Project name: IgeR

Status: done

Started: 2025-08-05 15:22:38
Settings
Chain sequence(s) A: MTRRADRLFQIVQILRGRRLTTAALLAQRLAVSERTIYRDIRDLSLSGVPVEGEAGSGYRLMAGFDLPPLMLTHRESEALMVAIRLLKTWGGDSLSRELESAQEKVLAILPEESRRKAEQTRIYAPDLGTSPHSRSAFDLIHQAVSAQQVLALHYRDEAGHLSSRDIQPLGLFFWGEHWLLVAWCERREDYRCFRLDRCLQITPLNRRFRETIDRSLRDFLRKVEHEKMP
B: MTRRADRLFQIVQILRGRRLTTAALLAQRLAVSERTIYRDIRDLSLSGVPVEGEAGSGYRLMAGFDLPPLMLTHRESEALMVAIRLLKTWGGDSLSRELESAQEKVLAILPEESRRKAEQTRIYAPDLGTSPHSRSAFDLIHQAVSAQQVLALHYRDEAGHLSSRDIQPLGLFFWGEHWLLVAWCERREDYRCFRLDRCLQITPLNRRFRETIDRSLRDFLRKVEHEKMP
input PDB
Selected Chain(s) A,B
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 all 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                                          (00:10:35)
[INFO]       Auto_mut: Residue number 46 from chain B and a score of 0.860 (leucine) selected for  
                       automated muatation                                                         (00:10:39)
[INFO]       Auto_mut: Residue number 46 from chain A and a score of 0.778 (leucine) selected for  
                       automated muatation                                                         (00:10:39)
[INFO]       Auto_mut: Residue number 213 from chain B and a score of 0.580 (isoleucine) selected  
                       for automated muatation                                                     (00:10:39)
[INFO]       Auto_mut: Residue number 213 from chain A and a score of 0.574 (isoleucine) selected  
                       for automated muatation                                                     (00:10:39)
[INFO]       Auto_mut: Residue number 124 from chain B and a score of 0.287 (tyrosine) selected    
                       for automated muatation                                                     (00:10:39)
[INFO]       Auto_mut: Residue number 1 from chain B and a score of 0.254 (methionine) selected    
                       for automated muatation                                                     (00:10:39)
[INFO]       Auto_mut: Mutating residue number 46 from chain B (leucine) into glutamic acid        (00:10:40)
[INFO]       Auto_mut: Mutating residue number 46 from chain B (leucine) into aspartic acid        (00:10:40)
[INFO]       Auto_mut: Mutating residue number 46 from chain A (leucine) into glutamic acid        (00:10:40)
[INFO]       Auto_mut: Mutating residue number 46 from chain A (leucine) into lysine               (00:14:59)
[INFO]       Auto_mut: Mutating residue number 46 from chain B (leucine) into lysine               (00:14:59)
[INFO]       Auto_mut: Mutating residue number 46 from chain B (leucine) into arginine             (00:15:04)
[INFO]       Auto_mut: Mutating residue number 46 from chain A (leucine) into aspartic acid        (00:19:13)
[INFO]       Auto_mut: Mutating residue number 213 from chain B (isoleucine) into glutamic acid    (00:19:20)
[INFO]       Auto_mut: Mutating residue number 213 from chain B (isoleucine) into aspartic acid    (00:19:33)
[INFO]       Auto_mut: Mutating residue number 213 from chain B (isoleucine) into lysine           (00:23:11)
[INFO]       Auto_mut: Mutating residue number 46 from chain A (leucine) into arginine             (00:23:19)
[INFO]       Auto_mut: Mutating residue number 213 from chain B (isoleucine) into arginine         (00:23:20)
[INFO]       Auto_mut: Mutating residue number 213 from chain A (isoleucine) into glutamic acid    (00:27:01)
[INFO]       Auto_mut: Mutating residue number 213 from chain A (isoleucine) into aspartic acid    (00:27:09)
[INFO]       Auto_mut: Mutating residue number 124 from chain B (tyrosine) into glutamic acid      (00:27:11)
[INFO]       Auto_mut: Mutating residue number 213 from chain A (isoleucine) into lysine           (00:30:48)
[INFO]       Auto_mut: Mutating residue number 213 from chain A (isoleucine) into arginine         (00:30:58)
