Project name: 2b5d3ca7702090c

Status: done

Started: 2025-02-06 20:02:37
Settings
Chain sequence(s) A: MVERNSGDLQLPQEIAMLVPNKTQVVPKSGGEGKVKDIFASPALVRAGGVMIAFVEGRTKNKLFPEVIDLSSSDIVAGYIKAPETWQSLVAEVTKEYWQAHTVLESANNSNHRVGVARLPTGITRGNKVFLLVGSYEERREIDDYIWKAEAWNIKVIEGEATQSTEVQPTQPINWSEPKPLFQTDSPNNKGDLKEFLGGGGSGIVMGNGTLVFPLTAKDESNKVFSLITYSTDDGQKWEIPGGVSSVACRSPRVTEWEEGTLLMVTYCEDGRKVFESRDMGKTWTEAFGTLPGVWLKSGPELPEKSLRVDALITATIEGRKVMLYTQKVRHFKEVDEPNALHLWVTDNNRTFHLGPFSVDSAENKTFANTLLYSDDALHLLQAKGDHESTAVSLARLTEELNTI
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode No
Automated mutations Yes
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]       FoldX:    Starting FoldX energy minimalization                                        (00:00:00)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:07:47)
[INFO]       Auto_mut: Residue number 288 from chain A and a score of 1.480 (phenylalanine)        
                       selected for automated muatation                                            (00:07:50)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 1.141 omitted from automated   
                       muatation (excluded by the user).                                           (00:07:50)
[INFO]       Auto_mut: Residue number 145 from chain A and a score of 0.815 (tyrosine) selected    
                       for automated muatation                                                     (00:07:50)
[INFO]       Auto_mut: Residue number 2 from chain A and a score of 0.735 (valine) selected for    
                       automated muatation                                                         (00:07:50)
[INFO]       Auto_mut: Residue number 68 from chain A and a score of 0.619 (isoleucine) selected   
                       for automated muatation                                                     (00:07:50)
[INFO]       Auto_mut: Residue number 146 from chain A and a score of 0.617 (isoleucine) selected  
                       for automated muatation                                                     (00:07:50)
[INFO]       Auto_mut: Residue number 142 from chain A and a score of 0.554 (isoleucine) selected  
                       for automated muatation                                                     (00:07:50)
[INFO]       Auto_mut: Mutating residue number 145 from chain A (tyrosine) into glutamic acid      (00:07:50)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 288 from chain A (phenylalanine) into glutamic acid (00:07:50)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 288 from chain A (phenylalanine) into aspartic acid (00:07:50)
[INFO]       Auto_mut: Mutating residue number 145 from chain A (tyrosine) into lysine             (00:11:22)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (phenylalanine) into arginine      (00:11:35)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (phenylalanine) into lysine        (00:11:38)
[INFO]       Auto_mut: Mutating residue number 145 from chain A (tyrosine) into aspartic acid      (00:15:25)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (valine) into glutamic acid          (00:15:26)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (valine) into aspartic acid          (00:15:31)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (valine) into lysine                 (00:18:51)
[INFO]       Auto_mut: Mutating residue number 145 from chain A (tyrosine) into arginine           (00:18:55)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (valine) into arginine               (00:18:59)
[INFO]       Auto_mut: Mutating residue number 68 from chain A (isoleucine) into glutamic acid     (00:22:20)
[INFO]       Auto_mut: Mutating residue number 68 from chain A (isoleucine) into aspartic acid     (00:22:33)
