Project name: 3cd902adb5304e6

Status: done

Started: 2026-03-11 02:46:18
Settings
Chain sequence(s) A: EVQLQQSGPELVKLGASVRVSCRTSGFTITEYTMHWVKQSHGKSLEWIGGINPITGGSRNNLKFKDKATLTGDKSSSTVYMDLRSLTSEGSTVNYCVRGRTMGPLDYWGQGTTLTVSS
B: DVVMTQTPLTLSVTIGQPVSISCKSSQSLLYTNGKTFLNWLFQRPGQSPKRLIYMVSKLESGVPDRFSGSGSGTDFTLKISRVEAEDLGIYYCMQSTHFPLTFGGGTKLELK
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]                                                (00:00:01)
[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 all chain(s) selected           (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:03:44)
[INFO]       Auto_mut: Residue number 9 from chain B and a score of 1.237 (leucine) selected for   
                       automated muatation                                                         (00:03:45)
[INFO]       Auto_mut: Residue number 3 from chain B and a score of 0.848 (valine) selected for    
                       automated muatation                                                         (00:03:45)
[INFO]       Auto_mut: Residue number 11 from chain A and a score of 0.716 (leucine) selected for  
                       automated muatation                                                         (00:03:45)
[INFO]       Auto_mut: Residue number 30 from chain B and a score of 0.711 (leucine) selected for  
                       automated muatation                                                         (00:03:45)
[INFO]       Auto_mut: Residue number 8 from chain B and a score of 0.500 (proline) selected for   
                       automated muatation                                                         (00:03:45)
[INFO]       Auto_mut: Residue number 54 from chain A and a score of 0.421 (isoleucine) selected   
                       for automated muatation                                                     (00:03:45)
[INFO]       Auto_mut: Mutating residue number 9 from chain B (leucine) into glutamic acid         (00:03:45)
[INFO]       Auto_mut: Mutating residue number 9 from chain B (leucine) into aspartic acid         (00:03:45)
[INFO]       Auto_mut: Mutating residue number 3 from chain B (valine) into glutamic acid          (00:03:45)
[INFO]       Auto_mut: Mutating residue number 9 from chain B (leucine) into arginine              (00:05:38)
[INFO]       Auto_mut: Mutating residue number 9 from chain B (leucine) into lysine                (00:05:40)
[INFO]       Auto_mut: Mutating residue number 3 from chain B (valine) into lysine                 (00:05:49)
[INFO]       Auto_mut: Mutating residue number 3 from chain B (valine) into aspartic acid          (00:07:52)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (leucine) into glutamic acid        (00:07:53)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (leucine) into aspartic acid        (00:08:03)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (leucine) into lysine               (00:09:50)
[INFO]       Auto_mut: Mutating residue number 3 from chain B (valine) into arginine               (00:09:51)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (leucine) into arginine             (00:09:58)
[INFO]       Auto_mut: Mutating residue number 30 from chain B (leucine) into glutamic acid        (00:11:55)
[INFO]       Auto_mut: Mutating residue number 30 from chain B (leucine) into aspartic acid        (00:12:03)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (proline) into glutamic acid         (00:12:06)
[INFO]       Auto_mut: Mutating residue number 30 from chain B (leucine) into lysine               (00:13:58)
[INFO]       Auto_mut: Mutating residue number 30 from chain B (leucine) into arginine             (00:14:02)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (proline) into lysine                (00:14:07)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (proline) into aspartic acid         (00:16:04)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into glutamic acid     (00:16:10)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into aspartic acid     (00:16:13)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (proline) into arginine              (00:17:57)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into arginine          (00:18:09)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into lysine            (00:18:15)
[INFO]       Auto_mut: Effect of mutation residue number 9 from chain B (leucine) into glutamic    
                       acid: Energy difference: -0.4866 kcal/mol, Difference in average score from 
                       the base case: -0.0557                                                      (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 9 from chain B (leucine) into lysine:     
                       Energy difference: -0.3590 kcal/mol, Difference in average score from the   
                       base case: -0.0535                                                          (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 9 from chain B (leucine) into aspartic    
                       acid: Energy difference: -0.3074 kcal/mol, Difference in average score from 
