Project name: Ire1_LD

Status: done

Started: 2024-06-13 14:10:08
Settings
Chain sequence(s) A: LLTLLLPGLGIFGSTSTVTLPETLLFVSTLDGSLHAVSKRTGSIKWTLKEDPVLQVPTHVEEPAFLPDPNDGSLYTLGSKNNEGLTKLPFTIPELVQASPCRSSDGILYMGKKQDIWYVIDLLTGEKQQTLSSAFADSLCPSTSLLYLGRTEYTITMYDTKTRELRWNATYFDYAASLPEDDVDYKMSHFVSNGDGLVVTVDSESGDVLWIQNYASPVVAFYVWQREGLRKVMHINVAVETLRYLTFMSGEVGRITKWKYPFPKETEAKSKLTPTLYVGKYSTSLYASPSMVHEGVAVVPRGSTLPLLEGPQTDGVTIGDKGECVITPSTDVKFDPGLKSKNKLNYLRNYWLLIGHHETPLSASTKMLERFPNNLPKHRENVIPADSEKKSFEEVINLVDQTSENAPTTVSRDVEEKPAHAPARPEAPVDSMLKDMATI
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]                                                (00:00:03)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:03)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:03)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:03)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:03)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:03:09)
[INFO]       Auto_mut: Residue number 12 from chain A and a score of 3.142 (leucine) selected for  
                       automated muatation                                                         (00:03:13)
[INFO]       Auto_mut: Residue number 334 from chain A and a score of 3.136 (isoleucine) selected  
                       for automated muatation                                                     (00:03:13)
[INFO]       Auto_mut: Residue number 13 from chain A and a score of 3.113 (leucine) selected for  
                       automated muatation                                                         (00:03:13)
[INFO]       Auto_mut: Residue number 333 from chain A and a score of 2.959 (valine) selected for  
                       automated muatation                                                         (00:03:13)
[INFO]       Auto_mut: Residue number 19 from chain A and a score of 2.940 (isoleucine) selected   
                       for automated muatation                                                     (00:03:13)
[INFO]       Auto_mut: Residue number 10 from chain A and a score of 2.785 (leucine) selected for  
                       automated muatation                                                         (00:03:13)
[INFO]       Auto_mut: Mutating residue number 12 from chain A (leucine) into glutamic acid        (00:03:13)
[INFO]       Auto_mut: Mutating residue number 12 from chain A (leucine) into aspartic acid        (00:03:13)
[INFO]       Auto_mut: Mutating residue number 334 from chain A (isoleucine) into glutamic acid    (00:03:13)
[INFO]       Auto_mut: Mutating residue number 12 from chain A (leucine) into arginine             (00:04:53)
[INFO]       Auto_mut: Mutating residue number 12 from chain A (leucine) into lysine               (00:04:54)
[INFO]       Auto_mut: Mutating residue number 334 from chain A (isoleucine) into lysine           (00:04:56)
[INFO]       Auto_mut: Mutating residue number 334 from chain A (isoleucine) into aspartic acid    (00:06:35)
[INFO]       Auto_mut: Mutating residue number 13 from chain A (leucine) into glutamic acid        (00:06:35)
[INFO]       Auto_mut: Mutating residue number 13 from chain A (leucine) into aspartic acid        (00:06:41)
[INFO]       Auto_mut: Mutating residue number 334 from chain A (isoleucine) into arginine         (00:08:15)
[INFO]       Auto_mut: Mutating residue number 13 from chain A (leucine) into lysine               (00:08:16)
[INFO]       Auto_mut: Mutating residue number 13 from chain A (leucine) into arginine             (00:08:21)
[INFO]       Auto_mut: Mutating residue number 333 from chain A (valine) into glutamic acid        (00:09:59)
[INFO]       Auto_mut: Mutating residue number 333 from chain A (valine) into aspartic acid        (00:10:00)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (isoleucine) into glutamic acid     (00:10:04)
