Project name: Ptp1b-open

Status: done

Started: 2025-04-30 08:30:19
Chain sequence(s) A: EMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDL
input PDB
Selected Chain(s) A
Distance of aggregation 5 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
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 minimization                                          (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:05:12)
[INFO]       AutoMut:  Residue number 182 from chain A and a score of 1.813 (phenylalanine)        
                       selected for automated mutation                                             (00:05:13)
[INFO]       AutoMut:  Residue number 149 from chain A and a score of 1.607 (isoleucine) selected  
                       for automated mutation                                                      (00:05:13)
[INFO]       AutoMut:  Residue number 119 from chain A and a score of 1.596 (leucine) selected for 
                       automated mutation                                                          (00:05:13)
[INFO]       AutoMut:  Residue number 134 from chain A and a score of 1.287 (isoleucine) selected  
                       for automated mutation                                                      (00:05:13)
[INFO]       AutoMut:  Residue number 299 from chain A and a score of 1.224 (leucine) selected for 
                       automated mutation                                                          (00:05:13)
[INFO]       AutoMut:  Residue number 294 from chain A and a score of 1.209 (leucine) selected for 
                       automated mutation                                                          (00:05:13)
[INFO]       AutoMut:  Mutating residue number 149 from chain A (isoleucine) into glutamic acid    (00:05:13)
[INFO]       AutoMut:  Mutating residue number 182 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 182 from chain A (phenylalanine) into glutamic acid (00:05:13)
[INFO]       AutoMut:  Mutating residue number 182 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 182 from chain A (phenylalanine) into aspartic acid (00:05:13)
[INFO]       AutoMut:  Mutating residue number 182 from chain A (phenylalanine) into arginine      (00:05:22)
[INFO]       AutoMut:  Mutating residue number 149 from chain A (isoleucine) into lysine           (00:05:25)
[INFO]       AutoMut:  Mutating residue number 149 from chain A (isoleucine) into aspartic acid    (00:05:35)
[INFO]       AutoMut:  Mutating residue number 182 from chain A (phenylalanine) into lysine        (00:05:37)
[INFO]       AutoMut:  Mutating residue number 149 from chain A (isoleucine) into arginine         (00:05:44)
[INFO]       AutoMut:  Mutating residue number 119 from chain A (leucine) into glutamic acid       (00:05:46)
[INFO]       AutoMut:  Mutating residue number 119 from chain A (leucine) into aspartic acid       (00:05:56)
[INFO]       AutoMut:  Mutating residue number 119 from chain A (leucine) into lysine              (00:05:59)
[INFO]       AutoMut:  Mutating residue number 134 from chain A (isoleucine) into glutamic acid    (00:06:07)
[INFO]       AutoMut:  Mutating residue number 119 from chain A (leucine) into arginine            (00:06:12)
[INFO]       AutoMut:  Mutating residue number 134 from chain A (isoleucine) into aspartic acid    (00:06:14)
[INFO]       AutoMut:  Mutating residue number 134 from chain A (isoleucine) into lysine           (00:06:21)
[INFO]       AutoMut:  Mutating residue number 299 from chain A (leucine) into glutamic acid       (00:06:23)
[INFO]       AutoMut:  Mutating residue number 134 from chain A (isoleucine) into arginine         (00:06:31)
[INFO]       AutoMut:  Mutating residue number 299 from chain A (leucine) into lysine              (00:06:33)
[INFO]       AutoMut:  Mutating residue number 299 from chain A (leucine) into aspartic acid       (00:06:42)
[INFO]       AutoMut:  Mutating residue number 294 from chain A (leucine) into glutamic acid       (00:06:46)
[INFO]       AutoMut:  Mutating residue number 294 from chain A (leucine) into aspartic acid       (00:06:49)
