Project name: hsanano-a6-5glp1

Status: done

Started: 2024-12-30 07:19:54
Settings
Chain sequence(s) A: EVQLLESGGGLVQPGGSLRLSCAASGFTFSNYYMTWARQAPGKGLEWVSGISVDGSVLDYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARASGPQALRRGAPWGQGTLVTVSSAAAAAAHGEGTFTSDVSSYLEGQAAKEFIAWLVKGRGAAAAAAHGEGTFTSDVSSYLEGQAAKEFIAWLVKGRGAAAAAAHGEGTFTSDVSSYLEGQAAKEFIAWLVKGRGAAAAAAHGEGTFTSDVSSYLEGQAAKEFIAWLVKGRGAAAAAAHGEGTFTSDVSSYLEGQAAKEFIAWLVKGRG
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                                          (00:01:56)
[INFO]       Auto_mut: Residue number 298 from chain A and a score of 1.522 (isoleucine) selected  
                       for automated muatation                                                     (00:01:58)
[INFO]       Auto_mut: Residue number 33 from chain A and a score of 0.873 (tyrosine) selected for 
                       automated muatation                                                         (00:01:58)
[INFO]       Auto_mut: Residue number 302 from chain A and a score of 0.856 (valine) selected for  
                       automated muatation                                                         (00:01:58)
[INFO]       Auto_mut: Residue number 57 from chain A and a score of 0.844 (valine) selected for   
                       automated muatation                                                         (00:01:58)
[INFO]       Auto_mut: Residue number 5 from chain A and a score of 0.716 (leucine) selected for   
                       automated muatation                                                         (00:01:58)
[INFO]       Auto_mut: Residue number 58 from chain A and a score of 0.620 (leucine) selected for  
                       automated muatation                                                         (00:01:58)
[INFO]       Auto_mut: Mutating residue number 298 from chain A (isoleucine) into glutamic acid    (00:01:58)
[INFO]       Auto_mut: Mutating residue number 298 from chain A (isoleucine) into aspartic acid    (00:01:58)
[INFO]       Auto_mut: Mutating residue number 33 from chain A (tyrosine) into glutamic acid       (00:01:58)
[INFO]       Auto_mut: Mutating residue number 298 from chain A (isoleucine) into arginine         (00:03:23)
[INFO]       Auto_mut: Mutating residue number 33 from chain A (tyrosine) into lysine              (00:03:26)
[INFO]       Auto_mut: Mutating residue number 298 from chain A (isoleucine) into lysine           (00:03:29)
[INFO]       Auto_mut: Mutating residue number 33 from chain A (tyrosine) into aspartic acid       (00:04:51)
[INFO]       Auto_mut: Mutating residue number 302 from chain A (valine) into glutamic acid        (00:04:53)
[INFO]       Auto_mut: Mutating residue number 302 from chain A (valine) into aspartic acid        (00:05:02)
[INFO]       Auto_mut: Mutating residue number 33 from chain A (tyrosine) into arginine            (00:06:17)
[INFO]       Auto_mut: Mutating residue number 302 from chain A (valine) into lysine               (00:06:20)
[INFO]       Auto_mut: Mutating residue number 302 from chain A (valine) into arginine             (00:06:32)
[INFO]       Auto_mut: Mutating residue number 57 from chain A (valine) into glutamic acid         (00:07:44)
[INFO]       Auto_mut: Mutating residue number 57 from chain A (valine) into aspartic acid         (00:07:57)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (leucine) into glutamic acid         (00:08:06)
[INFO]       Auto_mut: Mutating residue number 57 from chain A (valine) into lysine                (00:09:12)
[INFO]       Auto_mut: Mutating residue number 57 from chain A (valine) into arginine              (00:09:22)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (leucine) into lysine                (00:09:40)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (leucine) into aspartic acid         (00:10:52)
[INFO]       Auto_mut: Mutating residue number 58 from chain A (leucine) into glutamic acid        (00:11:01)
[INFO]       Auto_mut: Mutating residue number 58 from chain A (leucine) into aspartic acid        (00:11:26)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (leucine) into arginine              (00:12:19)
