Project name: 8dwy_A

Status: done

Started: 2024-06-14 20:42:48
Settings
Chain sequence(s) A: YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELQSVTLEPTLSLDYITCEYKTVIPSPYVKCCGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFASAYRAHTASASAKLRVLYQGNNITVAAYANGDHAVTVKDAKFVVGPMSSAWTPFDNKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNIPISIDIPDAAFTRVVDAPSVTDMSCEVPACTHSSDFGGVAIIKYTASKKGKCAVHSMTNAVTIREADVEVEGNSQLQISFSTALASAEFRVQVCSTQVHCAAACHPPKDHIVNYPASHTTLGVQDISTTAMSWVQKITGGVGLIVAVAALILIVVLCVSFSRH
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]                                                (00:00:01)
[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]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:03:24)
[INFO]       Auto_mut: Residue number 430 from chain A and a score of 5.159 (valine) selected for  
                       automated muatation                                                         (00:03:27)
[INFO]       Auto_mut: Residue number 427 from chain A and a score of 5.103 (isoleucine) selected  
                       for automated muatation                                                     (00:03:27)
[INFO]       Auto_mut: Residue number 429 from chain A and a score of 5.015 (isoleucine) selected  
                       for automated muatation                                                     (00:03:27)
[INFO]       Auto_mut: Residue number 428 from chain A and a score of 4.995 (leucine) selected for 
                       automated muatation                                                         (00:03:27)
[INFO]       Auto_mut: Residue number 431 from chain A and a score of 4.869 (valine) selected for  
                       automated muatation                                                         (00:03:27)
[INFO]       Auto_mut: Residue number 426 from chain A and a score of 4.615 (leucine) selected for 
                       automated muatation                                                         (00:03:27)
[INFO]       Auto_mut: Mutating residue number 430 from chain A (valine) into glutamic acid        (00:03:27)
[INFO]       Auto_mut: Mutating residue number 430 from chain A (valine) into aspartic acid        (00:03:27)
[INFO]       Auto_mut: Mutating residue number 427 from chain A (isoleucine) into glutamic acid    (00:03:27)
[INFO]       Auto_mut: Mutating residue number 430 from chain A (valine) into arginine             (00:04:57)
[INFO]       Auto_mut: Mutating residue number 430 from chain A (valine) into lysine               (00:04:58)
[INFO]       Auto_mut: Mutating residue number 427 from chain A (isoleucine) into lysine           (00:04:58)
[INFO]       Auto_mut: Mutating residue number 427 from chain A (isoleucine) into aspartic acid    (00:06:35)
[INFO]       Auto_mut: Mutating residue number 429 from chain A (isoleucine) into glutamic acid    (00:06:37)
[INFO]       Auto_mut: Mutating residue number 429 from chain A (isoleucine) into aspartic acid    (00:06:38)
[INFO]       Auto_mut: Mutating residue number 427 from chain A (isoleucine) into arginine         (00:08:05)
[INFO]       Auto_mut: Mutating residue number 429 from chain A (isoleucine) into lysine           (00:08:09)
[INFO]       Auto_mut: Mutating residue number 429 from chain A (isoleucine) into arginine         (00:08:09)
[INFO]       Auto_mut: Mutating residue number 428 from chain A (leucine) into glutamic acid       (00:09:39)
[INFO]       Auto_mut: Mutating residue number 428 from chain A (leucine) into aspartic acid       (00:09:42)
[INFO]       Auto_mut: Mutating residue number 431 from chain A (valine) into glutamic acid        (00:09:44)
[INFO]       Auto_mut: Mutating residue number 428 from chain A (leucine) into lysine              (00:11:10)