[INFO]       AutoMut:  Mutating residue number 299 from chain A (leucine) into arginine            (00:06:50)
[INFO]       AutoMut:  Mutating residue number 294 from chain A (leucine) into lysine              (00:06:55)
[INFO]       AutoMut:  Mutating residue number 294 from chain A (leucine) into arginine            (00:07:00)
[INFO]       AutoMut:  Effect of mutation residue number 182 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.9398 kcal/mol, Difference in average    
                       score from the base case: -0.0183                                           (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 182 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.5590 kcal/mol, Difference in average score     
                       from the base case: -0.0154                                                 (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 182 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 1.3214 kcal/mol, Difference in average    
                       score from the base case: -0.0179                                           (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 182 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.9421 kcal/mol, Difference in average score   
                       from the base case: -0.0183                                                 (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 149 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.8417 kcal/mol, Difference in average   
                       score from the base case: -0.0172                                           (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 149 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.6003 kcal/mol, Difference in average score    
                       from the base case: -0.0150                                                 (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 149 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: -0.5189 kcal/mol, Difference in average   
                       score from the base case: -0.0203                                           (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 149 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.6886 kcal/mol, Difference in average score  
                       from the base case: -0.0185                                                 (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 119 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.3745 kcal/mol, Difference in average score from  
                       the base case: -0.0165                                                      (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 119 from chain A (leucine) into lysine:   
                       Energy difference: 0.3184 kcal/mol, Difference in average score from the    
                       base case: -0.0172                                                          (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 119 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.4939 kcal/mol, Difference in average score from  
                       the base case: -0.0161                                                      (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 119 from chain A (leucine) into arginine: 
                       Energy difference: 0.4902 kcal/mol, Difference in average score from the    
                       base case: -0.0184                                                          (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 134 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 1.4408 kcal/mol, Difference in average    
                       score from the base case: -0.0147                                           (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 134 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.3408 kcal/mol, Difference in average score     
