Project name: ECD_946_AF2

Status: done

Started: 2024-06-13 15:36:07
Settings
Chain sequence(s) A: NFTLPPNFGKRPTDLELSVKLVEMLENIMLRDGCTLEESKIKKVLEKPKYINLALEAQFTIMPKTALELAKVFRLKNIEALAILVCGCSPTGNLSNIYSRRLKGDLNLSWVMTTCSTLCANERMPELLEKYSRGIYDGDLKDKVPYKGILISLELVTKPCTEGIELKSKRPQLLRKVMKELEEKVKELEEEVTRLSKENVGKSIMFAMTPKILKTSSLMPKLGYEKGLEISEKACLNGRCRRTVSMETGCRNVQLCSTILNVAFPPEVIGPLFFFPLLYMQNQKEEGDKIVKEYKEEEKKKE
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                                          (00:06:53)
[INFO]       Auto_mut: Residue number 206 from chain A and a score of 2.240 (phenylalanine)        
                       selected for automated muatation                                            (00:06:55)
[INFO]       Auto_mut: Residue number 205 from chain A and a score of 1.498 (methionine) selected  
                       for automated muatation                                                     (00:06:55)
[INFO]       Auto_mut: Residue number 19 from chain A and a score of 1.394 (valine) selected for   
                       automated muatation                                                         (00:06:55)
[INFO]       Auto_mut: Residue number 207 from chain A and a score of 1.357 (alanine) selected for 
                       automated muatation                                                         (00:06:55)
[INFO]       Auto_mut: Residue number 262 from chain A and a score of 1.266 (valine) selected for  
                       automated muatation                                                         (00:06:55)
[INFO]       Auto_mut: Residue number 208 from chain A and a score of 0.986 (methionine) selected  
                       for automated muatation                                                     (00:06:55)
[INFO]       Auto_mut: Mutating residue number 205 from chain A (methionine) into glutamic acid    (00:06:55)
[INFO]       Auto_mut: Mutating residue number 206 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 206 from chain A (phenylalanine) into glutamic acid (00:06:55)
[INFO]       Auto_mut: Mutating residue number 206 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 206 from chain A (phenylalanine) into aspartic acid (00:06:55)
[INFO]       Auto_mut: Mutating residue number 205 from chain A (methionine) into lysine           (00:10:00)
[INFO]       Auto_mut: Mutating residue number 206 from chain A (phenylalanine) into arginine      (00:10:03)
[INFO]       Auto_mut: Mutating residue number 206 from chain A (phenylalanine) into lysine        (00:10:07)
[INFO]       Auto_mut: Mutating residue number 205 from chain A (methionine) into aspartic acid    (00:13:21)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (valine) into glutamic acid         (00:13:25)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (valine) into aspartic acid         (00:13:50)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (valine) into lysine                (00:16:27)
[INFO]       Auto_mut: Mutating residue number 205 from chain A (methionine) into arginine         (00:16:29)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (valine) into arginine              (00:16:57)
[INFO]       Auto_mut: Mutating residue number 207 from chain A (alanine) into glutamic acid       (00:19:39)
[INFO]       Auto_mut: Mutating residue number 207 from chain A (alanine) into aspartic acid       (00:19:59)
[INFO]       Auto_mut: Mutating residue number 262 from chain A (valine) into glutamic acid        (00:20:09)
[INFO]       Auto_mut: Mutating residue number 207 from chain A (alanine) into lysine              (00:22:55)
[INFO]       Auto_mut: Mutating residue number 207 from chain A (alanine) into arginine            (00:23:09)
[INFO]       Auto_mut: Mutating residue number 262 from chain A (valine) into lysine               (00:23:15)
[INFO]       Auto_mut: Mutating residue number 262 from chain A (valine) into aspartic acid        (00:26:09)
[INFO]       Auto_mut: Mutating residue number 208 from chain A (methionine) into glutamic acid    (00:26:39)
[INFO]       Auto_mut: Mutating residue number 208 from chain A (methionine) into aspartic acid    (00:26:39)