[INFO]       Auto_mut: Mutating residue number 428 from chain A (leucine) into arginine            (00:11:11)
[INFO]       Auto_mut: Mutating residue number 431 from chain A (valine) into lysine               (00:11:15)
[INFO]       Auto_mut: Mutating residue number 431 from chain A (valine) into aspartic acid        (00:12:45)
[INFO]       Auto_mut: Mutating residue number 426 from chain A (leucine) into glutamic acid       (00:12:46)
[INFO]       Auto_mut: Mutating residue number 426 from chain A (leucine) into aspartic acid       (00:12:54)
[INFO]       Auto_mut: Mutating residue number 431 from chain A (valine) into arginine             (00:14:16)
[INFO]       Auto_mut: Mutating residue number 426 from chain A (leucine) into lysine              (00:14:16)
[INFO]       Auto_mut: Mutating residue number 426 from chain A (leucine) into arginine            (00:14:23)
[INFO]       Auto_mut: Effect of mutation residue number 430 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.0225 kcal/mol, Difference in average score from  
                       the base case: -0.0338                                                      (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 430 from chain A (valine) into lysine:    
                       Energy difference: -0.4272 kcal/mol, Difference in average score from the   
                       base case: -0.0344                                                          (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 430 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.5214 kcal/mol, Difference in average score from  
                       the base case: -0.0338                                                      (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 430 from chain A (valine) into arginine:  
                       Energy difference: -0.3278 kcal/mol, Difference in average score from the   
                       base case: -0.0354                                                          (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 427 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.3047 kcal/mol, Difference in average    
                       score from the base case: -0.0346                                           (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 427 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.0704 kcal/mol, Difference in average score     
                       from the base case: -0.0395                                                 (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 427 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.7011 kcal/mol, Difference in average    
                       score from the base case: -0.0321                                           (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 427 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.1990 kcal/mol, Difference in average score  
                       from the base case: -0.0346                                                 (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 429 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.8525 kcal/mol, Difference in average    
                       score from the base case: -0.0294                                           (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 429 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.4464 kcal/mol, Difference in average score     
                       from the base case: -0.0294                                                 (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 429 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 1.4591 kcal/mol, Difference in average    
