Project name: AAV3_1mer_M4

Status: done

Started: 2026-10-21 19:06:32
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                                          (00:05:47)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/9c33f8163bfff0/tmp/folded.pdb                 (00:05:47)
[INFO]       Main:     Simulation completed successfully.                                          (00:17:13)
Show buried residues

Minimal score value
-3.9096
Maximal score value
2.5944
Average score
-0.5869
Total score value
-304.6051

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 -1.2221
17 D A -2.0757
18 G A -1.0287
19 V A 0.4526
20 G A -0.6696
21 N A -1.7569
22 S A -1.5382
23 S A -1.4740
24 G A -1.2578
25 N A -1.2183
26 W A -0.3721
27 H A -1.3158
28 C A -1.1749
29 D A -2.1671
30 S A -1.4252
31 Q A -1.3312
32 W A -0.6138
33 L A -0.2385
34 G A -1.3580
35 D A -2.4313
36 R A -1.5411
37 V A 0.0000
38 I A -0.7139
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 0.4000
45 W A 0.0000
46 A A 0.6696
47 L A 0.0000
48 P A 0.0720
49 T A -0.2838
50 Y A -0.3077
51 N A -0.8256
52 N A -1.1386
53 H A -0.4237
54 L A -0.1328
55 Y A -0.3787
56 K A -1.3581
57 Q A -1.0042
58 I A -0.2607
59 S A -0.4347
60 S A 0.0000
61 Q A -1.5336
62 S A -1.1101
63 G A -1.2928
64 A A -1.5367
65 S A -1.9063
66 N A -2.7139
67 D A -2.6449
68 N A -2.4653
69 H A -2.0589
70 Y A -0.3069
71 F A 0.0000
72 G A 0.0000
73 Y A 0.0000
74 S A -0.3845
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 -0.6596
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 -1.0177
91 P A -1.3545
92 R A -2.4004
93 D A 0.0000
94 W A 0.0000
95 Q A -2.0341
96 R A -2.3786
97 L A 0.0000
98 I A 0.0000
99 N A -1.1421
100 N A -2.1125
101 N A 0.0000
102 W A 0.0000
103 G A 0.0000
104 F A 0.0000
105 R A -0.8869
106 P A 0.0000
107 K A -1.8450
108 K A -1.9348
109 L A 0.0000
110 S A -0.9456
111 F A 0.0000
112 K A -1.3104
113 L A 0.0000
114 F A 0.0000
115 N A -1.3462
116 I A 0.0000
117 Q A -1.2391
118 V A 0.0000
119 K A -0.6143
120 E A -0.2790
121 V A -0.1018
122 T A -0.7143
123 Q A -2.2356
124 N A -2.9069
125 D A -2.9325
126 G A -2.0916
127 T A -1.6917
128 T A -0.9616
129 T A -0.1029
130 I A 0.6301
131 A A -0.1846
132 N A -1.2671
133 N A -0.8666
134 L A -0.1801
135 T A -0.2842
136 S A 0.0000
137 T A -0.4203
138 V A 0.0000
139 Q A -0.3692
140 V A 0.0000
141 F A 0.0000
142 T A -0.5169
143 D A 0.0000
144 S A -1.3118
145 E A -2.2670
146 Y A -1.3786
147 Q A -1.4423
148 L A 0.0000
149 P A 0.3827
150 Y A 0.0611
151 V A 0.2935
152 L A 0.0000
153 G A -0.4047
154 S A -0.6034
155 A A -0.8548
156 H A -1.6091
157 Q A -1.8017
158 G A -0.7710
159 C A -0.5261
160 L A 0.0000
161 P A -0.0223
162 P A -0.0787
163 F A 0.6467
164 P A 0.0591
165 A A -0.1243
166 D A -0.4438
167 V A 1.2495
168 F A 0.0000
169 M A 1.2396
170 V A 0.0000
171 P A -0.3332
172 Q A -0.3706
173 Y A 0.0000
174 G A -0.0907
175 Y A 0.0000
176 L A 1.8578
177 T A 1.0635
178 L A 0.0131
179 N A -0.8126