[INFO]       Auto_mut: Mutating residue number 124 from chain B (tyrosine) into lysine             (00:31:24)
[INFO]       Auto_mut: Mutating residue number 124 from chain B (tyrosine) into aspartic acid      (00:34:41)
[INFO]       Auto_mut: Mutating residue number 1 from chain B (methionine) into glutamic acid      (00:34:42)
[INFO]       Auto_mut: Mutating residue number 1 from chain B (methionine) into aspartic acid      (00:35:47)
[INFO]       Auto_mut: Mutating residue number 1 from chain B (methionine) into lysine             (00:38:22)
[INFO]       Auto_mut: Mutating residue number 124 from chain B (tyrosine) into arginine           (00:38:33)
[INFO]       Auto_mut: Mutating residue number 1 from chain B (methionine) into arginine           (00:39:37)
[INFO]       Auto_mut: Effect of mutation residue number 46 from chain B (leucine) into glutamic   
                       acid: Energy difference: 0.3297 kcal/mol, Difference in average score from  
                       the base case: -0.0017                                                      (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 46 from chain B (leucine) into lysine:    
                       Energy difference: 0.4520 kcal/mol, Difference in average score from the    
                       base case: -0.0161                                                          (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 46 from chain B (leucine) into aspartic   
                       acid: Energy difference: 0.8583 kcal/mol, Difference in average score from  
                       the base case: -0.0107                                                      (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 46 from chain B (leucine) into arginine:  
                       Energy difference: -0.1463 kcal/mol, Difference in average score from the   
                       base case: -0.0121                                                          (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 46 from chain A (leucine) into glutamic   
                       acid: Energy difference: 0.4254 kcal/mol, Difference in average score from  
                       the base case: -0.0017                                                      (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 46 from chain A (leucine) into lysine:    
                       Energy difference: -0.2813 kcal/mol, Difference in average score from the   
                       base case: -0.0163                                                          (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 46 from chain A (leucine) into aspartic   
                       acid: Energy difference: 0.7826 kcal/mol, Difference in average score from  
                       the base case: -0.0178                                                      (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 46 from chain A (leucine) into arginine:  
                       Energy difference: -0.5102 kcal/mol, Difference in average score from the   
                       base case: -0.0160                                                          (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 213 from chain B (isoleucine) into        
                       glutamic acid: Energy difference: -0.4605 kcal/mol, Difference in average   
                       score from the base case: -0.0109                                           (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 213 from chain B (isoleucine) into        
                       lysine: Energy difference: -0.0899 kcal/mol, Difference in average score    
                       from the base case: -0.0179                                                 (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 213 from chain B (isoleucine) into        