[INFO]       Auto_mut: Mutating residue number 262 from chain A (valine) into arginine             (00:29:17)
[INFO]       Auto_mut: Mutating residue number 208 from chain A (methionine) into lysine           (00:29:45)
[INFO]       Auto_mut: Mutating residue number 208 from chain A (methionine) into arginine         (00:29:45)
[INFO]       Auto_mut: Effect of mutation residue number 206 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.3887 kcal/mol, Difference in average    
                       score from the base case: -0.0556                                           (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 206 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.1591 kcal/mol, Difference in average score     
                       from the base case: -0.0612                                                 (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 206 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.5553 kcal/mol, Difference in average    
                       score from the base case: -0.0524                                           (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 206 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.6620 kcal/mol, Difference in average score   
                       from the base case: -0.0533                                                 (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 205 from chain A (methionine) into        
                       glutamic acid: Energy difference: 0.6572 kcal/mol, Difference in average    
                       score from the base case: -0.0377                                           (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 205 from chain A (methionine) into        
                       lysine: Energy difference: 0.4503 kcal/mol, Difference in average score     
                       from the base case: -0.0406                                                 (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 205 from chain A (methionine) into        
                       aspartic acid: Energy difference: 1.0867 kcal/mol, Difference in average    
                       score from the base case: -0.0368                                           (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 205 from chain A (methionine) into        
                       arginine: Energy difference: 0.8642 kcal/mol, Difference in average score   
                       from the base case: -0.0385                                                 (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (valine) into glutamic    
                       acid: Energy difference: -0.0377 kcal/mol, Difference in average score from 
                       the base case: -0.0514                                                      (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (valine) into lysine:     
                       Energy difference: -0.6927 kcal/mol, Difference in average score from the   
                       base case: -0.0580                                                          (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.2863 kcal/mol, Difference in average score from  
                       the base case: -0.0519                                                      (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (valine) into arginine:   
                       Energy difference: -0.9199 kcal/mol, Difference in average score from the   
                       base case: -0.0580                                                          (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain A (alanine) into glutamic  
                       acid: Energy difference: 3.6700 kcal/mol, Difference in average score from  
                       the base case: -0.0110                                                      (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain A (alanine) into lysine:   
                       Energy difference: 3.7421 kcal/mol, Difference in average score from the    
                       base case: -0.0161                                                          (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain A (alanine) into aspartic  
