Project name: AAV1_1mer_M2

Status: done

Started: 2026-10-21 17:41:15
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]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[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                                          (00:02:18)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/1bf21ef1d0864f/tmp/folded.pdb                 (00:02:18)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:37)
Show buried residues

Minimal score value
-4.0091
Maximal score value
2.2777
Average score
-0.5436
Total score value
-281.6088

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 -2.3631
18 G A -1.3397
19 V A 0.3230
20 G A -0.6821
21 N A -1.7789
22 A A -1.3261
23 S A -1.4180
24 G A -1.2019
25 N A -1.1181
26 W A -0.2899
27 H A -1.1865
28 C A -1.0201
29 D A -1.8062
30 S A -0.8078
31 T A -0.0912
32 W A 0.0552
33 L A 0.2168
34 G A -1.1151
35 D A -2.2361
36 R A -1.2026
37 V A 0.0000
38 I A -0.1489
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 0.4085
45 W A 0.0000
46 A A 0.6997
47 L A 0.0000
48 P A 0.0808
49 T A -0.1803
50 Y A -0.1324
51 N A -0.5382
52 N A -0.8472
53 H A -0.0794
54 L A 0.6521
55 Y A 0.0342
56 K A -1.0972
57 Q A -0.7987
58 I A 0.1373
59 S A 0.0182
60 S A 0.0000
61 A A -0.2753
62 S A -0.2909
63 T A -0.5830
64 G A -0.9183
65 A A -1.2104
66 S A -1.6944
67 N A -2.6181
68 D A -2.5873
69 N A -2.3221
70 H A -1.7882
71 Y A -0.0280
72 F A 0.4659
73 G A 0.0000
74 Y A 0.3314
75 S A -0.1743
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 -0.5642
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 -1.0368
92 P A -1.5034
93 R A -2.4848
94 D A -1.7634
95 W A 0.0000
96 Q A -2.0485
97 R A -2.5414
98 L A 0.0000
99 I A 0.0000
100 N A -1.0685
101 N A -1.9777
102 N A 0.0000
103 W A -0.8985
104 G A 0.0000
105 F A 0.0000
106 R A -0.8998
107 P A 0.0000
108 K A -2.0314
109 R A -2.0439
110 L A 0.0000
111 N A -1.1310
112 F A 0.0000
113 K A -1.0846
114 L A 0.0000
115 F A 0.0000
116 N A -1.1259
117 I A 0.0000
118 Q A -1.0398
119 V A 0.0000
120 K A -0.4381
121 E A -0.0268
122 V A 0.4015
123 T A 0.2388
124 T A -0.4859
125 N A -1.7533
126 D A -2.1007
127 G A -0.9381
128 V A 0.4925
129 T A 0.4264
130 T A 0.7429
131 I A 1.0858
132 A A 0.0482
133 N A -1.0564
134 N A -0.5840
135 L A 0.3543
136 T A -0.0570
137 S A 0.0000
138 T A 0.0000
139 V A 0.0000
140 Q A -0.4466
141 V A 0.0000
142 F A 0.0000
143 S A -0.4314
144 D A 0.0000
145 S A -1.3045
146 E A -2.2657
147 Y A -1.5286
148 Q A -1.2858
149 L A 0.0000
150 P A 0.2501
151 Y A 0.0552
152 V A 0.2948
153 L A 0.0000
154 G A -0.4840
155 S A -0.5513
156 A A -0.7052
157 H A -1.2571
158 Q A -1.5477
159 G A -0.6143
160 C A -0.4239
161 L A 0.0000
162 P A -0.0165
163 P A -0.0809
164 F A 0.6258
165 P A 0.0508
166 A A -0.1661
167 D A -0.5786
168 V A 1.2257
169 F A 0.0000
170 M A 1.3537
171 I A 0.0000
172 P A -0.2588
173 Q A -0.3211
174 Y A 0.0000
175 G A -0.0226
176 Y A 0.0000
177 L A 2.0327
