Project name: Ptp1B open

Status: done

Started: 2025-04-30 12:32:40
Chain sequence(s) A: EMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKF
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]                                                (00:00:03)
[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 minimization                                          (00:00:03)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:04:19)
[INFO]       AutoMut:  Residue number 182 from chain A and a score of 1.688 (phenylalanine)        
                       selected for automated mutation                                             (00:04:21)
[INFO]       AutoMut:  Residue number 280 from chain A and a score of 1.628 (phenylalanine)        
                       selected for automated mutation                                             (00:04:21)
[INFO]       AutoMut:  Residue number 119 from chain A and a score of 1.590 (leucine) selected for 
                       automated mutation                                                          (00:04:21)
[INFO]       AutoMut:  Residue number 149 from chain A and a score of 1.429 (isoleucine) selected  
                       for automated mutation                                                      (00:04:21)
[INFO]       AutoMut:  Residue number 114 from chain A and a score of 1.251 (methionine) selected  
                       for automated mutation                                                      (00:04:21)
[INFO]       AutoMut:  Residue number 134 from chain A and a score of 1.036 (isoleucine) selected  
                       for automated mutation                                                      (00:04:21)
[INFO]       AutoMut:  Mutating residue number 182 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 182 from chain A (phenylalanine) into glutamic acid (00:04:21)
[INFO]       AutoMut:  Mutating residue number 182 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 182 from chain A (phenylalanine) into aspartic acid (00:04:21)
[INFO]       AutoMut:  Mutating residue number 280 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 280 from chain A (phenylalanine) into glutamic acid (00:04:21)
[INFO]       AutoMut:  Mutating residue number 182 from chain A (phenylalanine) into arginine      (00:04:30)
[INFO]       AutoMut:  Mutating residue number 182 from chain A (phenylalanine) into lysine        (00:04:31)
[INFO]       AutoMut:  Mutating residue number 280 from chain A (phenylalanine) into lysine        (00:04:41)
[INFO]       AutoMut:  Mutating residue number 280 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 280 from chain A (phenylalanine) into aspartic acid (00:04:49)
[INFO]       AutoMut:  Mutating residue number 119 from chain A (leucine) into glutamic acid       (00:04:50)
[INFO]       AutoMut:  Mutating residue number 119 from chain A (leucine) into lysine              (00:05:03)
[INFO]       AutoMut:  Mutating residue number 280 from chain A (phenylalanine) into arginine      (00:05:09)
[INFO]       AutoMut:  Mutating residue number 119 from chain A (leucine) into aspartic acid       (00:05:10)
[INFO]       AutoMut:  Mutating residue number 119 from chain A (leucine) into arginine            (00:05:21)
[INFO]       AutoMut:  Mutating residue number 149 from chain A (isoleucine) into glutamic acid    (00:05:26)
[INFO]       AutoMut:  Mutating residue number 149 from chain A (isoleucine) into aspartic acid    (00:05:36)
[INFO]       AutoMut:  Mutating residue number 149 from chain A (isoleucine) into lysine           (00:05:37)
[INFO]       AutoMut:  Mutating residue number 114 from chain A (methionine) into glutamic acid    (00:05:41)
[INFO]       AutoMut:  Mutating residue number 149 from chain A (isoleucine) into arginine         (00:05:44)
[INFO]       AutoMut:  Mutating residue number 114 from chain A (methionine) into lysine           (00:05:52)
[INFO]       AutoMut:  Mutating residue number 114 from chain A (methionine) into aspartic acid    (00:05:52)
[INFO]       AutoMut:  Mutating residue number 134 from chain A (isoleucine) into glutamic acid    (00:05:58)
[INFO]       AutoMut:  Mutating residue number 114 from chain A (methionine) into arginine         (00:06:06)
[INFO]       AutoMut:  Mutating residue number 134 from chain A (isoleucine) into aspartic acid    (00:06:07)
[INFO]       AutoMut:  Mutating residue number 134 from chain A (isoleucine) into lysine           (00:06:13)
[INFO]       AutoMut:  Mutating residue number 134 from chain A (isoleucine) into arginine         (00:06:22)
[INFO]       AutoMut:  Effect of mutation residue number 182 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: -0.0952 kcal/mol, Difference in average   
                       score from the base case: -0.0204                                           (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 182 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.0822 kcal/mol, Difference in average score     
                       from the base case: -0.0191                                                 (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 182 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.0502 kcal/mol, Difference in average    