[INFO]       Auto_mut: Mutating residue number 146 from chain A (isoleucine) into glutamic acid    (00:22:35)
[INFO]       Auto_mut: Mutating residue number 68 from chain A (isoleucine) into lysine            (00:25:49)
[INFO]       Auto_mut: Mutating residue number 68 from chain A (isoleucine) into arginine          (00:25:59)
[INFO]       Auto_mut: Mutating residue number 146 from chain A (isoleucine) into lysine           (00:26:12)
[INFO]       Auto_mut: Mutating residue number 146 from chain A (isoleucine) into aspartic acid    (00:29:37)
[INFO]       Auto_mut: Mutating residue number 142 from chain A (isoleucine) into glutamic acid    (00:29:46)
[INFO]       Auto_mut: Mutating residue number 142 from chain A (isoleucine) into aspartic acid    (00:30:05)
[INFO]       Auto_mut: Mutating residue number 146 from chain A (isoleucine) into arginine         (00:33:06)
[INFO]       Auto_mut: Mutating residue number 142 from chain A (isoleucine) into lysine           (00:33:27)
[INFO]       Auto_mut: Mutating residue number 142 from chain A (isoleucine) into arginine         (00:33:40)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: -0.0805 kcal/mol, Difference in average   
                       score from the base case: -0.0314                                           (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.2452 kcal/mol, Difference in average score     
                       from the base case: -0.0213                                                 (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: -0.0083 kcal/mol, Difference in average   
                       score from the base case: -0.0305                                           (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (phenylalanine) into     
                       arginine: Energy difference: -1.4006 kcal/mol, Difference in average score  
                       from the base case: -0.0314                                                 (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 145 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.4052 kcal/mol, Difference in average score from  
                       the base case: -0.0060                                                      (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 145 from chain A (tyrosine) into lysine:  
                       Energy difference: 0.2718 kcal/mol, Difference in average score from the    
                       base case: -0.0155                                                          (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 145 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: -0.0246 kcal/mol, Difference in average score from 
                       the base case: -0.0125                                                      (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 145 from chain A (tyrosine) into          
                       arginine: Energy difference: 0.2461 kcal/mol, Difference in average score   
                       from the base case: -0.0138                                                 (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (valine) into glutamic     
                       acid: Energy difference: -0.3047 kcal/mol, Difference in average score from 
                       the base case: -0.0063                                                      (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (valine) into lysine:      
                       Energy difference: -0.9708 kcal/mol, Difference in average score from the   
                       base case: -0.0069                                                          (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (valine) into aspartic     
                       acid: Energy difference: -0.7279 kcal/mol, Difference in average score from 