[INFO]       Auto_mut: Mutating residue number 333 from chain A (valine) into arginine             (00:11:42)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (isoleucine) into lysine            (00:11:42)
[INFO]       Auto_mut: Mutating residue number 333 from chain A (valine) into lysine               (00:11:44)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (isoleucine) into aspartic acid     (00:13:29)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (leucine) into glutamic acid        (00:13:32)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (leucine) into aspartic acid        (00:13:32)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (leucine) into lysine               (00:15:10)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (isoleucine) into arginine          (00:15:11)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (leucine) into arginine             (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain A (leucine) into glutamic   
                       acid: Energy difference: -0.0997 kcal/mol, Difference in average score from 
                       the base case: -0.0083                                                      (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain A (leucine) into lysine:    
                       Energy difference: -0.3882 kcal/mol, Difference in average score from the   
                       base case: -0.0072                                                          (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain A (leucine) into aspartic   
                       acid: Energy difference: -1.9885 kcal/mol, Difference in average score from 
                       the base case: -0.0077                                                      (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain A (leucine) into arginine:  
                       Energy difference: -2.3889 kcal/mol, Difference in average score from the   
                       base case: -0.0081                                                          (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 334 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.3491 kcal/mol, Difference in average   
                       score from the base case: -0.0173                                           (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 334 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.9269 kcal/mol, Difference in average score    
                       from the base case: -0.0156                                                 (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 334 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: -0.8475 kcal/mol, Difference in average   
                       score from the base case: -0.0146                                           (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 334 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.6742 kcal/mol, Difference in average score  
                       from the base case: -0.0136                                                 (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 13 from chain A (leucine) into glutamic   
                       acid: Energy difference: -0.6319 kcal/mol, Difference in average score from 
                       the base case: -0.0075                                                      (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 13 from chain A (leucine) into lysine:    
                       Energy difference: -0.3793 kcal/mol, Difference in average score from the   
                       base case: -0.0077                                                          (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 13 from chain A (leucine) into aspartic   