                       aspartic acid: Energy difference: -0.0223 kcal/mol, Difference in average   
                       score from the base case: -0.0108                                           (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 213 from chain B (isoleucine) into        
                       arginine: Energy difference: -0.4583 kcal/mol, Difference in average score  
                       from the base case: -0.0137                                                 (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 213 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.3896 kcal/mol, Difference in average   
                       score from the base case: -0.0197                                           (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 213 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.5755 kcal/mol, Difference in average score    
                       from the base case: -0.0149                                                 (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 213 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: -0.0508 kcal/mol, Difference in average   
                       score from the base case: -0.0196                                           (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 213 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.6411 kcal/mol, Difference in average score  
                       from the base case: -0.0090                                                 (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 124 from chain B (tyrosine) into glutamic 
                       acid: Energy difference: 1.0447 kcal/mol, Difference in average score from  
                       the base case: -0.0020                                                      (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 124 from chain B (tyrosine) into lysine:  
                       Energy difference: 0.7958 kcal/mol, Difference in average score from the    
                       base case: -0.0029                                                          (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 124 from chain B (tyrosine) into aspartic 
                       acid: Energy difference: 1.8264 kcal/mol, Difference in average score from  
                       the base case: -0.0005                                                      (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 124 from chain B (tyrosine) into          
                       arginine: Energy difference: 0.3859 kcal/mol, Difference in average score   
                       from the base case: 0.0016                                                  (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain B (methionine) into glutamic 
                       acid: Energy difference: 0.1430 kcal/mol, Difference in average score from  
                       the base case: 0.0066                                                       (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain B (methionine) into lysine:  
                       Energy difference: 0.3347 kcal/mol, Difference in average score from the    
                       base case: 0.0002                                                           (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain B (methionine) into aspartic 
                       acid: Energy difference: -0.9273 kcal/mol, Difference in average score from 
                       the base case: -0.0042                                                      (00:43:40)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain B (methionine) into          
                       arginine: Energy difference: 0.0643 kcal/mol, Difference in average score   
                       from the base case: 0.0042                                                  (00:43:40)