                       score from the base case: -0.0297                                           (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 429 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.2283 kcal/mol, Difference in average score   
                       from the base case: -0.0280                                                 (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 428 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.6384 kcal/mol, Difference in average score from  
                       the base case: -0.0284                                                      (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 428 from chain A (leucine) into lysine:   
                       Energy difference: 0.2991 kcal/mol, Difference in average score from the    
                       base case: -0.0302                                                          (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 428 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.1413 kcal/mol, Difference in average score from  
                       the base case: -0.0269                                                      (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 428 from chain A (leucine) into arginine: 
                       Energy difference: 0.3295 kcal/mol, Difference in average score from the    
                       base case: -0.0251                                                          (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 431 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.2702 kcal/mol, Difference in average score from  
                       the base case: -0.0322                                                      (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 431 from chain A (valine) into lysine:    
                       Energy difference: -0.1465 kcal/mol, Difference in average score from the   
                       base case: -0.0348                                                          (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 431 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.9197 kcal/mol, Difference in average score from  
                       the base case: -0.0313                                                      (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 431 from chain A (valine) into arginine:  
                       Energy difference: 0.2346 kcal/mol, Difference in average score from the    
                       base case: -0.0335                                                          (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 426 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.3295 kcal/mol, Difference in average score from  
                       the base case: -0.0301                                                      (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 426 from chain A (leucine) into lysine:   
                       Energy difference: 0.0131 kcal/mol, Difference in average score from the    
                       base case: -0.0302                                                          (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 426 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.7108 kcal/mol, Difference in average score from  
                       the base case: -0.0323                                                      (00:15:57)
[INFO]       Auto_mut: Effect of mutation residue number 426 from chain A (leucine) into arginine: 
                       Energy difference: 0.0187 kcal/mol, Difference in average score from the    
                       base case: -0.0304                                                          (00:15:57)
[INFO]       Main:     Simulation completed successfully.                                          (00:16:04)