                       the base case: -0.0553                                                      (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 9 from chain B (leucine) into arginine:   
                       Energy difference: -0.2657 kcal/mol, Difference in average score from the   
                       base case: -0.0442                                                          (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain B (valine) into glutamic     
                       acid: Energy difference: -0.0373 kcal/mol, Difference in average score from 
                       the base case: -0.0435                                                      (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain B (valine) into lysine:      
                       Energy difference: -0.1547 kcal/mol, Difference in average score from the   
                       base case: -0.0385                                                          (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain B (valine) into aspartic     
                       acid: Energy difference: 0.1739 kcal/mol, Difference in average score from  
                       the base case: -0.0393                                                      (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain B (valine) into arginine:    
                       Energy difference: -0.0801 kcal/mol, Difference in average score from the   
                       base case: -0.0410                                                          (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into glutamic   
                       acid: Energy difference: 0.5906 kcal/mol, Difference in average score from  
                       the base case: -0.0449                                                      (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into lysine:    
                       Energy difference: 0.0306 kcal/mol, Difference in average score from the    
                       base case: -0.0431                                                          (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into aspartic   
                       acid: Energy difference: 0.9264 kcal/mol, Difference in average score from  
                       the base case: -0.0395                                                      (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into arginine:  
                       Energy difference: -0.3682 kcal/mol, Difference in average score from the   
                       base case: -0.0399                                                          (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 30 from chain B (leucine) into glutamic   
                       acid: Energy difference: 0.1065 kcal/mol, Difference in average score from  
                       the base case: -0.0441                                                      (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 30 from chain B (leucine) into lysine:    
                       Energy difference: -0.6367 kcal/mol, Difference in average score from the   
                       base case: -0.0377                                                          (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 30 from chain B (leucine) into aspartic   
                       acid: Energy difference: 0.4077 kcal/mol, Difference in average score from  
                       the base case: -0.0502                                                      (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 30 from chain B (leucine) into arginine:  
                       Energy difference: -0.3754 kcal/mol, Difference in average score from the   
                       base case: -0.0426                                                          (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (proline) into glutamic    
                       acid: Energy difference: 3.5036 kcal/mol, Difference in average score from  
                       the base case: -0.0177                                                      (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (proline) into lysine:     
                       Energy difference: 3.2167 kcal/mol, Difference in average score from the    
                       base case: -0.0152                                                          (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (proline) into aspartic    
                       acid: Energy difference: 2.7667 kcal/mol, Difference in average score from  
                       the base case: -0.0272                                                      (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (proline) into arginine:   
                       Energy difference: 3.3267 kcal/mol, Difference in average score from the    
                       base case: -0.0174                                                          (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: -0.9976 kcal/mol, Difference in average   
