Project name: AAV6_1mer_M3

Status: done

Started: 2026-10-21 19:57:51
Settings
Chain sequence(s) GADGVGNASGNWHCDSTWLGDRVITTSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTTNDGVTTIANNLTSTVQVFSDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLNRTQNQSGSAQNKDLLFSRGSPAGMSVQPKNWLPGPCYRQQRVSKTKTDNNNSNFTWTGASKYNLNGRESIINPGTAMASHKDDKDKFFPMSGVMIFGKESAGASNTALDNVMITDEEEIKATNPVATERFGTVAVNLQSSSTDPATGDVHVMGALPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPPAEFSATKFASFITQYSTGQVSVEIEWELQKENSKRWNPEVQYTSNYAKSANVDFTVDNNGLYTEPRPIGTRYLTRPL 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                                          (00:04:25)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/83f010b797d0bb/tmp/folded.pdb                 (00:04:25)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:40)
Show buried residues

Minimal score value
-3.8787
Maximal score value
2.5373
Average score
-0.4894
Total score value
-254.49

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
15 G A -0.9179
16 A A -1.1102
17 D A -1.8655
18 G A -0.8585
19 V A 0.4553
20 G A -0.6461
21 N A -1.5303
22 A A -1.0934
23 S A -1.1273
24 G A -1.1079
25 N A -1.1562
26 W A -0.3357
27 H A -1.2534
28 C A -1.0394
29 D A -1.7993
30 S A -0.7704
31 T A -0.0899
32 W A 0.1440
33 L A 0.5103
34 G A -0.8644
35 D A -1.9781
36 R A -1.1036
37 V A 0.0000
38 I A -0.2441
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 0.4070
45 W A 0.0000
46 A A 0.6934
47 L A 0.0000
48 P A 0.1055
49 T A -0.2388
50 Y A -0.2370
51 N A -0.7235
52 N A -1.0807
53 H A -0.3629
54 L A 0.0600
55 Y A -0.2216
56 K A -1.2103
57 Q A -0.9048
58 I A 0.1136
59 S A -0.0702
60 S A 0.0000
61 A A -0.3039
62 S A -0.3777
63 T A -0.5796
64 G A -0.9159
65 A A -1.2047
66 S A -1.6929
67 N A -2.6314
68 D A -2.6401
69 N A -2.3517
70 H A -1.8719
71 Y A -0.1809
72 F A 0.0000
73 G A 0.0000
74 Y A 0.2466
75 S A -0.2188
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 -0.5476
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 -1.0172
92 P A -1.3108
93 R A -2.3870
94 D A 0.0000
95 W A 0.0000
96 Q A -2.0312
97 R A -2.4301
98 L A 0.0000
99 I A 0.0000
100 N A 0.0000
101 N A -2.0936
102 N A 0.0000
103 W A -0.9380
104 G A 0.0000
105 F A 0.0000
106 R A -1.0437
107 P A 0.0000
108 K A -2.3373
109 R A -2.1743
110 L A 0.0000
111 N A -1.0250
112 F A 0.0000
113 K A -0.8360
114 L A 0.0000
115 F A 0.0000
116 N A -0.8529
117 I A 0.0000
118 Q A -0.8726
119 V A 0.0000
120 K A -0.5430
121 E A -0.0721
122 V A 0.4786
123 T A 0.2638
124 T A -0.5042
125 N A -1.7798
126 D A -2.1088
127 G A -0.9266
128 V A 0.5015
129 T A 0.4176
130 T A 0.7263
131 I A 1.0065
132 A A -0.0311
133 N A -1.1279
134 N A -0.5555
135 L A 0.3839
136 T A 0.1623
137 S A 0.0000
138 T A -0.1003
139 V A 0.0000
140 Q A -0.3075
141 V A 0.0000
142 F A 0.0000
143 S A -0.4339
144 D A 0.0000
145 S A -1.3436
146 E A -2.3153
147 Y A -1.3921
148 Q A -1.5680
149 L A 0.0000
150 P A 0.3539
151 Y A 0.0567
152 V A 0.3208
153 L A 0.0000
154 G A -0.3849
155 S A -0.5498
156 A A -0.7606
157 H A -1.4053
158 Q A -1.6413
159 G A -0.6853