                       score from the base case: -0.0210                                           (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 182 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.0721 kcal/mol, Difference in average score  
                       from the base case: -0.0186                                                 (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 280 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 1.5773 kcal/mol, Difference in average    
                       score from the base case: -0.0176                                           (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 280 from chain A (phenylalanine) into     
                       lysine: Energy difference: 1.0983 kcal/mol, Difference in average score     
                       from the base case: -0.0159                                                 (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 280 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 1.7604 kcal/mol, Difference in average    
                       score from the base case: -0.0186                                           (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 280 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.5476 kcal/mol, Difference in average score  
                       from the base case: -0.0197                                                 (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 119 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.5009 kcal/mol, Difference in average score from  
                       the base case: -0.0181                                                      (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 119 from chain A (leucine) into lysine:   
                       Energy difference: 0.5889 kcal/mol, Difference in average score from the    
                       base case: -0.0175                                                          (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 119 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.3937 kcal/mol, Difference in average score from  
                       the base case: -0.0181                                                      (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 119 from chain A (leucine) into arginine: 
                       Energy difference: 1.0902 kcal/mol, Difference in average score from the    
                       base case: -0.0198                                                          (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 149 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.4954 kcal/mol, Difference in average   
                       score from the base case: -0.0193                                           (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 149 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.3312 kcal/mol, Difference in average score    
                       from the base case: -0.0182                                                 (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 149 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: -0.7444 kcal/mol, Difference in average   
                       score from the base case: -0.0209                                           (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 149 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.1721 kcal/mol, Difference in average score  
                       from the base case: -0.0188                                                 (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 114 from chain A (methionine) into        
                       glutamic acid: Energy difference: 0.1916 kcal/mol, Difference in average    
                       score from the base case: -0.0134                                           (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 114 from chain A (methionine) into        
                       lysine: Energy difference: -0.2374 kcal/mol, Difference in average score    
                       from the base case: -0.0131                                                 (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 114 from chain A (methionine) into        
                       aspartic acid: Energy difference: 1.1139 kcal/mol, Difference in average    
                       score from the base case: -0.0132                                           (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 114 from chain A (methionine) into        
                       arginine: Energy difference: 0.0984 kcal/mol, Difference in average score   
                       from the base case: -0.0146                                                 (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 134 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 1.2514 kcal/mol, Difference in average    
                       score from the base case: -0.0139                                           (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 134 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.1218 kcal/mol, Difference in average score     