                       the base case: -0.0073                                                      (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (valine) into arginine:    
                       Energy difference: -0.6309 kcal/mol, Difference in average score from the   
                       base case: -0.0086                                                          (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 68 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: -0.1380 kcal/mol, Difference in average   
                       score from the base case: -0.0136                                           (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 68 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.3909 kcal/mol, Difference in average score from the   
                       base case: -0.0154                                                          (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 68 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 0.2408 kcal/mol, Difference in average    
                       score from the base case: -0.0130                                           (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 68 from chain A (isoleucine) into         
                       arginine: Energy difference: -0.5187 kcal/mol, Difference in average score  
                       from the base case: -0.0109                                                 (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 146 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 1.1758 kcal/mol, Difference in average    
                       score from the base case: -0.0159                                           (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 146 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.1730 kcal/mol, Difference in average score    
                       from the base case: -0.0116                                                 (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 146 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 1.2882 kcal/mol, Difference in average    
                       score from the base case: -0.0100                                           (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 146 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.2535 kcal/mol, Difference in average score   
                       from the base case: -0.0147                                                 (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 142 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.1607 kcal/mol, Difference in average   
                       score from the base case: -0.0070                                           (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 142 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.2522 kcal/mol, Difference in average score    
                       from the base case: -0.0262                                                 (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 142 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.2708 kcal/mol, Difference in average    
                       score from the base case: -0.0163                                           (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 142 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.3448 kcal/mol, Difference in average score  
                       from the base case: -0.0206                                                 (00:37:29)
[INFO]       Main:     Simulation completed successfully.                                          (00:37:37)
Show buried residues
Minimal score value
-3.891
Maximal score value
1.4805
Average score
-0.9069
Total score value