160 C A -0.4726
161 L A 0.0000
162 P A -0.0679
163 P A -0.1556
164 F A 0.4892
165 P A -0.0204
166 A A -0.1762
167 D A -0.4711
168 V A 1.2559
169 F A 0.0000
170 M A 1.3452
171 I A 0.0000
172 P A -0.2810
173 Q A -0.3266
174 Y A 0.0000
175 G A -0.0177
176 Y A 0.0000
177 L A 1.9143
178 T A 1.1682
179 L A 0.2287
180 N A -0.6544
181 N A -1.7624
182 G A -1.6627
183 S A -1.2001
184 Q A -1.4126
185 A A -0.7991
186 V A -0.5051
187 G A -0.9240
188 R A -1.5678
189 S A -0.2422
190 S A 0.6511
191 F A 1.6457
192 Y A 1.2524
193 C A 0.9638
194 L A 0.0000
195 E A -0.1544
196 Y A 1.0844
197 F A 0.3290
198 P A -0.1652
199 S A -0.4275
200 Q A -0.7508
201 M A 0.2254
202 L A 0.0000
203 R A -0.4685
204 T A -0.6582
205 G A 0.0000
206 N A -0.9375
207 N A -0.9128
208 F A 0.0000
209 T A -0.4099
210 F A -0.0932
211 S A -0.5702
212 Y A -0.6148
213 T A -1.3994
214 F A 0.0000
215 E A -2.1263
216 D A -2.2120
217 V A 0.0000
218 P A -0.4339
219 F A 0.0098
220 H A 0.0000
221 S A -0.1215
222 S A 0.0000
223 Y A -0.4321
224 A A -0.6088
225 H A -0.8202
226 S A -0.8990
227 Q A -0.9528
228 S A -0.9112
229 L A -0.5381
230 D A -1.5685
231 R A -1.4588
232 L A -0.5681
233 M A -0.5226
234 N A -0.5782
235 P A 0.1367
236 L A 1.6180
237 I A 1.5467
238 D A -0.6489
239 Q A 0.0312
240 Y A 1.3596
241 L A 1.2731
242 Y A 2.2120
243 Y A 1.6843
244 L A 1.8505
245 N A 0.5178
246 R A -0.5637
247 T A -0.9814
248 Q A -2.5899
249 N A -2.5440
250 Q A -2.2675
251 S A -1.5960
252 G A -1.4288
253 S A -1.0062
254 A A -1.6140
255 Q A -2.9146
256 N A -3.4377
257 K A -3.0083
258 D A -1.6161
259 L A 1.1753
260 L A 1.2114
261 F A 2.5373
262 S A 1.1981
263 R A 0.3162
264 G A 0.0000
265 S A -0.1366
266 P A 0.0676
267 A A -0.0258
268 G A -0.1405
269 M A -0.3277
270 S A -0.2062
271 V A 0.6248
272 Q A 0.0000
273 P A -0.2521
274 K A -1.3426
275 N A -1.3520
276 W A 0.0095
277 L A 0.5154
278 P A 0.4347
279 G A 0.0000
280 P A 0.6325
281 C A 0.0000
282 Y A 0.6561
283 R A -0.6546
284 Q A 0.0000
285 Q A -1.4570
286 R A -1.7783
287 V A -1.5790
288 S A 0.0000
289 K A -1.8122
290 T A -1.8038
291 K A -2.7670
292 T A -2.2395
293 D A -2.8361
294 N A -2.8129
295 N A -2.8089
296 N A -2.6867
297 S A -1.7828
298 N A -1.6141
299 F A -0.6848
300 T A -0.0262
301 W A 0.3552
302 T A -0.0263
303 G A -0.4441
304 A A 0.0657
305 S A -0.0406
306 K A 0.1219
307 Y A 0.5471
308 N A -0.9749
309 L A -0.0628
310 N A -1.5246
311 G A -1.5159
312 R A -2.0438
313 E A -1.5579
314 S A -0.3652
315 I A 0.3668
316 I A 0.2552
317 N A -0.7608
318 P A 0.0000
319 G A 0.0000
320 T A 0.1191
321 A A 0.1802
322 M A 0.0000
323 A A 0.0000
324 S A 0.0000
325 H A 0.0000
326 K A -3.0027
327 D A -3.7704
328 D A -3.8037
329 K A -3.6178
330 D A -3.8787
331 K A -2.5967
332 F A -2.0767
333 F A 0.0000
334 P A 0.0000
335 M A -0.5364
336 S A -0.3383
337 G A 0.0000
338 V A 0.0000
339 M A 0.0000
340 I A 1.3300
341 F A 0.3740
342 G A -0.9247
343 K A -1.8429
344 E A -1.7890
345 S A -1.5297
346 A A -1.4672
347 G A -1.1812
348 A A -0.6130
349 S A -0.9409
350 N A -1.3683
351 T A -1.0358
352 A A -0.6038
353 L A -0.6111
354 D A -1.6385