                       from the base case: -0.0141                                                 (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 134 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 2.2574 kcal/mol, Difference in average    
                       score from the base case: -0.0137                                           (00:06:46)
[INFO]       AutoMut:  Effect of mutation residue number 134 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.2033 kcal/mol, Difference in average score   
                       from the base case: -0.0147                                                 (00:06:46)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:52)
Show buried residues
Minimal score value
-2.471
Maximal score value
1.6877
Average score
-0.4173
Total score value
-116.421
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 -1.9189
3 M A 0.0000
4 E A -1.4481
5 K A -2.0333
6 E A -1.1147
7 F A -0.3764
8 E A -1.9336
9 Q A -1.3999
10 I A 0.0000
11 D A -0.9145
12 K A -1.8496
13 S A -0.6099
14 G A -0.5172
15 S A -0.1495
16 W A 0.0000
17 A A 0.0657
18 A A 0.1188
19 I A 0.3793
20 Y A 0.0000
21 Q A -0.9837
22 D A -1.9097
23 I A 0.0000
24 R A -1.9074
25 H A -1.6469
26 E A -2.0008
27 A A -0.3347
28 S A -0.3887
29 D A -1.6339
30 F A 0.5398
31 P A -0.0005
32 C A -0.2697
33 R A -1.7659
34 V A -0.0242
35 A A 0.0000
36 K A -1.6010
37 L A 0.1823
38 P A -0.4650
39 K A -1.7463
40 N A 0.0000
41 K A -1.9335
42 N A -1.6256
43 R A -0.4881
44 N A -0.2774
45 R A -0.2945
46 Y A -0.0317
47 R A -2.1032
48 D A -2.1260
49 V A 0.0000
50 S A 0.0000
51 P A 0.0000
52 F A 0.0000
53 D A -0.4656
54 H A -1.0423
55 S A 0.0000
56 R A -0.3056
57 I A 0.0000
58 K A -1.7000
59 L A 0.0000
60 H A -1.1255
61 Q A -1.2544
62 E A -2.2818
63 D A -2.1727
64 N A -0.6699
65 D A -0.3951
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 0.2082
72 I A 0.0000
73 K A -1.6069
74 M A 0.0000
75 E A -2.0021
76 E A -1.3200
77 A A -0.3942
78 Q A -1.2498
79 R A -0.5191
80 S A -0.3417
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 0.1580
89 P A -0.4502
90 N A -1.3197
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 -0.6033
102 Q A -0.6594
103 K A -1.7523
104 S A 0.0000
105 R A -0.3518
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 -0.3501
113 V A 0.3866
114 M A 1.2511
115 E A 0.0000
116 K A -1.7859
117 G A -0.8004
118 S A 0.0815
119 L A 1.5896
120 K A -0.0797
121 C A 0.0000
122 A A -0.0790
123 Q A -0.4632
124 Y A 0.0000
125 W A 0.0000
126 P A 0.0000
127 Q A -1.5105
128 K A -2.2538
129 E A -2.4684
130 E A -2.4710
131 K A -2.2959
132 E A -1.6795
133 M A 0.1480
134 I A 1.0362
135 F A 0.0000
136 E A -2.2200
137 D A -2.1279
138 T A 0.0000
139 N A -0.7988
140 L A 0.0000
141 K A -0.3239
142 L A 0.0000
143 T A -0.1797
144 L A 0.0000
145 I A 0.6135
146 S A -0.1314
147 E A -1.0583
148 D A -1.5446
149 I A 1.4295
150 K A -1.0405
151 S A -0.4067
152 Y A 0.2957
153 Y A 0.0000
154 T A 0.0000
155 V A 0.0000
156 R A -0.3683
157 Q A -0.4301
158 L A 0.0000
159 E A -0.7576
160 L A 0.0000
161 E A 0.0000
162 N A -0.0800
163 L A 0.2957
164 T A 0.0018
165 T A -0.3020
166 Q A -1.3763
167 E A -1.3949
168 T A -0.3632
169 R A -0.6609
170 E A -0.8741
171 I A 0.0000
172 L A 0.1735
173 H A 0.0000
174 F A 0.0000
175 H A 0.0000
176 Y A 0.0000
177 T A -0.0227
178 T A -0.0493
179 W A 0.0000
180 P A -0.2242
181 D A -0.5579
182 F A 1.6877
183 G A -0.0372
184 V A 0.2737
185 P A 0.0000
186 E A -1.8486
187 S A -0.4916
188 P A 0.0000
189 A A 0.0269
190 S A -0.0480
191 F A 0.0000
192 L A 0.0000
193 N A -1.0282
194 F A 0.0000
195 L A 0.0000
196 F A 0.2389
197 K A -0.4378
198 V A 0.0000
199 R A -0.8573
200 E A -1.9322
201 S A -0.4111
202 G A -0.1618
203 S A 0.0000
204 L A 0.0000
205 S A -0.0797
206 P A -0.5948
207 E A -1.9554
208 H A -0.8274
209 G A -0.3703
210 P A -0.0412
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 0.0077
218 G A 0.0000
219 I A 0.0000
220 G A 0.0000
221 R A -0.2178
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 0.2578
234 L A 0.0000
235 M A -0.1949
236 D A -2.0740
237 K A -2.1490
238 R A -1.2726
239 K A -2.0148
240 D A -1.4001
241 P A -0.3340
242 S A -0.1906
243 S A -0.1488
244 V A 0.0000
245 D A -0.5098
246 I A 0.0000
247 K A -0.7473
248 K A -1.7798
249 V A 0.0000
250 L A 0.0000
251 L A -0.0022
252 E A -1.2608
253 M A 0.0000
254 R A 0.0000
255 K A -0.8359
256 F A 0.1125
257 R A 0.0000
258 M A 0.2592
259 G A -0.0243
260 L A 0.0000
261 I A 0.0000
262 Q A -1.2019
263 T A -0.2345
264 A A -0.2953
265 D A -1.7082
266 Q A 0.0000
267 L A 0.0000
268 R A -0.7970
269 F A 0.0000
270 S A 0.0000
271 Y A 0.0000
272 L A 0.2538
273 A A 0.0000
274 V A 0.0000
275 I A 0.0797
276 E A -0.7220
277 G A 0.0000
278 A A -0.2874
279 K A -1.3384
280 F A 1.6284
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
ID149A -0.7444 -0.0209 View CSV PDB
FR280A -0.5476 -0.0197 View CSV PDB
IE149A -0.4954 -0.0193 View CSV PDB
FE182A -0.0952 -0.0204 View CSV PDB
FR182A -0.0721 -0.0186 View CSV PDB
MK114A -0.2374 -0.0131 View CSV PDB
MR114A 0.0984 -0.0146 View CSV PDB
IK134A 0.1218 -0.0141 View CSV PDB
IR134A 0.2033 -0.0147 View CSV PDB
LD119A 0.3937 -0.0181 View CSV PDB
LE119A 0.5009 -0.0181 View CSV PDB
FK280A 1.0983 -0.0159 View CSV PDB