-366.378
Download the table (csv)

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
1 M A 1.1406
2 V A 0.7352
3 E A -1.9089
4 R A -2.8079
5 N A -2.7234
6 S A -1.9613
7 G A -1.7713
8 D A -1.7810
9 L A -0.1193
10 Q A -0.8968
11 L A -0.0080
12 P A -0.7387
13 Q A -0.9714
14 E A -0.7013
15 I A -0.1415
16 A A 0.1416
17 M A 0.0000
18 L A 0.0000
19 V A -0.2398
20 P A -1.1161
21 N A -2.1003
22 K A -2.3441
23 T A 0.0000
24 Q A -1.7733
25 V A 0.0000
26 V A -1.5670
27 P A -1.9629
28 K A -2.0134
29 S A -1.5483
30 G A -1.6398
31 G A -2.0657
32 E A -2.7072
33 G A -2.2693
34 K A -2.4646
35 V A -1.0871
36 K A 0.0000
37 D A -1.3329
38 I A -0.8815
39 F A 0.0000
40 A A -0.0668
41 S A -0.0133
42 P A 0.0000
43 A A 0.0000
44 L A 0.0000
45 V A 0.0000
46 R A -1.0056
47 A A 0.0000
48 G A -1.5945
49 G A -1.4754
50 V A 0.0000
51 M A 0.0000
52 I A 0.0000
53 A A 0.0000
54 F A 0.0000
55 V A 0.0000
56 E A 0.0000
57 G A 0.0000
58 R A -0.6580
59 T A -1.2036
60 K A -1.6683
61 N A -1.7001
62 K A -1.9914
63 L A -0.7940
64 F A 0.0000
65 P A -1.2761
66 E A -1.5340
67 V A 0.2152
68 I A 0.6192
69 D A -1.5794
70 L A 0.0000
71 S A 0.0000
72 S A 0.0000
73 S A 0.0000
74 D A -0.7223
75 I A 0.0000
76 V A 0.0000
77 A A 0.0000
78 G A 0.0000
79 Y A 0.0000
80 I A 0.0000
81 K A -1.6460
82 A A -1.2812
83 P A -1.4248
84 E A -2.4340
85 T A -1.2585
86 W A -0.9501
87 Q A -1.2915
88 S A -1.0847
89 L A 0.0000
90 V A -0.0891
91 A A -0.2763
92 E A 0.0000
93 V A 0.0000
94 T A -0.5392
95 K A -1.1382
96 E A -1.5567
97 Y A 0.0200
98 W A -0.3859
99 Q A -0.8111
100 A A 0.0000
101 H A -0.9332
102 T A 0.0000
103 V A 0.0000
104 L A 0.0000
105 E A -1.4751
106 S A -1.1740
107 A A -1.3197
108 N A -2.4984
109 N A -2.6680
110 S A -2.3487
111 N A -2.4415
112 H A -2.0747
113 R A -2.8966
114 V A 0.0000
115 G A 0.0000
116 V A 0.0000
117 A A 0.0000
118 R A -0.4769
119 L A -0.0412
120 P A 0.0000
121 T A 0.0000
122 G A 0.0000
123 I A 0.0000
124 T A -1.0932
125 R A -1.9609
126 G A -1.7545
127 N A -2.0777
128 K A -2.4865
129 V A 0.0000
130 F A 0.0000
131 L A 0.0000
132 L A 0.0000
133 V A 0.0000
134 G A 0.0000
135 S A -0.7457
136 Y A 0.0000
137 E A -1.9270
138 E A -2.1124
139 R A -2.2995
140 R A -1.2617
141 E A -0.9506
142 I A 0.5536
143 D A -1.4260
144 D A -1.3096
145 Y A 0.8146
146 I A 0.6169
147 W A -0.4203
148 K A -1.4700
149 A A -1.5163
150 E A -2.0984
151 A A -1.1882
152 W A -1.1528
153 N A -1.4468
154 I A 0.0000
155 K A -0.9195
156 V A 0.0000
157 I A 0.0000
158 E A -1.4350
159 G A 0.0000
160 E A -2.6313
161 A A 0.0000
162 T A -1.7923
163 Q A -1.8254
164 S A -1.3124
165 T A -1.0281
166 E A -1.6549
167 V A 0.2740
168 Q A -1.1383
169 P A -1.3103
170 T A -0.6927
171 Q A -1.0733
172 P A 0.0000
173 I A 0.0000
174 N A -1.8975
175 W A -1.6323
176 S A -1.5997
177 E A -2.0871
178 P A -1.3568
179 K A -1.3847
180 P A -1.0784
181 L A 0.0000
182 F A -1.3274
183 Q A -2.0941
184 T A -1.5936
185 D A -2.4972
186 S A -2.3209
187 P A -2.3925
188 N A -3.4516
189 N A -3.2102
190 K A -3.3392
191 G A -3.0899
192 D A -3.8910
193 L A -3.0208
194 K A -2.9807
195 E A -1.9347
196 F A -0.6667
197 L A -0.3189
198 G A 0.0000
199 G A 0.0000
200 G A 0.0000
201 G A 0.0000
202 S A 0.1654
203 G A 0.0000
204 I A 0.4029
205 V A 0.2593
206 M A 0.0000
207 G A -1.5551
208 N A -1.7575
209 G A -1.1648
210 T A 0.0000
211 L A 0.0000
212 V A 0.0000
213 F A 0.0000
214 P A 0.0000
215 L A 0.0000
216 T A 0.0000
217 A A 0.0000
218 K A -2.3451
219 D A -3.1846
220 E A -3.6259
221 S A -2.5043
222 N A -2.9848
223 K A -2.0743
224 V A 0.0000
225 F A -0.2507
226 S A 0.0000
227 L A 0.0000
228 I A 0.0000
229 T A 0.0000
230 Y A -0.6836
231 S A 0.0000
232 T A -1.6227
233 D A -1.9994
234 D A -2.5765
235 G A 0.0000
236 Q A -2.6280
237 K A -3.0741
238 W A -2.0793
239 E A -2.0989
240 I A -1.1073
241 P A 0.0000
242 G A -1.5144
243 G A -0.7506