[INFO]       Main:     Simulation completed successfully.                                          (00:43:49)
Show buried residues
Minimal score value
-4.9
Maximal score value
0.8596
Average score
-1.1099
Total score value
-510.5457
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 M A 0.1438
2 T A -1.0483
3 R A -2.1691
4 R A -1.7121
5 A A 0.0000
6 D A 0.0000
7 R A -1.0283
8 L A -0.7881
9 F A -0.3415
10 Q A -0.6056
11 I A 0.0000
12 V A 0.0000
13 Q A 0.0000
14 I A -0.4673
15 L A 0.0000
16 R A 0.0000
17 G A -2.2923
18 R A -2.7989
19 R A -2.7743
20 L A -1.7882
21 T A 0.0000
22 T A -0.6125
23 A A 0.0000
24 A A -0.8583
25 L A -0.5707
26 L A 0.0000
27 A A 0.0000
28 Q A -1.9388
29 R A -2.1426
30 L A -1.0706
31 A A -0.7257
32 V A -0.6981
33 S A -1.1386
34 E A -2.1552
35 R A -2.6435
36 T A -1.8771
37 I A 0.0000
38 Y A -2.1261
39 R A -2.9753
40 D A 0.0000
41 I A 0.0000
42 R A -2.1681
43 D A -1.1717
44 L A 0.0000
45 S A -0.4275
46 L A 0.7783
47 S A -0.1673
48 G A -0.1073
49 V A 0.0000
50 P A -0.2508
51 V A -0.8192
52 E A -1.3725
53 G A -1.9223
54 E A -2.4294
55 A A -1.3935
56 G A -1.1848
57 S A -1.1949
58 G A 0.0000
59 Y A 0.0000
60 R A -2.4656
61 L A -1.2164
62 M A -0.2274
63 A A -0.3204
64 G A -0.8780
65 F A 0.0000
66 D A -1.9828
67 L A 0.0000
68 P A -0.7178
69 P A 0.0000
70 L A 0.0000
71 M A -0.0794
72 L A 0.0000
73 T A -0.9950
74 H A -1.4719
75 R A -2.2780
76 E A 0.0000
77 S A 0.0000
78 E A -1.8871
79 A A 0.0000
80 L A 0.0000
81 M A 0.0000
82 V A 0.0000
83 A A 0.0000
84 I A 0.0000
85 R A -0.6882
86 L A 0.0000
87 L A 0.0000
88 K A -1.5804
89 T A -0.8606
90 W A 0.0000
91 G A 0.0000
92 G A 0.0000
93 D A -2.1868
94 S A -1.9259
95 L A 0.0000
96 S A -2.2179
97 R A -3.1861
98 E A -2.4985
99 L A 0.0000
100 E A -2.9783
101 S A -2.2583
102 A A 0.0000
103 Q A -1.9812
104 E A -2.3313
105 K A 0.0000
106 V A 0.0000
107 L A 0.0000
108 A A -0.8033
109 I A 0.0000
110 L A 0.0000
111 P A -2.2299
112 E A -3.6139
113 E A -3.9914
114 S A -3.4949
115 R A -3.6718
116 R A -4.5679
117 K A -4.2557
118 A A 0.0000
119 E A -3.0304
120 Q A -2.8220
121 T A -1.8065
122 R A -0.7396
123 I A 0.0000
124 Y A 0.2529
125 A A 0.0000
126 P A -0.6838
127 D A -1.8788
128 L A 0.0000
129 G A -1.4388
130 T A -1.5467
131 S A -1.1860
132 P A -1.0790
133 H A -1.2877
134 S A 0.0000
135 R A -1.4406
136 S A -1.0991
137 A A 0.0000
138 F A 0.0000
139 D A -1.0148
140 L A -0.4321
141 I A 0.0000
142 H A -0.8061
143 Q A -1.3445
144 A A 0.0000
145 V A 0.0000
146 S A -1.1238
147 A A -1.2767
148 Q A -1.7599
149 Q A -1.9743
150 V A 0.0000
151 L A 0.0000
152 A A -0.5000
153 L A 0.0000
154 H A -0.8796
155 Y A 0.0000
156 R A -2.2411
157 D A -2.2018
158 E A -2.5269
159 A A -1.3849
160 G A -1.5024
161 H A -1.4869
162 L A -0.5923
163 S A -0.4775
164 S A -0.8641
165 R A -1.5502
166 D A -1.4115
167 I A 0.0000
168 Q A 0.0000
169 P A 0.0000
170 L A 0.0000
171 G A 0.0000
172 L A 0.0000
173 F A 0.0000
174 F A 0.0000
175 W A -0.6635
176 G A 0.0000
177 E A -2.2948
178 H A -1.6639
179 W A 0.0000
180 L A -0.5572
181 L A 0.0000
182 V A 0.0000
183 A A 0.0000
184 W A 0.0000
185 C A 0.0000
186 E A -2.8599
187 R A -3.7946
188 R A -4.1357
189 E A -3.8113
190 D A -2.8061
191 Y A -1.6280
192 R A -1.4537
193 C A -0.4351
194 F A 0.0000
195 R A -1.7142
196 L A 0.0000
197 D A -2.5768
198 R A -2.3026
199 C A 0.0000
200 L A -0.8136
201 Q A -1.2176
202 I A -0.3636
203 T A -0.3822
204 P A -0.7300
205 L A -1.0422
206 N A -1.9749
207 R A -2.2808
208 R A -2.9563
209 F A -2.0801
210 R A -2.5320
211 E A -1.5325
212 T A -0.6757
213 I A 0.5743
214 D A -1.4333
215 R A -1.6797
216 S A -1.3426
217 L A 0.0000
218 R A -2.3570
219 D A -1.9711
220 F A -1.6528
221 L A -2.1522
222 R A -3.5306
223 K A -3.0485
224 V A -2.5746
225 E A -3.6044
226 H A -3.5934
227 E A -3.7345
228 K A -2.8806
229 M A -1.0283
230 P A -0.6091
1 M B 0.2540
2 T B -1.0270
3 R B -2.0559
4 R B -1.3411
5 A B -0.8580
6 D B -1.2570
7 R B -1.0531
8 L B -0.7161
9 F B 0.0000