                       from the base case: -0.0154                                                 (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 134 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 1.6007 kcal/mol, Difference in average    
                       score from the base case: -0.0140                                           (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 134 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.3968 kcal/mol, Difference in average score   
                       from the base case: -0.0132                                                 (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 299 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.0275 kcal/mol, Difference in average score from  
                       the base case: -0.0133                                                      (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 299 from chain A (leucine) into lysine:   
                       Energy difference: -0.4044 kcal/mol, Difference in average score from the   
                       base case: -0.0129                                                          (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 299 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.0986 kcal/mol, Difference in average score from  
                       the base case: -0.0132                                                      (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 299 from chain A (leucine) into arginine: 
                       Energy difference: -1.0352 kcal/mol, Difference in average score from the   
                       base case: -0.0134                                                          (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 294 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.8011 kcal/mol, Difference in average score from  
                       the base case: -0.0159                                                      (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 294 from chain A (leucine) into lysine:   
                       Energy difference: 0.0922 kcal/mol, Difference in average score from the    
                       base case: -0.0152                                                          (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 294 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.1733 kcal/mol, Difference in average score from  
                       the base case: -0.0166                                                      (00:07:15)
[INFO]       AutoMut:  Effect of mutation residue number 294 from chain A (leucine) into arginine: 
                       Energy difference: 0.1063 kcal/mol, Difference in average score from the    
                       base case: -0.0159                                                          (00:07:15)
[INFO]       Main:     Simulation completed successfully.                                          (00:07:20)
Show buried residues
Minimal score value
-2.4638
Maximal score value
1.8133
Average score
-0.4163
Total score value
-124.0711
Download the table (csv)

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan4D score mutation
2 E A -1.8434
3 M A 0.0000
4 E A -1.1259
5 K A -2.0537
6 E A -1.4843
7 F A -0.4367
8 E A -2.0765
9 Q A -1.6488
10 I A 0.0000
11 D A -1.2138
12 K A -1.8594
13 S A -0.6122
14 G A -0.5869
15 S A -0.1329
16 W A 0.0000
17 A A 0.0686
18 A A 0.0746
19 I A 0.4474
20 Y A 0.0000
21 Q A -1.1378
22 D A -1.7194
23 I A 0.0000
24 R A -1.5827
25 H A -1.5681
26 E A -1.9996
27 A A -0.3333
28 S A -0.3875
29 D A -1.6062
30 F A 0.6652
31 P A -0.0449
32 C A -0.2907
33 R A -1.7878
34 V A -0.1309
35 A A 0.0000
36 K A -1.6230
37 L A 0.0598
38 P A -0.4918
39 K A -1.7469
40 N A 0.0000
41 K A -1.9333
42 N A -1.6212
43 R A -0.4728
44 N A -0.3116
45 R A -0.2954
46 Y A -0.0148
47 R A -2.1029
48 D A -2.1298
49 V A 0.0000
50 S A -0.0218
51 P A 0.0000
52 F A 0.0000
53 D A -0.5149
54 H A -1.0513
55 S A 0.0000
56 R A -0.1983
57 I A 0.0000
58 K A -1.7000
59 L A 0.0000
60 H A -1.0401
61 Q A -0.7885
62 E A -2.1986
63 D A -2.1570
64 N A -0.5794
65 D A -0.4198
66 Y A 0.0000
67 I A 0.0000
68 N A 0.0000
69 A A 0.0000