244 V A 0.4715
245 S A 0.0000
246 S A -0.0241
247 V A 0.3958
248 A A -1.0092
249 C A 0.0000
250 R A -1.9022
251 S A -0.8946
252 P A 0.0000
253 R A 0.0000
254 V A 0.0000
255 T A 0.0000
256 E A -0.9139
257 W A 0.0000
258 E A -2.7603
259 E A -3.1557
260 G A -2.3697
261 T A 0.0000
262 L A 0.0000
263 L A 0.0000
264 M A 0.0000
265 V A 0.0000
266 T A 0.0000
267 Y A -1.7022
268 C A 0.0000
269 E A -3.2742
270 D A -3.1608
271 G A 0.0000
272 R A 0.0000
273 K A -0.6528
274 V A 0.0000
275 F A 0.0000
276 E A -0.7916
277 S A 0.0000
278 R A -2.8652
279 D A -1.9713
280 M A -1.1232
281 G A 0.0000
282 K A -2.0317
283 T A -1.2740
284 W A -0.8023
285 T A -0.3377
286 E A -0.2149
287 A A 0.3701
288 F A 1.4805
289 G A 0.1473
290 T A 0.0000
291 L A 0.0000
292 P A -0.4382
293 G A -0.2828
294 V A 0.0000
295 W A 0.1474
296 L A -0.6962
297 K A -2.2277
298 S A -2.3632
299 G A -1.7443
300 P A -1.2071
301 E A -2.1650
302 L A -1.8678
303 P A -1.9763
304 E A -3.1922
305 K A -2.6374
306 S A -1.6325
307 L A 0.0000
308 R A -1.2616
309 V A 0.0000
310 D A 0.0000
311 A A 0.0000
312 L A 0.0000
313 I A 0.2875
314 T A -0.0768
315 A A 0.0000
316 T A -1.7394
317 I A -2.0058
318 E A -2.7862
319 G A -2.4084
320 R A -3.0376
321 K A -2.3670
322 V A 0.0000
323 M A 0.0000
324 L A 0.0000
325 Y A 0.0000
326 T A 0.0000
327 Q A 0.0000
328 K A 0.0000
329 V A -0.1186
330 R A -1.2249
331 H A -1.3878
332 F A -0.0178
333 K A -2.0429
334 E A -2.5272
335 V A -0.5024
336 D A -2.4875
337 E A -2.7053
338 P A -1.4976
339 N A -1.0161
340 A A 0.0000
341 L A 0.0000
342 H A 0.0000
343 L A 0.0000
344 W A 0.1837
345 V A 0.0000
346 T A 0.0000
347 D A -1.9050
348 N A -2.0008
349 N A -2.5952
350 R A -2.5300
351 T A -1.0917
352 F A 0.2847
353 H A -0.0818
354 L A 0.0583
355 G A 0.0614
356 P A 0.3012
357 F A 0.0000
358 S A 0.2344
359 V A 0.5371
360 D A -0.8536
361 S A -1.4088
362 A A -1.5030
363 E A -3.1333
364 N A -2.6618
365 K A -1.9113
366 T A 0.0000
367 F A -0.7858
368 A A 0.0000
369 N A 0.0000
370 T A 0.0000
371 L A 0.0000
372 L A 0.0684
373 Y A -0.4384
374 S A -1.3546
375 D A -2.8933
376 D A -2.7750
377 A A 0.0000
378 L A 0.0000
379 H A 0.0000
380 L A 0.0000
381 L A 0.0000
382 Q A 0.0000
383 A A 0.0000
384 K A -1.4839
385 G A 0.0000
386 D A -2.8307
387 H A -2.7447
388 E A -3.1214
389 S A -2.0972
390 T A 0.0000
391 A A -0.3094
392 V A 0.0000
393 S A 0.0000
394 L A 0.0000
395 A A 0.0000
396 R A -0.7844
397 L A 0.0000
398 T A -1.5700
399 E A -2.3248
400 E A -1.4301
401 L A -1.1949
402 N A -1.7669
403 T A -0.9034
404 I A -0.3058
Download PDB file
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Automated mutations analysis

In the automated mutations mode, the server selects aggregation prone resides and each selected residue is mutated to glutamic acid, lysine, aspartic acid and arginine. The table below shows 2 best scored mutants for each mutated residue. Protein variants are ordered according to the mutation effect they had on protein stability (energetic effect) together with the difference in the average per-residue aggregation score between the wild type and the mutant (in the table green values indicate a positive change, grey are neutral, and orange/red mean destabilizing or more aggregation prone mutants).
Summary for all the mutants can be found in this CSV file.

Mutant
Energetic effect
Score comparison
FR288A -1.4006 -0.0314 View CSV PDB
IK142A -0.2522 -0.0262 View CSV PDB
FE288A -0.0805 -0.0314 View CSV PDB
IR142A -0.3448 -0.0206 View CSV PDB
IK68A -0.3909 -0.0154 View CSV PDB
IR68A -0.5187 -0.0109 View CSV PDB
VK2A -0.9708 -0.0069 View CSV PDB
VR2A -0.6309 -0.0086 View CSV PDB
IK146A -0.173 -0.0116 View CSV PDB
YD145A -0.0246 -0.0125 View CSV PDB
IR146A 0.2535 -0.0147 View CSV PDB
YK145A 0.2718 -0.0155 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018