178 T A 1.2993
179 L A 0.3083
180 N A -0.6303
181 N A -1.8169
182 G A -1.6525
183 S A -1.2398
184 Q A -1.4495
185 A A -0.9488
186 V A -0.9269
187 G A -1.1324
188 R A -1.6559
189 S A -0.3892
190 S A 0.6943
191 F A 1.7972
192 Y A 1.2758
193 C A 0.9511
194 L A 0.0000
195 E A -0.2064
196 Y A 1.0309
197 F A 0.2898
198 P A -0.2108
199 S A -0.4882
200 Q A -1.0732
201 M A -0.1268
202 L A 0.0000
203 R A -1.5593
204 T A -1.3707
205 G A -1.6544
206 N A -1.9817
207 N A -1.6430
208 F A -0.5861
209 T A -0.4585
210 F A -0.1705
211 S A -0.6626
212 Y A -0.7922
213 T A -1.4086
214 F A 0.0000
215 E A -2.2029
216 E A -2.1907
217 V A 0.0000
218 P A -0.4668
219 F A 0.0438
220 H A 0.0000
221 S A -0.0018
222 S A 0.0000
223 Y A -0.3046
224 A A -0.7953
225 H A -0.8656
226 S A -0.9093
227 Q A -1.1048
228 S A -0.9967
229 L A 0.0000
230 D A -1.3905
231 R A -1.2518
232 L A -0.4110
233 M A -0.1913
234 N A -0.0125
235 P A 0.4365
236 L A 1.8016
237 I A 1.7109
238 D A -0.6778
239 Q A -0.0845
240 Y A 1.1753
241 L A 0.9978
242 Y A 1.8138
243 Y A 1.4677
244 L A 1.7139
245 N A 0.1984
246 R A -0.7000
247 T A -1.0088
248 Q A -2.5978
249 N A -2.6186
250 Q A -2.4989
251 S A -1.6801
252 G A -1.2789
253 S A -1.0951
254 A A -1.7103
255 Q A -2.9071
256 N A -3.3405
257 K A -3.0836
258 D A -1.4793
259 L A 1.1800
260 L A 1.0991
261 F A 2.2777
262 S A 0.6704
263 R A -0.4407
264 G A 0.0000
265 S A -0.1967
266 P A 0.0807
267 A A 0.0222
268 G A 0.0647
269 M A 0.0097
270 S A 0.0255
271 V A 0.9712
272 Q A 0.0000
273 P A -0.3958
274 K A -1.3332
275 N A -1.3777
276 W A 0.1007
277 L A 0.4563
278 P A 0.3655
279 G A 0.0000
280 P A 0.3056
281 C A 0.0000
282 Y A -0.0251
283 R A -1.1036
284 Q A 0.0000
285 Q A -1.2909
286 R A -1.8543
287 V A -1.5984
288 S A 0.0000
289 K A -1.8127
290 T A -1.7533
291 K A -2.7166
292 T A -2.1267
293 D A -2.6333
294 N A -2.7463
295 N A -2.7684
296 N A -2.6667
297 S A -1.8240
298 N A -1.6499
299 F A -0.7343
300 T A -0.0514
301 W A 0.3057
302 T A -0.0804
303 G A -0.4297
304 A A -0.1021
305 S A -0.0401
306 K A 0.0737
307 Y A 0.4566
308 N A -0.9730
309 L A -0.0148
310 N A -1.4858
311 G A -1.4729
312 R A -1.9651
313 E A -1.5387
314 S A -0.4028
315 I A 0.2346
316 I A 0.1781
317 N A -0.7706
318 P A 0.0000
319 G A 0.0876
320 T A 0.1133
321 A A 0.2242
322 M A 0.0000
323 A A 0.0000
324 S A 0.0000
325 H A 0.0000
326 K A -3.2396
327 D A -4.0091
328 D A -3.8322
329 E A -3.4829
330 D A -3.9107
331 K A -2.5233
332 F A -1.9967
333 F A 0.0000
334 P A 0.0000
335 M A -0.4531
336 S A 0.0000
337 G A 0.0000
338 V A 0.0000
339 M A 0.0000
340 I A 1.3339
341 F A 0.1568
342 G A -1.1920
343 K A -2.3060
344 E A -2.3678
345 S A -1.7698
346 A A -1.6449
347 G A -1.2508
348 A A -0.6098
349 S A -0.9397
350 N A -1.3805
351 T A -1.0708
352 A A -0.7039
353 L A -0.7185
354 D A -1.6988
355 N A -1.5837
356 V A -0.6740
357 M A 0.0000
358 I A 0.2549
359 T A 0.0000
360 D A -1.5520
361 E A 0.0000
362 E A -3.0420
363 E A -2.1829