70 S A 0.0000
71 L A 0.2499
72 I A 0.0000
73 K A -1.2193
74 M A 0.0000
75 E A -2.1550
76 E A -2.1550
77 A A 0.0000
78 Q A -1.2432
79 R A -0.4750
80 S A -0.2647
81 Y A 0.0000
82 I A 0.0000
83 L A 0.0000
84 T A 0.0000
85 Q A 0.0000
86 G A 0.0000
87 P A 0.0000
88 L A 0.1244
89 P A -0.4186
90 N A -1.1129
91 T A 0.0000
92 C A 0.0000
93 G A 0.0000
94 H A 0.0000
95 F A 0.0000
96 W A 0.0000
97 E A 0.0000
98 M A 0.0000
99 V A 0.0000
100 W A 0.0000
101 E A -0.7239
102 Q A -0.7170
103 K A -1.4931
104 S A 0.0000
105 R A -0.3270
106 G A 0.0000
107 V A 0.0000
108 V A 0.0000
109 M A 0.0000
110 L A 0.0000
111 N A 0.0000
112 R A -1.4961
113 V A 0.2208
114 M A 1.0719
115 E A -0.3387
116 K A -1.8193
117 G A -0.8016
118 S A 0.0829
119 L A 1.5963
120 K A 0.0692
121 C A 0.0000
122 A A -0.1089
123 Q A -0.6334
124 Y A 0.0000
125 W A 0.0000
126 P A 0.0000
127 Q A -1.3987
128 K A -1.6456
129 E A -2.3461
130 E A -2.4638
131 K A -2.2668
132 E A -1.5399
133 M A 0.2249
134 I A 1.2869
135 F A 0.0000
136 E A -2.2174
137 D A -2.1286
138 T A -0.4415
139 N A -0.7820
140 L A 0.0000
141 K A -0.2720
142 L A 0.0000
143 T A -0.1761
144 L A 0.0000
145 I A 0.6538
146 S A -0.1471
147 E A -1.1650
148 D A -1.5620
149 I A 1.6066
150 K A -0.0569
151 S A -0.2314
152 Y A 0.0000
153 Y A 0.0000
154 T A 0.0000
155 V A 0.0000
156 R A -0.3692
157 Q A -0.3601
158 L A 0.0000
159 E A -1.1549
160 L A 0.0000
161 E A -0.3147
162 N A -0.1651
163 L A 0.2147
164 T A -0.0056
165 T A -0.2836
166 Q A -1.4830
167 E A -1.9764
168 T A -0.5250
169 R A -0.7460
170 E A -1.0065
171 I A 0.0000
172 L A 0.1380
173 H A 0.0000
174 F A 0.0000
175 H A 0.0000
176 Y A 0.0000
177 T A -0.0162
178 T A -0.0182
179 W A 0.0000
180 P A -0.2531
181 D A 0.0099
182 F A 1.8133
183 G A 0.3410
184 V A 0.4559
185 P A 0.0000
186 E A -1.8328
187 S A -0.4144
188 P A -0.0601
189 A A 0.0000
190 S A 0.0000
191 F A 0.0000
192 L A 0.0000
193 N A 0.0000
194 F A 0.0000
195 L A 0.0000
196 F A 0.0000
197 K A -0.6155
198 V A 0.0000
199 R A -0.6102
200 E A -1.8784
201 S A -0.3947
202 G A -0.1035
203 S A 0.0000
204 L A 0.0000
205 S A -0.0901
206 P A -0.5967
207 E A -1.9221
208 H A -0.6478
209 G A -0.3072
210 P A -0.0416
211 V A 0.0000
212 V A 0.0000
213 V A 0.0000
214 H A 0.0000
215 C A 0.0000
216 S A 0.0000
217 A A 0.0000
218 G A 0.0000
219 I A 0.0000
220 G A 0.0000
221 R A 0.0000
222 S A 0.0000
223 G A 0.0000
224 T A 0.0000
225 F A 0.0000
226 C A 0.0000
227 L A 0.0000
228 A A 0.0000
229 D A 0.0000
230 T A 0.0000
231 C A 0.0000
232 L A 0.0000
233 L A 0.1518
234 L A 0.0000
235 M A 0.0000
236 D A -1.1727
237 K A -1.9635
238 R A -1.3480
239 K A -2.0487
240 D A -1.0980
241 P A -0.2401
242 S A -0.4444
243 S A -0.1456
244 V A 0.0000
245 D A -1.0851
246 I A 0.0000
247 K A -0.6910
248 K A -1.7191
249 V A 0.0000
250 L A 0.0000
251 L A -0.0429
252 E A -1.3352
253 M A 0.0000
254 R A 0.0000
255 K A -0.8065
256 F A 0.1080
257 R A 0.0000
258 M A 0.2191
259 G A -0.0291
260 L A 0.0000
261 I A 0.0000
262 Q A -0.2400
263 T A -0.0514
264 A A -0.3234
265 D A -1.8446
266 Q A 0.0000
267 L A 0.0000
268 R A -0.7264
269 F A 0.0000
270 S A 0.0000
271 Y A 0.0000
272 L A 0.3891
273 A A 0.0000
274 V A 0.0000
275 I A 0.3273
276 E A -0.2267
277 G A 0.0000
278 A A -0.2430
279 K A -1.2781
280 F A 0.0602
281 I A 0.0000
282 M A 0.3987
283 G A -0.6319
284 D A -1.4573
285 S A -0.5080
286 S A -0.2520
287 V A 0.0000
288 Q A -0.5487
289 D A -1.9664
290 Q A -1.0694
291 W A 0.0000
292 K A -1.5283
293 E A -1.7549
294 L A 1.2089
295 S A 0.0823
296 H A -1.0280
297 E A -0.7118
298 D A -1.5433
299 L A 1.2239
Download PDB file
View in 3Dmol

Automated mutations analysis - charged mutations

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
IE149A -0.8417 -0.0172 View CSV PDB
IR149A -0.6886 -0.0185 View CSV PDB
LR299A -1.0352 -0.0134 View CSV PDB
LK299A -0.4044 -0.0129 View CSV PDB
LK294A 0.0922 -0.0152 View CSV PDB
LR294A 0.1063 -0.0159 View CSV PDB
LK119A 0.3184 -0.0172 View CSV PDB
IK134A 0.3408 -0.0154 View CSV PDB
LE119A 0.3745 -0.0165 View CSV PDB
IR134A 0.3968 -0.0132 View CSV PDB
FK182A 0.559 -0.0154 View CSV PDB
FE182A 0.9398 -0.0183 View CSV PDB