A 0.2512
432 L A 0.8664
433 M A 0.4390
434 G A 0.0000
435 G A -0.0020
436 F A 0.0000
437 G A -0.7289
438 L A 0.0000
439 K A -2.2501
440 H A -2.1659
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 0.1448
451 P A 0.0803
452 V A 0.3980
453 P A 0.1202
454 A A -0.2722
455 N A -1.3335
456 P A -0.6099
457 P A -0.3304
458 T A -0.0055
459 T A 0.6736
460 F A 1.6646
461 S A 0.3980
462 P A -0.1670
463 A A -0.4549
464 K A -1.3068
465 F A 0.0800
466 A A -0.0581
467 S A -0.2242
468 F A 0.2984
469 I A 0.5640
470 T A 0.1255
471 Q A 0.0000
472 Y A 0.3063
473 S A 0.0000
474 T A 0.0470
475 G A 0.0000
476 Q A -0.3688
477 V A 0.0000
478 S A -0.7198
479 V A 0.0000
480 E A -1.3840
481 I A 0.0000
482 E A -1.2965
483 W A 0.0000
484 E A -1.1917
485 L A 0.0000
486 Q A -1.6992
487 K A -2.2613
488 E A -2.2890
489 N A -2.5711
490 S A -2.2027
491 K A -2.3336
492 R A -1.6698
493 W A 0.0865
494 N A -0.3953
495 P A -0.1267
496 E A 0.2597
497 I A 1.3380
498 Q A -0.5181
499 Y A 0.0000
500 T A -0.4135
501 S A -0.9511
502 N A -1.3364
503 Y A -0.3880
504 N A -1.9315
505 K A -1.8756
506 S A -0.5757
507 V A 0.9252
508 N A -0.0819
509 V A 0.6946
510 D A -0.4360
511 F A 0.0000
512 T A 0.4205
513 V A 0.5466
514 D A -0.3830
515 T A -0.9163
516 N A -1.2502
517 G A -0.6816
518 V A 0.0583
519 Y A -0.0142
520 S A -0.6027
521 E A -1.1449
522 P A -1.1736
523 R A -1.1836
524 P A -0.4761
525 I A 0.0000
526 G A -0.2310
527 T A 0.0000
528 R A 0.0000
529 Y A 0.2912
530 L A 0.0000
531 T A -0.6033
532 R A -1.9199
533 N A -1.5210
534 L A -0.2553
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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 -0.2215 4.8776 View CSV PDB
4.5 -0.2665 4.8776 View CSV PDB
5.0 -0.3182 4.8776 View CSV PDB
5.5 -0.3685 4.8776 View CSV PDB
6.0 -0.4101 4.8776 View CSV PDB
6.5 -0.4385 4.8776 View CSV PDB
7.0 -0.4554 4.8776 View CSV PDB
7.5 -0.4659 4.8776 View CSV PDB
8.0 -0.4722 4.8776 View CSV PDB
8.5 -0.4729 4.8776 View CSV PDB
9.0 -0.4654 4.8776 View CSV PDB