                       score from the base case: -0.0469                                           (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into lysine: 
                       Energy difference: -1.3401 kcal/mol, Difference in average score from the   
                       base case: -0.0411                                                          (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: -0.0099 kcal/mol, Difference in average   
                       score from the base case: -0.0401                                           (00:20:23)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into         
                       arginine: Energy difference: -1.8015 kcal/mol, Difference in average score  
                       from the base case: -0.0428                                                 (00:20:23)
[INFO]       Main:     Simulation completed successfully.                                          (00:20:30)
Show buried residues
Minimal score value
-3.0506
Maximal score value
1.2369
Average score
-0.6562
Total score value
-150.9183
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 -2.0539
2 V A -1.2371
3 Q A -1.9504
4 L A 0.0000
5 Q A -2.0408
6 Q A 0.0000
7 S A -1.2263
8 G A -1.0984
9 P A -0.5826
10 E A -0.5738
11 L A 0.7163
12 V A -0.3493
13 K A -1.5689
14 L A -1.0547
15 G A -1.0084
16 A A -0.7993
17 S A -1.3553
18 V A 0.0000
19 R A -1.7402
20 V A 0.0000
21 S A -0.9404
22 C A 0.0000
23 R A -2.1035
24 T A 0.0000
25 S A -1.2955
26 G A -1.1782
27 F A -0.6268
28 T A -0.6310
29 I A 0.0000
30 T A -0.7017
31 E A -1.7888
32 Y A -1.1343
33 T A -1.0333
34 M A 0.0000
35 H A 0.0000
36 W A 0.0000
37 V A 0.0000
38 K A -0.4514
39 Q A 0.0000
40 S A -1.0461
41 H A -1.4964
42 G A -1.3306
43 K A -1.4117
44 S A -0.9991
45 L A -0.5729
46 E A -0.7643
47 W A 0.0000
48 I A 0.0000
49 G A 0.0000
50 G A 0.0000
51 I A 0.0000
52 N A -1.1224
53 P A 0.0000
54 I A 0.4212
55 T A 0.0906
56 G A -0.7347
57 G A -1.0185
58 S A -1.5755
59 R A -2.0657
60 N A -1.6672
61 N A 0.0000
62 L A -0.5804
63 K A -1.7458
64 F A -1.7616
65 K A -2.8444
66 D A -3.0506
67 K A -2.4442
68 A A 0.0000
69 T A -1.4887
70 L A 0.0000
71 T A -0.6772
72 G A -1.0829
73 D A -1.6015
74 K A -1.6802
75 S A -1.2097
76 S A -1.2419
77 S A -1.3410
78 T A 0.0000
79 V A 0.0000
80 Y A -0.6091
81 M A 0.0000
82 D A -1.4536
83 L A 0.0000
84 R A -2.0705
85 S A -1.2078
86 L A 0.0000
87 T A -1.0205
88 S A -1.4175
89 E A -2.3222
90 G A -1.4856
91 S A -0.8126
92 T A -0.5393
93 V A -0.0844
94 N A 0.0000
95 Y A 0.0000
96 C A 0.0000
97 V A 0.0000
98 R A -0.4775
99 G A 0.0000
100 R A -2.1608
101 T A -1.0462
102 M A -0.4434
103 G A 0.0000
104 P A -0.3885
105 L A 0.0000
106 D A -0.7315
107 Y A -0.2033
108 W A 0.0000
109 G A 0.0000
110 Q A -1.7202
111 G A -0.9740
112 T A 0.0000
113 T A -0.2716
114 L A 0.0000
115 T A -0.4002
116 V A 0.0000
117 S A -1.1177
118 S A -1.1125
1 D B -1.2702
2 V B 0.0000
3 V B 0.8478
4 M B 0.0000
5 T B -0.0516
6 Q B 0.0000
7 T B 0.1927
8 P B 0.5000
9 L B 1.2369
10 T B 0.3059
11 L B -0.0040
12 S B -0.6783
13 V B 0.0000
14 T B -0.2720
15 I B 0.0370
16 G B -0.9249
17 Q B -1.3350
18 P B -1.6226
19 V B 0.0000
20 S B -0.6668
21 I B 0.0000
22 S B -0.6855
23 C B 0.0000
24 K B -1.6529
25 S B 0.0000
26 S B -0.8714
27 Q B -1.4540
28 S B -0.6834
29 L B 0.0000
30 L B 0.7112
31 Y B 0.3153
32 T B -0.4341
33 N B -1.4799
34 G B -1.1571
35 K B -1.1756
36 T B -0.0978
37 F B 0.0000
38 L B 0.0000
39 N B 0.0000
40 W B 0.0000
41 L B 0.0000
42 F B 0.0000
43 Q B 0.0000
44 R B -1.7368
45 P B -1.1923
46 G B -1.4329
47 Q B -2.1331
48 S B -1.4034
49 P B 0.0000
50 K B -1.3868
51 R B -0.6929
52 L B 0.0000
53 I B 0.0000
54 Y B -0.2402
55 M B -0.0506
56 V B -0.3824
57 S B -0.8560
58 K B -1.5021
59 L B -0.9583
60 E B -0.9307
61 S B -0.6863
62 G B -0.7525
63 V B -0.8218
64 P B -1.1188
65 D B -1.9890
66 R B -2.0241
67 F B 0.0000
68 S B -1.1895
69 G B -0.6918
70 S B -0.8944
71 G B -1.1658
72 S B -0.7955
73 G B -0.6631
74 T B -1.4907
75 D B -2.3951
76 F B 0.0000
77 T B -0.9688
78 L B 0.0000
79 K B -1.4239
80 I B 0.0000
81 S B -2.1115
82 R B -2.5336
83 V B 0.0000
84 E B -1.8670
85 A B -0.9058
86 E B -2.0409
87 D B 0.0000
88 L B -0.6097
89 G B 0.0000
90 I B -0.3648
91 Y B 0.0000
92 Y B 0.0000
93 C B 0.0000
94 M B 0.0000
95 Q B 0.0000
96 S B 0.0000
97 T B 0.0000
98 H B -0.2064
99 F B 0.0474
100 P B -0.4088
101 L B 0.0000
102 T B 0.0609
103 F B 0.3309
104 G B 0.0000
105 G B 0.0119
106 G B 0.0000
107 T B 0.0000
108 K B -0.4850
109 L B 0.0000
110 E B -0.5859
111 L B 0.1930
112 K B -1.1812
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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
IR54A -1.8015 -0.0428 View CSV PDB
IK54A -1.3401 -0.0411 View CSV PDB
LE9B -0.4866 -0.0557 View CSV PDB
LK9B -0.359 -0.0535 View CSV PDB
LK30B -0.6367 -0.0377 View CSV PDB
LR30B -0.3754 -0.0426 View CSV PDB
LR11A -0.3682 -0.0399 View CSV PDB
VK3B -0.1547 -0.0385 View CSV PDB
VR3B -0.0801 -0.041 View CSV PDB
LK11A 0.0306 -0.0431 View CSV PDB
PD8B 2.7667 -0.0272 View CSV PDB
PR8B 3.3267 -0.0174 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018