                       acid: Energy difference: 3.2247 kcal/mol, Difference in average score from  
                       the base case: -0.0092                                                      (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain A (alanine) into arginine: 
                       Energy difference: 3.1519 kcal/mol, Difference in average score from the    
                       base case: -0.0142                                                          (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 262 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.7086 kcal/mol, Difference in average score from  
                       the base case: -0.0315                                                      (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 262 from chain A (valine) into lysine:    
                       Energy difference: -0.5844 kcal/mol, Difference in average score from the   
                       base case: -0.0356                                                          (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 262 from chain A (valine) into aspartic   
                       acid: Energy difference: 1.2423 kcal/mol, Difference in average score from  
                       the base case: -0.0369                                                      (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 262 from chain A (valine) into arginine:  
                       Energy difference: -0.3751 kcal/mol, Difference in average score from the   
                       base case: -0.0344                                                          (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 208 from chain A (methionine) into        
                       glutamic acid: Energy difference: 2.1999 kcal/mol, Difference in average    
                       score from the base case: -0.0165                                           (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 208 from chain A (methionine) into        
                       lysine: Energy difference: 1.6050 kcal/mol, Difference in average score     
                       from the base case: -0.0224                                                 (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 208 from chain A (methionine) into        
                       aspartic acid: Energy difference: 3.4558 kcal/mol, Difference in average    
                       score from the base case: -0.0117                                           (00:33:07)
[INFO]       Auto_mut: Effect of mutation residue number 208 from chain A (methionine) into        
                       arginine: Energy difference: 1.9116 kcal/mol, Difference in average score   
                       from the base case: -0.0217                                                 (00:33:07)
[INFO]       Main:     Simulation completed successfully.                                          (00:33:13)
Show buried residues
Minimal score value
-5.8217
Maximal score value
2.2401
Average score
-1.2021
Total score value
-363.0399
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 N A -0.5762
2 F A 0.6481
3 T A 0.2298
4 L A -0.2098
5 P A -0.2581
6 P A -1.0321
7 N A -2.1685
8 F A -1.5269
9 G A -1.3286
10 K A -2.2015
11 R A -1.4053
12 P A -0.7928
13 T A -0.6020
14 D A 0.0000
15 L A 0.7713
16 E A -0.3208
17 L A 0.0000
18 S A 0.8526
19 V A 1.3942
20 K A -0.2929
21 L A 0.0000
22 V A -0.0397
23 E A -1.0400
24 M A 0.0000
25 L A 0.0000
26 E A -1.4722
27 N A 0.0000
28 I A 0.0000
29 M A 0.0000
30 L A -0.8834
31 R A -0.9375
32 D A 0.0000
33 G A 0.0000
34 C A 0.0000
35 T A -0.4298
36 L A 0.0000
37 E A -2.2934
38 E A -3.1347
39 S A -2.5185
40 K A -2.6466
41 I A -2.3953
42 K A -3.4778
43 K A -3.5324
44 V A -2.2397
45 L A -1.7744
46 E A -3.2256
47 K A -3.2726
48 P A -2.3707
49 K A -2.6371
50 Y A -1.7004
51 I A 0.0000
52 N A -2.2224
53 L A -1.2425
54 A A 0.0000
55 L A -0.9355
56 E A -1.9127
57 A A 0.0000
58 Q A 0.0000
59 F A 0.0000
60 T A -0.7965
61 I A -0.6197
62 M A 0.0000
63 P A 0.0000
64 K A -1.7401
65 T A 0.0000
66 A A 0.0000
67 L A -1.2478
68 E A -2.3993