                       acid: Energy difference: -0.9421 kcal/mol, Difference in average score from 
                       the base case: -0.0073                                                      (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 13 from chain A (leucine) into arginine:  
                       Energy difference: -0.2575 kcal/mol, Difference in average score from the   
                       base case: -0.0077                                                          (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 333 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.0081 kcal/mol, Difference in average score from  
                       the base case: -0.0176                                                      (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 333 from chain A (valine) into lysine:    
                       Energy difference: -0.2587 kcal/mol, Difference in average score from the   
                       base case: -0.0142                                                          (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 333 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.2895 kcal/mol, Difference in average score from 
                       the base case: -0.0149                                                      (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 333 from chain A (valine) into arginine:  
                       Energy difference: -0.3778 kcal/mol, Difference in average score from the   
                       base case: -0.0178                                                          (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: -0.3113 kcal/mol, Difference in average   
                       score from the base case: -0.0109                                           (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.0867 kcal/mol, Difference in average score from the   
                       base case: -0.0116                                                          (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 0.0426 kcal/mol, Difference in average    
                       score from the base case: -0.0107                                           (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (isoleucine) into         
                       arginine: Energy difference: 0.0097 kcal/mol, Difference in average score   
                       from the base case: -0.0111                                                 (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (leucine) into glutamic   
                       acid: Energy difference: 1.7563 kcal/mol, Difference in average score from  
                       the base case: -0.0055                                                      (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (leucine) into lysine:    
                       Energy difference: 1.7835 kcal/mol, Difference in average score from the    
                       base case: -0.0059                                                          (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (leucine) into aspartic   
                       acid: Energy difference: -0.1975 kcal/mol, Difference in average score from 
                       the base case: -0.0049                                                      (00:16:54)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (leucine) into arginine:  
                       Energy difference: 1.7537 kcal/mol, Difference in average score from the    
                       base case: -0.0052                                                          (00:16:54)