[INFO]       Auto_mut: Mutating residue number 58 from chain A (leucine) into lysine               (00:12:30)
[INFO]       Auto_mut: Mutating residue number 58 from chain A (leucine) into arginine             (00:12:51)
[INFO]       Auto_mut: Effect of mutation residue number 298 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.2487 kcal/mol, Difference in average    
                       score from the base case: -0.0532                                           (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 298 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.1040 kcal/mol, Difference in average score     
                       from the base case: -0.0528                                                 (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 298 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.5931 kcal/mol, Difference in average    
                       score from the base case: -0.0532                                           (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 298 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.2500 kcal/mol, Difference in average score   
                       from the base case: -0.0562                                                 (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 33 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: -0.6896 kcal/mol, Difference in average score from 
                       the base case: -0.0257                                                      (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 33 from chain A (tyrosine) into lysine:   
                       Energy difference: 0.1144 kcal/mol, Difference in average score from the    
                       base case: -0.0269                                                          (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 33 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: -0.3293 kcal/mol, Difference in average score from 
                       the base case: -0.0229                                                      (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 33 from chain A (tyrosine) into arginine: 
                       Energy difference: 0.0498 kcal/mol, Difference in average score from the    
                       base case: -0.0341                                                          (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 302 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.1896 kcal/mol, Difference in average score from 
                       the base case: -0.0542                                                      (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 302 from chain A (valine) into lysine:    
                       Energy difference: -0.7171 kcal/mol, Difference in average score from the   
                       base case: -0.0520                                                          (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 302 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.6469 kcal/mol, Difference in average score from  
                       the base case: -0.0510                                                      (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 302 from chain A (valine) into arginine:  
                       Energy difference: -0.5873 kcal/mol, Difference in average score from the   
                       base case: -0.0539                                                          (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 57 from chain A (valine) into glutamic    
                       acid: Energy difference: 0.6803 kcal/mol, Difference in average score from  
                       the base case: -0.0388                                                      (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 57 from chain A (valine) into lysine:     
                       Energy difference: -0.8970 kcal/mol, Difference in average score from the   
                       base case: -0.0260                                                          (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 57 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.6283 kcal/mol, Difference in average score from  