10 Q B -0.6210
11 I B 0.0000
12 V B 0.0000
13 Q B 0.0000
14 I B -0.4666
15 L B 0.0000
16 R B 0.0000
17 G B -2.2411
18 R B -2.8981
19 R B -2.8189
20 L B -1.7782
21 T B 0.0000
22 T B -0.5809
23 A B 0.0000
24 A B -0.8955
25 L B -0.5940
26 L B 0.0000
27 A B 0.0000
28 Q B -1.9588
29 R B -2.1260
30 L B -1.0420
31 A B -0.7378
32 V B -0.7434
33 S B -1.2420
34 E B -2.1727
35 R B -2.5516
36 T B -1.7253
37 I B 0.0000
38 Y B -1.8463
39 R B -2.3630
40 D B 0.0000
41 I B 0.0000
42 R B -1.8918
43 D B -0.9294
44 L B 0.0000
45 S B -0.1766
46 L B 0.8596
47 S B -0.0766
48 G B -0.0481
49 V B 0.0000
50 P B -0.2511
51 V B -0.8411
52 E B -1.4704
53 G B -1.9349
54 E B -2.4181
55 A B -1.4936
56 G B -1.1687
57 S B -1.1605
58 G B 0.0000
59 Y B -1.7497
60 R B -2.4353
61 L B -1.1597
62 M B -0.1867
63 A B -0.2602
64 G B -0.7116
65 F B 0.0000
66 D B -1.6148
67 L B 0.0000
68 P B -0.4440
69 P B 0.0000
70 L B 0.0000
71 M B 0.0000
72 L B 0.0000
73 T B -1.1780
74 H B -1.6541
75 R B -2.5366
76 E B 0.0000
77 S B 0.0000
78 E B -2.0743
79 A B 0.0000
80 L B 0.0000
81 M B 0.0000
82 V B 0.0000
83 A B 0.0000
84 I B 0.0000
85 R B -0.6754
86 L B 0.0000
87 L B 0.0000
88 K B -1.5187
89 T B -0.7866
90 W B 0.0000
91 G B 0.0000
92 G B 0.0000
93 D B -2.7034
94 S B -2.0218
95 L B 0.0000
96 S B -2.1761
97 R B -3.0357
98 E B -2.3041
99 L B 0.0000
100 E B -2.2474
101 S B -1.8589
102 A B 0.0000
103 Q B -1.8202
104 E B -2.1287
105 K B 0.0000
106 V B 0.0000
107 L B 0.0000
108 A B -0.8048
109 I B 0.0000
110 L B 0.0000
111 P B -2.1161
112 E B -3.4593
113 E B -4.0206
114 S B -3.6424
115 R B -3.9920
116 R B -4.9000
117 K B -4.4581
118 A B 0.0000
119 E B -4.0259
120 Q B -3.2421
121 T B -2.0051
122 R B 0.0000
123 I B 0.0000
124 Y B 0.2873
125 A B 0.0000
126 P B -0.7959
127 D B -1.7587
128 L B -1.1463
129 G B -1.2809
130 T B -1.4853
131 S B -1.2545
132 P B -1.3006
133 H B -1.6199
134 S B -1.5157
135 R B -1.5242
136 S B -1.2778
137 A B -1.0973
138 F B 0.0000
139 D B -1.1063
140 L B -0.3015
141 I B 0.0000
142 H B -0.8710
143 Q B -1.3818
144 A B 0.0000
145 V B 0.0000
146 S B -1.2273
147 A B -1.3387
148 Q B -1.8306
149 Q B -2.0220
150 V B 0.0000
151 L B 0.0000
152 A B -0.4975
153 L B 0.0000
154 H B -0.6876
155 Y B 0.0000
156 R B -2.1159
157 D B -2.3697
158 E B -2.6043
159 A B -1.4518
160 G B -1.5526
161 H B -1.5112
162 L B -0.4443
163 S B -0.4024
164 S B -0.7638
165 R B -1.5161
166 D B -1.4233
167 I B 0.0000
168 Q B 0.0000
169 P B 0.0000
170 L B 0.0000
171 G B 0.0000
172 L B 0.0000
173 F B 0.0000
174 F B 0.0000
175 W B -0.6648
176 G B 0.0000
177 E B -1.9776
178 H B -1.4639
179 W B 0.0000
180 L B -0.4443
181 L B 0.0000
182 V B 0.0000
183 A B 0.0000
184 W B 0.0000
185 C B 0.0000
186 E B -2.9404
187 R B -3.8326
188 R B -4.1792
189 E B -3.9005
190 D B -2.9926
191 Y B 0.0000
192 R B -1.2698
193 C B -0.2986
194 F B 0.0000
195 R B -1.5954
196 L B 0.0000
197 D B -2.4643
198 R B -2.0260
199 C B -1.0578
200 L B -0.2941
201 Q B -0.9837
202 I B -0.2288
203 T B -0.3851
204 P B -0.7453
205 L B -1.0506
206 N B -1.9716
207 R B -2.2830
208 R B -2.9805
209 F B -2.0759
210 R B -2.4929
211 E B -1.4263
212 T B -0.6219
213 I B 0.5804
214 D B -1.4835
215 R B -1.7417
216 S B -1.3744
217 L B 0.0000
218 R B -2.4161
219 D B -2.0941
220 F B 0.0000
221 L B -2.2744
222 R B -3.6070
223 K B -3.1945
224 V B -2.7089
225 E B -3.6724
226 H B -3.6250
227 E B -3.8101
228 K B -2.9853
229 M B -1.2650
230 P B -0.7184
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
IE213A -0.3896 -0.0197 View CSV PDB
LR46A -0.5102 -0.016 View CSV PDB
IK213A -0.5755 -0.0149 View CSV PDB
IR213B -0.4583 -0.0137 View CSV PDB
LK46A -0.2813 -0.0163 View CSV PDB
IK213B -0.0899 -0.0179 View CSV PDB
LR46B -0.1463 -0.0121 View CSV PDB
MD1B -0.9273 -0.0042 View CSV PDB
LK46B 0.452 -0.0161 View CSV PDB
YK124B 0.7958 -0.0029 View CSV PDB
YE124B 1.0447 -0.002 View CSV PDB
MK1B 0.3347 0.0002 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018