355 N A -1.4808
356 V A -0.4694
357 M A 0.0000
358 I A 0.4171
359 T A 0.0000
360 D A -1.5503
361 E A 0.0000
362 E A -2.8178
363 E A -2.2805
364 I A 0.0000
365 K A -1.9312
366 A A -1.1976
367 T A 0.0000
368 N A 0.0000
369 P A -0.6136
370 V A 0.0000
371 A A 0.0000
372 T A -1.3899
373 E A -1.9780
374 R A -1.9789
375 F A -0.5314
376 G A -0.6566
377 T A -0.3072
378 V A 1.0342
379 A A 1.0387
380 V A 1.6426
381 N A 0.4042
382 L A 0.6189
383 Q A -1.2805
384 S A -1.1456
385 S A -1.2167
386 S A -1.0398
387 T A -1.4108
388 D A -2.3022
389 P A -1.1930
390 A A -0.0882
391 T A 0.2848
392 G A -0.3008
393 D A -1.6616
394 V A -0.6304
395 H A -0.5675
396 V A 1.2488
397 M A 0.7921
398 G A 0.3254
399 A A 0.4722
400 L A 0.6526
401 P A 0.2502
402 G A 0.0731
403 M A 0.6450
404 V A 1.0154
405 W A 0.3717
406 Q A -0.4228
407 D A -0.4427
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 -0.3624
416 I A 0.0000
417 W A 0.0000
418 A A -0.5175
419 K A -1.3781
420 I A 0.0000
421 P A -1.5905
422 H A -2.0588
423 T A -1.8250
424 D A -2.4751
425 G A -1.5893
426 H A -1.0109
427 F A 1.0074
428 H A -0.1110
429 P A -0.2927
430 S A -0.0567
431 P A 0.2594
432 L A 0.9653
433 M A 0.3639
434 G A 0.0000
435 G A -0.0099
436 F A 0.0000
437 G A -0.8284
438 L A 0.0000
439 K A -2.6237
440 H A -2.2450
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 0.1498
451 P A 0.0038
452 V A 0.2972
453 P A 0.0317
454 A A -0.2928
455 N A -1.3261
456 P A -0.9241
457 P A -0.8437
458 A A -0.7480
459 E A -1.0156
460 F A 0.9088
461 S A 0.0880
462 A A 0.0535
463 T A -0.5079
464 K A -1.4558
465 F A -0.2879
466 A A -0.2620
467 S A -0.2881
468 F A 0.3249
469 I A 0.7543
470 T A 0.3586
471 Q A 0.0000
472 Y A 0.3493
473 S A 0.0000
474 T A 0.0249
475 G A 0.0000
476 Q A -0.3236
477 V A 0.0000
478 S A -0.6273
479 V A 0.0000
480 E A -1.2347
481 I A 0.0000
482 E A -1.3580
483 W A 0.0000
484 E A -1.3924
485 L A 0.0000
486 Q A -1.7640
487 K A -2.4044
488 E A -2.4589
489 N A -2.6180
490 S A -2.1108
491 K A -2.2832
492 R A -1.5044
493 W A 0.1009
494 N A -0.2378
495 P A -0.1733
496 E A 0.1807
497 V A 1.2615
498 Q A -0.0345
499 Y A -0.2801
500 T A -0.2619
501 S A -0.4925
502 N A -0.9185
503 Y A 0.2341
504 A A -0.6227
505 K A -1.5813
506 S A -1.0210
507 A A -0.6440
508 N A -0.7316
509 V A 0.5990
510 D A -0.2361
511 F A 0.0158
512 T A 0.5978
513 V A 0.5793
514 D A -0.7805
515 N A -1.9212
516 N A -1.6734
517 G A -0.8229
518 L A 0.3891
519 Y A 0.2967
520 T A 0.0955
521 E A 0.0000
522 P A -0.5792
523 R A -0.6940
524 P A -0.1850
525 I A 0.0000
526 G A -0.2441
527 T A 0.0000
528 R A 0.0000
529 Y A 0.2627
530 L A 0.0000
531 T A -0.3913
532 R A -1.3245
533 P A -0.3535
534 L A 0.6798
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 -0.1005 4.6873 View CSV PDB
4.5 -0.1494 4.6711 View CSV PDB
5.0 -0.2046 4.6531 View CSV PDB
5.5 -0.2584 4.6345 View CSV PDB
6.0 -0.303 4.6157 View CSV PDB
6.5 -0.333 4.5968 View CSV PDB
7.0 -0.35 4.5781 View CSV PDB
7.5 -0.3592 4.5596 View CSV PDB
8.0 -0.3631 4.5422 View CSV PDB
8.5 -0.3594 4.5272 View CSV PDB
9.0 -0.3452 4.5165 View CSV PDB