Show buried residues
Minimal score value
-4.1008
Maximal score value
5.1588
Average score
-0.4602
Total score value
-202.0325
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 Y A -1.0785
2 E A -1.7136
3 H A -0.3465
4 V A 1.5310
5 T A 1.7213
6 V A 1.9378
7 I A 0.0000
8 P A 0.0369
9 N A -0.1581
10 T A -0.2175
11 V A -0.1213
12 G A -0.3031
13 V A -0.0839
14 P A -0.5457
15 Y A -0.4890
16 K A -0.6450
17 T A 0.4285
18 L A 0.2503
19 V A 0.0000
20 N A -1.0168
21 R A -0.9136
22 P A -0.8256
23 G A -0.4516
24 Y A -0.3808
25 S A -0.2722
26 P A -0.1001
27 M A -0.1308
28 V A -0.1022
29 L A 0.0000
30 E A -0.4824
31 M A 0.0000
32 E A -0.8818
33 L A 0.0000
34 Q A -1.3729
35 S A -0.8197
36 V A 0.0000
37 T A -0.4059
38 L A -0.4744
39 E A -1.3516
40 P A -0.9975
41 T A -0.6437
42 L A -0.1850
43 S A 0.0325
44 L A 0.4262
45 D A -0.3374
46 Y A 0.0000
47 I A 0.0000
48 T A 0.0000
49 C A 0.0000
50 E A -1.3021
51 Y A -1.4759
52 K A -2.1099
53 T A -0.6916
54 V A 0.1242
55 I A 0.7489
56 P A 0.2025
57 S A 0.1187
58 P A 0.4129
59 Y A 0.9457
60 V A 0.8368
61 K A -0.4219
62 C A 0.1706
63 C A -0.0863
64 G A -0.4516
65 T A -0.7115
66 A A -0.8072
67 E A -2.0563
68 C A -2.0853
69 K A -3.0835
70 D A -3.0390
71 K A -2.3132
72 S A -0.8669
73 L A -0.2131
74 P A -0.5383
75 D A -0.8379
76 Y A -0.5962
77 S A -0.6482
78 C A -1.1736
79 K A -1.3023
80 V A -0.3056
81 F A -0.2547
82 T A -0.4362
83 G A -0.8521
84 V A -0.2835
85 Y A 1.1219
86 P A 0.0000
87 F A 2.4450
88 M A 1.8274
89 W A 1.5195
90 G A 0.5356
91 G A 0.7507
92 A A 1.6430
93 Y A 2.3583
94 C A 1.7986
95 F A 2.1025
96 C A 0.3659
97 D A -1.1364
98 A A -1.1901
99 E A -2.0281
100 N A 0.0000
101 T A 0.0000
102 Q A 0.0000
103 L A -0.0157
104 S A 0.0000
105 E A -0.4491
106 A A 0.0000
107 H A -0.3403
108 V A 0.0000
109 E A -2.0918
110 K A -2.2541
111 S A -2.2144
112 E A -2.8228
113 S A -1.7992
114 C A -1.6054
115 K A -2.3785
116 T A -1.2117
117 E A -1.0615
118 F A -0.1327
119 A A 0.0000
120 S A 0.0000
121 A A 0.0000
122 Y A -0.2722
123 R A -1.8234
124 A A -1.8089
125 H A -1.8495
126 T A -0.6844
127 A A -0.7189
128 S A -0.4757
129 A A -0.1466
130 S A -0.0281
131 A A -0.2934
132 K A -1.3731
133 L A 0.0000
134 R A -1.4514
135 V A 0.0000
136 L A -0.9566
137 Y A 0.0000
138 Q A -1.7142
139 G A -1.8354
140 N A -1.9464
141 N A -1.9241
142 I A -0.9522
143 T A -0.6271
144 V A 0.0000
145 A A -0.1697
146 A A 0.0747
147 Y A 0.3740
148 A A 0.0000
149 N A -1.5966
150 G A -1.7062
151 D A -2.2048
152 H A -1.1115
153 A A -0.5524
154 V A -0.0889
155 T A -1.2880
156 V A -1.3154
157 K A -2.5909
158 D A -2.9636
159 A A 0.0000
160 K A -2.2319
161 F A 0.0000
162 V A -0.2845
163 V A -0.1297
164 G A -0.7474
165 P A -0.8287
166 M A -0.3682
167 S A -0.3821
168 S A -0.1534
169 A A 0.1817
170 W A 0.4038
171 T A -0.1332
172 P A -0.0041
173 F A -1.5197
174 D A -3.2320
175 N A -3.2125
176 K A -2.7862
177 I A 0.0000
178 V A 0.0000
179 V A -0.2793
180 Y A -0.6720
181 K A -1.9515
182 G A -1.4719
183 D A -0.9191
184 V A 0.0000
185 Y A 0.0000
186 N A -2.1689
187 M A -1.8002
188 D A -2.4934
189 Y A 0.0000
190 P A -0.6854
191 P A -0.3259
192 F A 0.0592
193 G A -0.4389
194 A A -0.5647
195 G A 0.0000
196 R A -2.4435
197 P A -1.8892
198 G A -1.4108
199 Q A -1.5789
200 F A -0.5781
201 G A 0.0000
202 D A 0.0000
203 I A 0.0000
204 Q A 0.0000
205 S A 0.0000
206 R A -2.3960
207 T A -1.8953
208 P A -1.9391
209 E A -2.9722
210 S A -2.7076
211 K A -3.3511
212 D A -3.0953
213 V A -1.4518
214 Y A -0.5677
215 A A -0.8647
216 N A -1.5427
217 T A 0.0000
218 Q A -1.1355
219 L A 0.2305
220 V A 1.3599
221 L A 0.0351
222 Q A -1.4615
223 R A -2.2902
224 P A -0.9060
225 A A -0.3569
226 A A 0.2236
227 G A 0.7354
228 T A 0.7952
229 V A 1.2394
230 H A -0.1938
231 V A -0.0997
232 P A -0.0276
233 Y A 0.7290
234 S A 0.2623
235 Q A -0.1809