180 N A -1.8797
181 G A -1.9207
182 S A -1.5435
183 Q A -1.4723
184 A A -1.1573
185 V A -0.9323
186 G A -1.1193
187 R A -1.7052
188 S A -0.3948
189 S A 0.5770
190 F A 1.6470
191 Y A 1.1931
192 C A 0.9491
193 L A 0.0000
194 E A -0.1124
195 Y A 1.0711
196 F A 0.3099
197 P A -0.1561
198 S A -0.3826
199 Q A -0.8930
200 M A -0.0029
201 L A 0.0000
202 R A -1.4691
203 T A -1.3325
204 G A 0.0000
205 N A -1.6607
206 N A -2.0005
207 F A 0.0000
208 Q A -1.5513
209 F A -0.5081
210 S A -0.6910
211 Y A -0.4861
212 T A -1.2349
213 F A 0.0000
214 E A -2.0582
215 D A -2.1290
216 V A 0.0000
217 P A -0.5049
218 F A -0.0637
219 H A 0.0000
220 S A -0.1208
221 S A 0.0000
222 Y A -0.2562
223 A A -0.4201
224 H A -0.8005
225 S A -0.9205
226 Q A -0.9689
227 S A -0.8792
228 L A 0.0000
229 D A -1.2456
230 R A -1.3429
231 L A -0.2713
232 M A -0.0481
233 N A 0.0094
234 P A 0.2240
235 L A 1.7906
236 I A 1.7533
237 D A -0.5809
238 Q A 0.2897
239 Y A 1.5078
240 L A 1.7112
241 Y A 2.5944
242 Y A 1.7911
243 L A 1.8911
244 N A 0.4049
245 R A -1.4785
246 T A -1.4520
247 Q A -2.9029
248 G A -2.1161
249 T A -1.5823
250 T A -1.2053
251 S A -0.6500
252 G A -0.8467
253 T A -0.8117
254 T A -1.2408
255 N A -2.6586
256 Q A -2.7003
257 S A -2.3422
258 R A -2.2231
259 L A 0.4490
260 L A 1.0879
261 F A 2.5109
262 S A 1.3651
263 Q A 0.5239
264 A A 0.0000
265 G A 0.0000
266 P A -0.4185
267 Q A -1.4090
268 S A -0.6699
269 M A -0.5865
270 S A -0.2561
271 L A 0.7091
272 Q A 0.0000
273 A A 0.1923
274 R A -0.7895
275 N A -1.0552
276 W A 0.4191
277 L A 0.7776
278 P A 0.5350
279 G A 0.0000
280 P A -0.2369
281 C A 0.0000
282 Y A -1.2024
283 R A -1.7756
284 Q A 0.0000
285 Q A -1.2599
286 R A -1.5705
287 L A -1.3688
288 S A 0.0000
289 K A -2.0771
290 T A -1.5144
291 A A -1.6492
292 N A -2.6611
293 D A -2.9564
294 N A -2.7779
295 N A -2.8390
296 N A -2.6943
297 S A -1.8391
298 N A -1.6641
299 F A -0.7237
300 P A -0.1343
301 W A 0.3547
302 T A 0.0215
303 A A -0.2221
304 A A -0.0143
305 S A -0.2130
306 K A -0.0288
307 Y A 0.4902
308 H A -0.7368
309 L A 0.0194
310 N A -1.4701
311 G A -1.6189
312 R A -2.1300
313 D A -1.4235
314 S A -0.4637
315 L A 0.1305
316 V A 0.0000
317 N A -0.9513
318 P A 0.0000
319 G A 0.0000
320 P A 0.0040
321 A A 0.1614
322 M A 0.0000
323 A A 0.0000
324 S A 0.0000
325 H A 0.0000
326 K A -2.7436
327 D A -3.6613
328 D A -3.7432
329 E A -3.4304
330 E A -3.9096
331 K A -2.8595
332 F A -2.1695
333 F A 0.0000
334 P A 0.0000
335 M A 0.0000
336 H A -0.5301
337 G A 0.0000
338 N A 0.0000
339 L A 0.6058
340 I A 1.4195
341 F A 0.2707
342 G A -1.3603
343 K A -2.3930
344 E A -2.4777
345 G A -1.6089
346 T A -1.9041
347 T A -1.1666
348 A A -0.4654
349 S A -1.0375
350 N A -1.7118
351 A A -1.8595
352 E A -2.4224
353 L A -1.2306
354 D A -2.3454
355 N A -2.2485
356 V A -0.9240
357 M A 0.0000
358 I A 0.4121
359 T A 0.0000
360 D A -1.3071
361 E A 0.0000
362 E A -2.3125
363 E A -1.4860
364 I A 0.0000
365 R A -1.2428
366 T A -0.7661