[INFO]       Main:     Simulation completed successfully.                                          (00:17:01)
Show buried residues
Minimal score value
-3.6376
Maximal score value
3.1417
Average score
-0.5938
Total score value
-260.6971
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
9 L A 2.4913
10 L A 2.7854
11 T A 2.1952
12 L A 3.1417
13 L A 3.1128
14 L A 2.4085
15 P A 1.0716
16 G A 0.7518
17 L A 1.7664
18 G A 1.5487
19 I A 2.9399
20 F A 2.6958
21 G A 0.7657
22 S A 0.1180
23 T A -0.3592
24 S A -0.3291
25 T A -0.6832
26 V A -0.3076
27 T A -0.8110
28 L A 0.0000
29 P A -0.9774
30 E A -2.0284
31 T A -1.4774
32 L A 0.0000
33 L A 0.0000
34 F A 0.0000
35 V A 0.0000
36 S A 0.0000
37 T A 0.0000
38 L A 0.0000
39 D A -0.9105
40 G A 0.0000
41 S A 0.0000
42 L A 0.0000
43 H A 0.0000
44 A A 0.0000
45 V A 0.0000
46 S A -1.2074
47 K A -1.3529
48 R A -1.9299
49 T A -0.7191
50 G A 0.0000
51 S A -0.4222
52 I A 0.1380
53 K A -0.9788
54 W A 0.0000
55 T A -0.8836
56 L A 0.0000
57 K A -2.2768
58 E A -1.7913
59 D A -2.0197
60 P A -1.2087
61 V A 0.0000
62 L A 0.0000
63 Q A -0.7152
64 V A -0.3590
65 P A -0.5872
66 T A -0.3800
67 H A -0.9964
68 V A 0.0444
69 E A -2.2544
70 E A -2.5351
71 P A -1.6218
72 A A -0.7220
73 F A 0.0257
74 L A 0.0000
75 P A 0.0000
76 D A 0.0000
77 P A 0.0000
78 N A 0.0000
79 D A -0.5792
80 G A 0.0000
81 S A 0.0000
82 L A 0.0000
83 Y A 0.0000
84 T A 0.0000
85 L A -0.4967
86 G A -1.6926
87 S A -2.1804
88 K A -3.0595
89 N A -3.0320
90 N A -2.7489
91 E A -2.4391
92 G A -1.4679
93 L A 0.0000
94 T A 0.0000
95 K A -0.1336
96 L A -0.0739
97 P A -0.5247
98 F A 0.0000
99 T A -0.5046
100 I A 0.0000
101 P A -0.9994
102 E A -1.0007
103 L A 0.0000
104 V A 0.0000
105 Q A -1.7809
106 A A -0.7720
107 S A -1.0789
108 P A -0.7252
109 C A -0.7581
110 R A -1.7721
111 S A 0.0000
112 S A -1.6504
113 D A -2.2631
114 G A 0.0000
115 I A -1.1077
116 L A -0.1987
117 Y A 0.0000
118 M A -0.3195
119 G A -1.2086
120 K A -2.1347
121 K A -3.0399
122 Q A -2.4067
123 D A -2.0255
124 I A -0.3333
125 W A 0.7039
126 Y A 0.0000
127 V A 0.0000
128 I A 0.0000
129 D A -0.9089
130 L A 0.0000
131 L A 0.8817
132 T A -0.4282
133 G A 0.0000
134 E A -2.5048
135 K A -2.6664
136 Q A -2.2598
137 Q A -1.0797
138 T A 0.0341
139 L A 0.5936
140 S A 0.2674
141 S A 0.1731
142 A A 0.7435
143 F A 1.4867
144 A A 0.1497
145 D A -1.1801
146 S A -0.5469
147 L A -0.0470
148 C A 0.5060
149 P A 0.0885
150 S A -0.1329
151 T A -0.1519
152 S A 0.1884
153 L A -0.1368
154 L A 0.0000
155 Y A 0.4232
156 L A 0.0000
157 G A 0.0000
158 R A 0.0000
159 T A 0.0000
160 E A -1.5106
161 Y A -1.4160
162 T A -1.0379
163 I A 0.0000
164 T A -0.1294
165 M A 0.0000
166 Y A -0.5746
167 D A 0.0000
168 T A -1.8645
169 K A -2.7390
170 T A -2.1597
171 R A -2.9702
172 E A -2.3656
173 L A -0.1022
174 R A -1.4498
175 W A 0.0000
176 N A -0.7949
177 A A 0.0000
178 T A -0.7438
179 Y A 0.0000
180 F A -0.7373
181 D A -0.2838
182 Y A 0.0000
183 A A -0.0931
184 A A -0.0637
185 S A -0.3539
186 L A 0.1901
187 P A -1.2193
188 E A -2.9156
189 D A -3.4370
190 D A -3.2108
191 V A -1.9241
192 D A -2.3424
193 Y A -1.5234
194 K A -2.3759
195 M A -1.1160
196 S A -0.2659
197 H A 0.0000
198 F A 0.0000
199 V A 0.0000
200 S A 0.0000
201 N A 0.0000
202 G A -0.6704
203 D A -0.5215
204 G A 0.0000
205 L A 0.0000
206 V A 0.0000
207 V A 0.0000
208 T A 0.0000
209 V A 0.0000
210 D A 0.0000
211 S A -1.4545
212 E A -2.2690
213 S A -1.3428
214 G A 0.0000
215 D A -1.1068
216 V A 0.0917
217 L A 0.2997
218 W A 0.0000
219 I A 0.7194
220 Q A -0.1601
221 N A -0.7655
222 Y A 0.0000
223 A A -0.3651
224 S A 0.0000
225 P A 0.0000
226 V A 0.0000
227 V A 0.0000
228 A A 0.0000
229 F A 0.0000
230 Y A 0.0000
231 V A 0.0000
232 W A -1.3844
233 Q A -2.3592
234 R A -3.0470
235 E A -2.8072
236 G A -1.6258
237 L A 0.0000
238 R A -0.8408
239 K A 0.0314
240 V A 0.0000