                       the base case: -0.0419                                                      (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 57 from chain A (valine) into arginine:   
                       Energy difference: -0.3604 kcal/mol, Difference in average score from the   
                       base case: -0.0418                                                          (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (leucine) into glutamic    
                       acid: Energy difference: 0.6924 kcal/mol, Difference in average score from  
                       the base case: -0.0472                                                      (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (leucine) into lysine:     
                       Energy difference: -0.2406 kcal/mol, Difference in average score from the   
                       base case: -0.0412                                                          (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (leucine) into aspartic    
                       acid: Energy difference: 1.0310 kcal/mol, Difference in average score from  
                       the base case: -0.0419                                                      (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (leucine) into arginine:   
                       Energy difference: -0.3035 kcal/mol, Difference in average score from the   
                       base case: -0.0427                                                          (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 58 from chain A (leucine) into glutamic   
                       acid: Energy difference: 0.4495 kcal/mol, Difference in average score from  
                       the base case: -0.0329                                                      (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 58 from chain A (leucine) into lysine:    
                       Energy difference: 0.4361 kcal/mol, Difference in average score from the    
                       base case: -0.0298                                                          (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 58 from chain A (leucine) into aspartic   
                       acid: Energy difference: 1.4297 kcal/mol, Difference in average score from  
                       the base case: -0.0280                                                      (00:14:18)
[INFO]       Auto_mut: Effect of mutation residue number 58 from chain A (leucine) into arginine:  
                       Energy difference: 0.4193 kcal/mol, Difference in average score from the    
                       base case: -0.0328                                                          (00:14:18)
[INFO]       Main:     Simulation completed successfully.                                          (00:14:25)
Show buried residues
Minimal score value
-3.5788
Maximal score value
1.5222
Average score
-0.8069
Total score value
-246.9245
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 E A -1.9651
2 V A -1.0632
3 Q A -0.8724
4 L A 0.0000
5 L A 0.7156
6 E A 0.0000
7 S A -0.4650
8 G A -0.9360
9 G A -0.6927
10 G A -0.2796
11 L A -0.2203
12 V A 0.0000
13 Q A -1.5285
14 P A -1.6773
15 G A -1.3818
16 G A -1.1620
17 S A -1.3593
18 L A -1.2120
19 R A -2.0544
20 L A 0.0000
21 S A -0.3626
22 C A 0.0000
23 A A -0.1460
24 A A -0.4488
25 S A -0.6433
26 G A -1.0244
27 F A -0.5628
28 T A -0.5731
29 F A 0.0000
30 S A -1.1831
31 N A -1.0321
32 Y A 0.2087
33 Y A 0.8730
34 M A 0.0000
35 T A 0.0000
36 W A 0.0000
37 A A 0.0000
38 R A 0.0000
39 Q A -0.4849
40 A A 0.0000
41 P A -1.1178
42 G A -1.3825
43 K A -2.0367
44 G A -1.0453
45 L A 0.1524
46 E A -0.3184
47 W A 0.0172
48 V A 0.0000
49 S A 0.0000
50 G A 0.0000
51 I A 0.0000
52 S A 0.0000
53 V A -0.5295
54 D A -1.7270
55 G A -0.5998
56 S A -0.2726
57 V A 0.8441
58 L A 0.6201
59 D A -1.0988
60 Y A -1.2678
61 A A -1.6119
62 D A -2.5423
63 S A -1.7010
64 V A 0.0000
65 K A -2.8191
66 G A -1.7955
67 R A -1.4339
68 F A 0.0000
69 T A -0.8232
70 I A 0.0000
71 S A -0.1734
72 R A -1.1215
73 D A -1.5133