69 L A 0.0000
70 A A 0.0000
71 K A -2.2399
72 V A -0.2322
73 F A -1.2490
74 R A -2.6564
75 L A -1.9915
76 K A -2.6221
77 N A -2.1116
78 I A -0.5321
79 E A 0.0000
80 A A 0.0000
81 L A 0.0000
82 A A 0.0000
83 I A 0.0000
84 L A 0.0000
85 V A 0.0000
86 C A 0.0000
87 G A 0.0000
88 C A 0.0000
89 S A 0.0000
90 P A 0.0000
91 T A 0.0000
92 G A 0.0000
93 N A 0.2427
94 L A 0.2501
95 S A 0.0000
96 N A 0.0000
97 I A 0.5863
98 Y A 0.0000
99 S A 0.0000
100 R A -2.4580
101 R A -2.3922
102 L A 0.0000
103 K A -3.3177
104 G A 0.0000
105 D A -1.8694
106 L A -0.8750
107 N A -0.6914
108 L A 0.0000
109 S A 0.0000
110 W A -0.0131
111 V A 0.0000
112 M A 0.0000
113 T A 0.0000
114 T A 0.0000
115 C A 0.3262
116 S A 0.0000
117 T A 0.0000
118 L A -0.2196
119 C A -0.3304
120 A A 0.0000
121 N A -1.7389
122 E A -2.6441
123 R A -2.3948
124 M A 0.0000
125 P A -2.2219
126 E A -3.1404
127 L A 0.0000
128 L A 0.0000
129 E A -2.8760
130 K A -2.6857
131 Y A -1.8398
132 S A 0.0000
133 R A -3.0499
134 G A -2.0046
135 I A -1.3990
136 Y A -1.9033
137 D A -2.7059
138 G A -2.6495
139 D A -3.4962
140 L A -3.1100
141 K A -3.3418
142 D A -3.1930
143 K A -2.3372
144 V A 0.0000
145 P A -1.1557
146 Y A -1.2044
147 K A -1.1765
148 G A -0.2995
149 I A 0.0000
150 L A -0.3059
151 I A 0.3935
152 S A 0.0000
153 L A 0.0000
154 E A -1.8042
155 L A -1.0850
156 V A 0.0000
157 T A -1.6383
158 K A -2.6243
159 P A 0.0000
160 C A 0.0000
161 T A -1.6477
162 E A -2.6929
163 G A 0.0000
164 I A -2.0235
165 E A -2.8490
166 L A -2.2367
167 K A -2.6886
168 S A -2.9033
169 K A -3.1634
170 R A -3.1289
171 P A -2.4795
172 Q A -2.2359
173 L A -1.3092
174 L A 0.0000
175 R A -3.2321
176 K A -3.4284
177 V A -2.4180
178 M A -2.6901
179 K A -4.3233
180 E A -4.4755
181 L A 0.0000
182 E A -3.9413
183 E A -4.6351
184 K A -4.3145
185 V A 0.0000
186 K A -4.8349
187 E A -4.6803
188 L A 0.0000
189 E A -4.0844
190 E A -4.1722
191 E A -3.6244
192 V A -2.4898
193 T A -2.6976
194 R A -3.6909
195 L A -2.7804
196 S A 0.0000
197 K A -3.5659
198 E A -3.3462
199 N A 0.0000
200 V A 0.0000
201 G A -2.3080
202 K A -1.5834
203 S A 0.1880
204 I A 0.5125
205 M A 1.4978
206 F A 2.2401
207 A A 1.3573
208 M A 0.9861
209 T A 0.2043
210 P A -0.7026
211 K A -1.4486
212 I A 0.0000
213 L A -0.5729
214 K A -1.5706
215 T A 0.0000
216 S A 0.0000
217 S A -1.0043
218 L A -0.3103
219 M A 0.0000
220 P A 0.0000
221 K A -1.3632
222 L A -0.7421
223 G A 0.0000
224 Y A 0.0000
225 E A -2.5671
226 K A -2.3103
227 G A 0.0000
228 L A -2.0363
229 E A -3.1520
230 I A -1.8752
231 S A 0.0000
232 E A -2.9150
233 K A -2.5131
234 A A -1.4370
235 C A -0.9070
236 L A 0.0000
237 N A -2.1798
238 G A -2.3218
239 R A -3.0988
240 C A 0.0000
241 R A -2.1790
242 R A -2.0963
243 T A 0.0000
244 V A 0.0000
245 S A 0.0000
246 M A 0.0000
247 E A 0.0000
248 T A 0.0000
249 G A 0.0000
250 C A 0.0000
251 R A 0.0000
252 N A 0.0000
253 V A 0.0000
254 Q A -0.0810
255 L A 0.0000
256 C A 0.0000
257 S A 0.0000
258 T A 0.0000
259 I A 0.0000
260 L A 0.0000
261 N A 0.3558
262 V A 1.2657
263 A A 0.2434
264 F A 0.0000
265 P A -0.2069
266 P A -0.8399
267 E A -1.5105
268 V A 0.4391
269 I A 0.0000
270 G A 0.0000
271 P A 0.0000
272 L A 0.0000
273 F A 0.0000
274 F A 0.0000
275 F A 0.0000
276 P A 0.0000
277 L A 0.7708
278 L A 0.4118
279 Y A 0.0000
280 M A -0.5386
281 Q A -1.6093
282 N A -1.7858
283 Q A 0.0000
284 K A -2.6083
285 E A -3.3988
286 E A -2.7505
287 G A 0.0000
288 D A -3.0293
289 K A -3.2166
290 I A -2.8057
291 V A 0.0000
292 K A -4.3600
293 E A -4.3886
294 Y A -3.9413
295 K A -5.0630
296 E A -5.7031
297 E A -5.8217
298 E A -5.5858
299 K A -5.6176
300 K A -5.4436
301 K A -5.0447
302 E A -4.1970
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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
VR19A -0.9199 -0.058 View CSV PDB
VK19A -0.6927 -0.058 View CSV PDB
VK262A -0.5844 -0.0356 View CSV PDB
VR262A -0.3751 -0.0344 View CSV PDB
FK206A 0.1591 -0.0612 View CSV PDB
FE206A 0.3887 -0.0556 View CSV PDB
MK205A 0.4503 -0.0406 View CSV PDB
ME205A 0.6572 -0.0377 View CSV PDB
MK208A 1.605 -0.0224 View CSV PDB
MR208A 1.9116 -0.0217 View CSV PDB
AR207A 3.1519 -0.0142 View CSV PDB
AK207A 3.7421 -0.0161 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018