241 M A 0.3187
242 H A 0.3323
243 I A 0.6314
244 N A 0.2374
245 V A 0.0000
246 A A 0.0000
247 V A -0.8624
248 E A -1.8979
249 T A 0.0000
250 L A 0.0000
251 R A -0.5125
252 Y A 0.4600
253 L A 0.0000
254 T A 0.0000
255 F A 2.2745
256 M A 1.3669
257 S A 0.0854
258 G A -0.6522
259 E A -1.2628
260 V A 0.3740
261 G A -0.8692
262 R A -1.9242
263 I A -0.3127
264 T A -1.2517
265 K A -1.5837
266 W A 0.0000
267 K A -1.6068
268 Y A -0.4347
269 P A -1.1183
270 F A 0.3326
271 P A -0.9952
272 K A -2.3656
273 E A -3.0248
274 T A -2.5012
275 E A -3.0381
276 A A -2.4708
277 K A -2.7436
278 S A -2.3554
279 K A -2.5717
280 L A -1.3582
281 T A -0.8517
282 P A -0.2361
283 T A 0.0000
284 L A 0.0000
285 Y A 0.4776
286 V A 0.0000
287 G A 0.0000
288 K A -1.1920
289 Y A -0.6752
290 S A -0.5174
291 T A -0.5512
292 S A 0.0000
293 L A 0.0280
294 Y A 0.0000
295 A A 0.0000
296 S A 0.0000
297 P A 0.2199
298 S A 0.0000
299 M A 0.1159
300 V A 0.0000
301 H A -1.6253
302 E A -2.3176
303 G A -1.1617
304 V A -0.6456
305 A A 0.0401
306 V A 0.1040
307 V A 0.1539
308 P A -0.8717
309 R A -1.7671
310 G A -1.7269
311 S A -0.2318
312 T A 0.4581
313 L A 1.8772
314 P A 0.8964
315 L A 1.0448
316 L A 1.0462
317 E A -1.2222
318 G A -0.8312
319 P A -1.2794
320 Q A -2.2804
321 T A -1.5093
322 D A -2.2543
323 G A -0.8806
324 V A 1.6763
325 T A 1.1962
326 I A 1.7007
327 G A -0.7662
328 D A -2.7450
329 K A -3.0503
330 G A -1.9040
331 E A -1.4967
332 C A 1.4297
333 V A 2.9592
334 I A 3.1363
335 T A 1.3243
336 P A -0.0110
337 S A -0.7023
338 T A -0.9468
339 D A -1.7550
340 V A 0.2100
341 K A -0.9744
342 F A 0.4534
343 D A -1.1777
344 P A -1.0255
345 G A -0.7445
346 L A -0.2140
347 K A -1.9440
348 S A -1.9185
349 K A -2.9570
350 N A -2.9968
351 K A -2.0039
352 L A 0.0239
353 N A -0.8115
354 Y A 0.8511
355 L A 1.1225
356 R A -1.1215
357 N A -0.5855
358 Y A 0.7830
359 W A 1.5669
360 L A 1.7642
361 L A 1.9314
362 I A 1.8533
363 G A 0.9189
364 H A 0.0000
365 H A 0.0000
366 E A -0.8252
367 T A -0.6111
368 P A 0.0000
369 L A -0.3603
370 S A -0.3564
371 A A -0.4235
372 S A -0.6251
373 T A -0.9061
374 K A -2.2481
375 M A -1.6718
376 L A -1.4739
377 E A -2.6445
378 R A -2.5644
379 F A -0.9166
380 P A -1.1554
381 N A -2.1354
382 N A -1.8717
383 L A -1.1703
384 P A -1.8401
385 K A -3.2596
386 H A -3.2255
387 R A -3.6376
388 E A -3.1391
389 N A -1.7442
390 V A -0.6116
391 I A -0.1457
392 P A -0.9930
393 A A -0.9738
394 D A -2.4112
395 S A -2.5893
396 E A -3.4255
397 K A -3.4149
398 K A -2.5376
399 S A -1.1137
400 F A 0.5126
401 E A -1.0601
402 E A -0.5051
403 V A 2.3995
404 I A 2.1998
405 N A 0.4592
406 L A 1.7334
407 V A 1.6152
408 D A -1.2816
409 Q A -1.7464
410 T A -1.3304
411 S A -2.0909
412 E A -2.9995
413 N A -2.2475
414 A A -1.0625
415 P A -0.7564
416 T A 0.1288
417 T A 0.6337
418 V A 1.1924
419 S A -0.6223
420 R A -2.1844
421 D A -2.3852
422 V A -0.7807
423 E A -2.5751
424 E A -3.2615
425 K A -3.0168
426 P A -1.5385
427 A A -0.8273
428 H A -1.0298
429 A A -0.5728
430 P A -0.7726
431 A A -1.0876
432 R A -2.3179
433 P A -1.9576
434 E A -2.2992
435 A A -0.7473
436 P A -0.2469
437 V A 1.0776
438 D A -0.9877
439 S A -0.5022
440 M A 0.5955
441 L A 0.6653
442 K A -1.3801
443 D A -1.1383
444 M A 0.8249
445 A A 0.4170
446 T A 0.3046
447 I A 1.5604
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
LR12A -2.3889 -0.0081 View CSV PDB
IK334A -0.9269 -0.0156 View CSV PDB
ID334A -0.8475 -0.0146 View CSV PDB
LD12A -1.9885 -0.0077 View CSV PDB
VR333A -0.3778 -0.0178 View CSV PDB
VD333A -0.2895 -0.0149 View CSV PDB
LD13A -0.9421 -0.0073 View CSV PDB
IE19A -0.3113 -0.0109 View CSV PDB
LE13A -0.6319 -0.0075 View CSV PDB
IK19A -0.0867 -0.0116 View CSV PDB
LD10A -0.1975 -0.0049 View CSV PDB
LK10A 1.7835 -0.0059 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018