236 A A -0.8508
237 P A -0.6742
238 S A -0.6045
239 G A 0.0000
240 F A 0.0000
241 K A -0.9939
242 Y A -0.3157
243 W A -1.0862
244 L A -1.2474
245 K A -2.5511
246 E A -2.9889
247 R A -2.3769
248 G A -1.7075
249 A A -1.0136
250 S A 0.0000
251 L A -0.9656
252 Q A -1.6973
253 H A -1.6055
254 T A -0.7538
255 A A -0.4047
256 P A 0.2104
257 F A 1.4630
258 G A -0.1636
259 C A 0.0000
260 Q A -1.4197
261 I A -0.9375
262 A A -0.8377
263 T A -1.1833
264 N A -1.7547
265 P A -1.3973
266 V A 0.0000
267 R A -1.1160
268 A A 0.0000
269 V A -0.4441
270 N A -0.4019
271 C A 0.2597
272 A A 0.4275
273 V A 0.3900
274 G A -0.4812
275 N A -0.3724
276 I A 0.0000
277 P A 0.7907
278 I A 0.0000
279 S A 0.1621
280 I A -0.7286
281 D A -2.2518
282 I A 0.0000
283 P A -1.7386
284 D A -1.7350
285 A A -0.7614
286 A A -0.6194
287 F A -0.6190
288 T A -0.7667
289 R A -1.0296
290 V A 0.9297
291 V A 1.0769
292 D A -1.0927
293 A A -0.9480
294 P A -1.3132
295 S A -0.7722
296 V A -0.9619
297 T A -1.0023
298 D A -1.9566
299 M A -1.4101
300 S A -1.3013
301 C A -0.9714
302 E A -1.7492
303 V A -0.4552
304 P A -0.3603
305 A A -0.1935
306 C A -0.1359
307 T A -0.6861
308 H A -0.8498
309 S A -1.3788
310 S A -0.7546
311 D A -1.7036
312 F A -0.8937
313 G A -0.4698
314 G A 0.0000
315 V A 0.0902
316 A A 0.0000
317 I A -0.8864
318 I A 0.0000
319 K A -2.3929
320 Y A 0.0000
321 T A -2.0536
322 A A -2.0605
323 S A -1.8420
324 K A -3.3070
325 K A -3.8669
326 G A -2.9658
327 K A -3.4776
328 C A 0.0000
329 A A -1.2096
330 V A 0.0000
331 H A -0.8478
332 S A -0.6057
333 M A -0.4290
334 T A -0.9936
335 N A -1.2447
336 A A -0.7236
337 V A 0.0000
338 T A -0.8761
339 I A 0.0000
340 R A -2.5637
341 E A -2.5233
342 A A -1.7516
343 D A -2.7869
344 V A -2.2649
345 E A -3.3849
346 V A 0.0000
347 E A -4.1008
348 G A -2.6423
349 N A -2.4462
350 S A -2.1118
351 Q A -2.3123
352 L A -1.3590
353 Q A -1.3346
354 I A 0.0000
355 S A -0.6654
356 F A 0.0000
357 S A 0.0000
358 T A 0.0000
359 A A -0.1351
360 L A 0.0000
361 A A -0.3570
362 S A -0.5515
363 A A 0.0000
364 E A -2.2414
365 F A 0.0000
366 R A -2.0828
367 V A 0.0000
368 Q A -0.8928
369 V A 0.0000
370 C A -0.6092
371 S A -0.2788
372 T A -0.6771
373 Q A -1.1953
374 V A -1.1809
375 H A -1.9530
376 C A 0.0000
377 A A -1.2420
378 A A -0.5482
379 A A -0.3916
380 C A 0.0000
381 H A -1.1638
382 P A -1.3971
383 P A -1.9586
384 K A -2.6938
385 D A -2.3679
386 H A -1.0287
387 I A 1.3520
388 V A 1.3762
389 N A 0.2039
390 Y A 0.5042
391 P A -0.1489
392 A A -0.3248
393 S A -0.4506
394 H A -0.6452
395 T A -0.3060
396 T A 0.0636
397 L A 0.7245
398 G A 0.3733
399 V A 1.0858
400 Q A -0.4444
401 D A -0.4126
402 I A 0.9739
403 S A 0.3662
404 T A 0.4604
405 T A 0.7231
406 A A 1.1179
407 M A 1.0217
408 S A 0.5990
409 W A 1.3233
410 V A 1.1624
411 Q A -0.6725
412 K A -0.7181
413 I A 1.0938
414 T A 0.6190
415 G A 0.3316
416 G A 1.2912
417 V A 2.9920
418 G A 2.5251
419 L A 3.4631
420 I A 4.2092
421 V A 3.9591
422 A A 3.2204
423 V A 3.5039
424 A A 3.4270
425 A A 3.5079
426 L A 4.6152
427 I A 5.1027
428 L A 4.9951
429 I A 5.0152
430 V A 5.1588
431 V A 4.8685
432 L A 3.8264
433 C A 3.1664
434 V A 2.4145
435 S A 1.5768
436 F A 1.7585
437 S A -0.0052
438 R A -1.5159
439 H A -1.3095
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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
VK430A -0.4272 -0.0344 View CSV PDB
VR430A -0.3278 -0.0354 View CSV PDB
IR427A -0.199 -0.0346 View CSV PDB
VK431A -0.1465 -0.0348 View CSV PDB
LK426A 0.0131 -0.0302 View CSV PDB
LR426A 0.0187 -0.0304 View CSV PDB
IK427A 0.0704 -0.0395 View CSV PDB
VR431A 0.2346 -0.0335 View CSV PDB
IR429A 0.2283 -0.028 View CSV PDB
LK428A 0.2991 -0.0302 View CSV PDB
LR428A 0.3295 -0.0251 View CSV PDB
IK429A 0.4464 -0.0294 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018