367 T A 0.0000
368 N A 0.0000
369 P A -0.3679
370 V A -0.5877
371 A A 0.0000
372 T A -1.2247
373 E A -1.5080
374 Q A -1.6002
375 Y A -0.8955
376 G A -0.7100
377 T A -0.4194
378 V A 0.1766
379 A A -0.5446
380 N A -1.5893
381 N A -0.8290
382 L A 0.3701
383 Q A -1.1784
384 S A -1.0362
385 S A -1.2202
386 N A -1.6716
387 T A -0.9961
388 A A -0.6733
389 P A -0.8993
390 T A -0.8593
391 T A -1.1155
392 R A -1.7750
393 T A -1.2387
394 V A 0.0000
395 N A -2.2063
396 D A -2.4541
397 Q A -1.3856
398 G A -0.7410
399 A A 0.3619
400 L A 0.6668
401 P A 0.3200
402 G A 0.2180
403 M A 0.0000
404 V A 0.9905
405 W A 0.3697
406 Q A -0.3001
407 D A -0.3704
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 -0.3801
416 I A 0.0000
417 W A 0.0000
418 A A -0.4992
419 K A -1.3176
420 I A 0.0000
421 P A -1.5866
422 H A -2.0634
423 T A -1.8226
424 D A -2.4748
425 G A -1.5873
426 H A -1.0058
427 F A 1.0107
428 H A -0.0720
429 P A -0.2942
430 S A 0.0657
431 P A 0.2470
432 L A 0.8736
433 M A 0.3823
434 G A 0.0000
435 G A -0.0065
436 F A 0.0000
437 G A -0.8080
438 L A 0.0000
439 K A -2.6042
440 H A -2.2291
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 0.2002
451 P A 0.1874
452 V A 0.5353
453 P A 0.2730
454 A A -0.1865
455 N A -1.3131
456 P A -0.5619
457 P A -0.3253
458 T A -0.0071
459 T A 0.6753
460 F A 1.6694
461 S A 0.4383
462 P A -0.1313
463 A A -0.3991
464 K A -1.2032
465 F A 0.3284
466 A A 0.0711
467 S A -0.1106
468 F A 0.4363
469 I A 0.5613
470 T A 0.1088
471 Q A 0.0000
472 Y A 0.3051
473 S A 0.0000
474 T A 0.0539
475 G A 0.0000
476 Q A -0.3653
477 V A 0.0000
478 S A -0.7243
479 V A 0.0000
480 E A -1.2897
481 I A 0.0000
482 E A -1.1722
483 W A 0.0000
484 E A -1.4017
485 L A 0.0000
486 Q A -2.1113
487 K A -3.1335
488 E A -2.3984
489 N A -2.6366
490 S A -2.2336
491 K A -2.3880
492 R A -1.8703
493 W A -0.1475
494 N A -0.8217
495 P A -0.3322
496 E A 0.1804
497 I A 1.5347
498 Q A 0.0956
499 Y A -0.2241
500 T A -0.2235
501 S A -0.8563
502 N A -1.3209
503 Y A -0.3802
504 N A -1.9270
505 K A -1.8494
506 S A -0.5158
507 V A 1.0220
508 N A 0.1561
509 V A 0.8288
510 D A -0.3152
511 F A -0.1170
512 T A 0.6163
513 V A 0.7461
514 D A -0.2431
515 T A -0.8440
516 N A -1.1828
517 G A -0.5549
518 V A 0.3164
519 Y A 0.1924
520 S A -0.4150
521 E A -0.9472
522 P A -0.9603
523 R A -0.8652
524 P A -0.3554
525 I A 0.0000
526 G A -0.2291
527 T A 0.0000
528 R A 0.0000
529 Y A 0.4424
530 L A 0.0000
531 T A -0.4779
532 R A -1.6162
533 N A -1.2192
534 L A 0.3036
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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 -0.2126 4.9171 View CSV PDB
4.5 -0.2568 4.9171 View CSV PDB
5.0 -0.3084 4.9171 View CSV PDB
5.5 -0.3592 4.9171 View CSV PDB
6.0 -0.401 4.9171 View CSV PDB
6.5 -0.4288 4.9171 View CSV PDB
7.0 -0.4441 4.9171 View CSV PDB
7.5 -0.453 4.9171 View CSV PDB
8.0 -0.4582 4.9171 View CSV PDB
8.5 -0.4583 4.9171 View CSV PDB
9.0 -0.4505 4.9171 View CSV PDB