74 N A -2.1373
75 S A -1.7208
76 K A -2.5322
77 N A -2.0304
78 T A -1.1227
79 L A 0.0000
80 Y A -0.2873
81 L A 0.0000
82 Q A -1.1313
83 M A 0.0000
84 N A -1.4666
85 S A -1.2392
86 L A 0.0000
87 R A -2.4322
88 A A -1.9243
89 E A -2.2922
90 D A 0.0000
91 T A 0.0000
92 A A 0.0000
93 V A 0.0000
94 Y A 0.0000
95 Y A 0.1819
96 C A 0.0000
97 A A 0.0000
98 R A 0.1121
99 A A 0.0000
100 S A 0.1884
101 G A 0.0000
102 P A -1.4366
103 Q A -2.0621
104 A A 0.0000
105 L A -1.8388
106 R A -3.1468
107 R A -3.1248
108 G A -1.8598
109 A A 0.0000
110 P A -0.5442
111 W A 0.0730
112 G A -0.1369
113 Q A -0.9226
114 G A 0.0000
115 T A 0.0000
116 L A 0.0000
117 V A 0.0000
118 T A 0.0000
119 V A 0.0000
120 S A 0.0000
121 S A -0.9476
122 A A 0.0000
123 A A -0.5821
124 A A -0.5521
125 A A -0.7548
126 A A -0.6124
127 A A -0.8545
128 H A -1.5487
129 G A -1.9186
130 E A -2.4716
131 G A -1.4959
132 T A -0.7025
133 F A 0.0000
134 T A -0.5962
135 S A 0.0000
136 D A -1.9009
137 V A 0.0000
138 S A -0.5066
139 S A 0.0000
140 Y A 0.0447
141 L A 0.0000
142 E A -1.1286
143 G A -1.6411
144 Q A -1.8587
145 A A 0.0000
146 A A 0.0000
147 K A -2.6965
148 E A -1.3593
149 F A 0.0000
150 I A 0.0000
151 A A -0.9171
152 W A -0.6319
153 L A 0.0000
154 V A -0.5871
155 K A -1.4585
156 G A 0.0000
157 R A 0.0000
158 G A 0.0000
159 A A -0.3629
160 A A 0.0000
161 A A 0.0000
162 A A -0.2289
163 A A -0.0496
164 A A -0.3848
165 H A -1.0705
166 G A -1.9555
167 E A -3.0251
168 G A -1.8328
169 T A -0.8757
170 F A -0.2092
171 T A -0.3977
172 S A 0.0000
173 D A -1.7305
174 V A 0.0000
175 S A -0.4384
176 S A 0.0000
177 Y A 0.4038
178 L A 0.0000
179 E A -1.7582
180 G A -2.2500
181 Q A -2.6503
182 A A 0.0000
183 A A 0.0000
184 K A -3.1175
185 E A -2.5164
186 F A 0.0000
187 I A 0.0000
188 A A -0.8312
189 W A -0.3174
190 L A 0.0000
191 V A 0.0031
192 K A -0.9179
193 G A 0.0000
194 R A -0.4335
195 G A -0.6222
196 A A -0.4804
197 A A -0.3769
198 A A -0.3575
199 A A -0.4922
200 A A 0.0000
201 A A 0.0000
202 H A -2.5850
203 G A -2.9854
204 E A -3.5788
205 G A -2.0170
206 T A -0.8517
207 F A 0.0000
208 T A -0.3257
209 S A -0.6160
210 D A -1.4585
211 V A 0.0000
212 S A -0.3014
213 S A 0.0000
214 Y A 0.3724
215 L A 0.0000
216 E A -2.2060
217 G A -2.5915
218 Q A -2.8969
219 A A 0.0000
220 A A 0.0000
221 K A -3.1346
222 E A -2.6102
223 F A 0.0000
224 I A 0.0000
225 A A -1.0876
226 W A 0.0000
227 L A 0.0000
228 V A -0.7510
229 K A -1.4325
230 G A 0.0000
231 R A -0.7646
232 G A -0.7266
233 A A -0.4306
234 A A -0.3835
235 A A 0.0000
236 A A -0.4716
237 A A -0.6727
238 A A 0.0000
239 H A -2.6587
240 G A -3.1720
241 E A -3.4714
242 G A -2.0284
243 T A -0.5441
244 F A 0.1178
245 T A -0.4043
246 S A 0.0000
247 D A -1.8681
248 V A 0.0000
249 S A -0.4356
250 S A 0.0000
251 Y A 0.3075
252 L A 0.0000
253 E A -3.0560
254 G A -2.7977
255 Q A -3.0511
256 A A 0.0000
257 A A 0.0000
258 K A -3.1859
259 E A -2.2493
260 F A 0.0000
261 I A 0.0000
262 A A -1.0458
263 W A -0.6920
264 L A 0.0000
265 V A -0.5097
266 K A -1.9135
267 G A -1.3159
268 R A -2.0916
269 G A -1.5369
270 A A -0.8706
271 A A -1.0272
272 A A -0.5537
273 A A -0.3998
274 A A -0.3093
275 A A -0.8829
276 H A -1.7025
277 G A -2.3234
278 E A -2.7818
279 G A -2.1552
280 T A -0.5618
281 F A 0.2798
282 T A -0.3494
283 S A -1.3840
284 D A -2.2180
285 V A 0.0000
286 S A -0.2185
287 S A 0.1988
288 Y A 0.1636
289 L A -1.5312
290 E A -3.0510
291 G A -2.4520
292 Q A -2.9380
293 A A 0.0000
294 A A -1.8366
295 K A -2.3496
296 E A -1.8028
297 F A 0.0000
298 I A 1.5222
299 A A 0.4502
300 W A 0.1560
301 L A 0.4936
302 V A 0.8562
303 K A -1.3458
304 G A -1.5471
305 R A -2.1557
306 G A -1.5678
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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
VK302A -0.7171 -0.052 View CSV PDB
VR302A -0.5873 -0.0539 View CSV PDB
VK57A -0.897 -0.026 View CSV PDB
VR57A -0.3604 -0.0418 View CSV PDB
LR5A -0.3035 -0.0427 View CSV PDB
YE33A -0.6896 -0.0257 View CSV PDB
LK5A -0.2406 -0.0412 View CSV PDB
YD33A -0.3293 -0.0229 View CSV PDB
IK298A 0.104 -0.0528 View CSV PDB
IR298A 0.25 -0.0562 View CSV PDB
LR58A 0.4193 -0.0328 View CSV PDB
LE58A 0.4495 -0.0329 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018