364 I A 0.0000
365 K A -2.3473
366 A A 0.0000
367 T A 0.0000
368 N A 0.0000
369 P A -0.5183
370 V A -0.8094
371 A A 0.0000
372 T A -1.3009
373 E A -1.7874
374 R A -2.0437
375 F A -0.7786
376 G A -0.8168
377 T A -0.3305
378 V A 0.9769
379 A A 1.0902
380 V A 1.7380
381 N A 0.6513
382 F A 1.0394
383 Q A -1.0757
384 S A -1.0434
385 S A -1.1737
386 S A -1.0472
387 T A -1.3400
388 D A -2.2380
389 P A -1.0617
390 A A -0.0172
391 T A 0.2719
392 G A -0.3215
393 D A -1.8347
394 V A -1.1155
395 H A -1.4247
396 A A -0.4940
397 M A -0.0691
398 G A -0.0965
399 A A 0.4109
400 L A 0.6020
401 P A 0.1923
402 G A 0.0520
403 M A 0.5903
404 V A 0.9486
405 W A 0.3029
406 Q A -0.4322
407 D A -0.4072
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 -0.3580
416 I A 0.0000
417 W A 0.0000
418 A A -0.5938
419 K A -1.4456
420 I A 0.0000
421 P A -1.5806
422 H A -2.1816
423 T A -1.7928
424 D A -2.4436
425 G A -1.5742
426 H A -0.8406
427 F A 1.1142
428 H A -0.0468
429 P A -0.2557
430 S A -0.0097
431 P A 0.2705
432 L A 0.9893
433 M A 0.4427
434 G A 0.0000
435 G A 0.0108
436 F A 0.0000
437 G A -0.8696
438 L A 0.0000
439 K A -2.7362
440 N A -2.6057
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 0.1860
451 P A 0.1024
452 V A 0.4590
453 P A 0.1339
454 A A -0.2942
455 N A -1.2398
456 P A -0.8603
457 P A -0.8311
458 A A -0.7437
459 E A -1.0161
460 F A 0.8911
461 S A 0.0592
462 A A 0.0500
463 T A -0.4611
464 K A -1.3398
465 F A -0.1352
466 A A -0.0472
467 S A -0.2652
468 F A 0.2487
469 I A 0.4380
470 T A 0.1418
471 Q A 0.0000
472 Y A 0.3501
473 S A 0.0000
474 T A 0.0275
475 G A 0.0000
476 Q A -0.3803
477 V A 0.0000
478 S A 0.0000
479 V A 0.0000
480 E A -1.1897
481 I A 0.0000
482 E A 0.0000
483 W A 0.0000
484 E A -1.3797
485 L A 0.0000
486 Q A -1.9086
487 K A -2.4440
488 E A -2.3861
489 N A -2.5769
490 S A -2.0881
491 K A -2.3540
492 R A -1.6398
493 W A -0.0749
494 N A -0.5632
495 P A -0.3161
496 E A 0.0901
497 V A 1.2125
498 Q A -0.1633
499 Y A -0.3143
500 T A -0.4400
501 S A -0.8329
502 N A -1.0026
503 Y A 0.2948
504 A A -0.4068
505 K A -1.6194
506 S A -1.2187
507 A A -0.9001
508 N A -1.2564
509 V A -0.0255
510 D A -1.5523
511 F A -0.6774
512 T A 0.1482
513 V A 0.2317
514 D A -1.2487
515 N A -2.1179
516 N A -1.8748
517 G A -1.1157
518 L A -0.2282
519 Y A -0.1548
520 T A -0.5476
521 E A -1.3294
522 P A -1.3952
523 R A -1.7587
524 P A 0.0000
525 I A 0.0000
526 G A -0.3304
527 T A 0.0000
528 R A 0.0000
529 Y A 0.2229
530 L A 0.0000
531 T A -0.4888
532 R A -1.3911
533 P A -0.7504
534 L A 0.0621
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 -0.1246 4.255 View CSV PDB
4.5 -0.1741 4.2292 View CSV PDB
5.0 -0.2313 4.2145 View CSV PDB
5.5 -0.2883 4.1993 View CSV PDB
6.0 -0.3373 4.1839 View CSV PDB
6.5 -0.3724 4.1685 View CSV PDB
7.0 -0.3935 4.1531 View CSV PDB
7.5 -0.4049 4.1381 View CSV PDB
8.0 -0.4095 4.1239 View CSV PDB
8.5 -0.4062 4.1118 View CSV PDB
9.0 -0.3928 4.1032 View CSV PDB