Project name: SS1

Status: done

Started: 2025-03-04 07:38:14
Settings
Chain sequence(s) A: QVQLQESGPGLVKPSETLSLTCTASGYTFTSYGISWVRQTPGKGLEWIGEIYPRSGNTYYNEKFKGRATLSADKSKNQASLKLKSVTAADTAIYFCARESISRRLGWNFDVWGRGTLVTVS
B: DIQMTQTPSSLSASVGDRVTITCRASENIYSFLAWYQQKPGEAPKRVVYNAKTLTEGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQHHYGPPLTFGQGTKLEIK
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                                          (00:02:05)
[INFO]       Auto_mut: Residue number 11 from chain A and a score of 0.999 (leucine) selected for  
                       automated muatation                                                         (00:02:07)
[INFO]       Auto_mut: Residue number 30 from chain B and a score of 0.910 (tyrosine) selected for 
                       automated muatation                                                         (00:02:07)
[INFO]       Auto_mut: Residue number 117 from chain A and a score of 0.860 (leucine) selected for 
                       automated muatation                                                         (00:02:07)
[INFO]       Auto_mut: Residue number 10 from chain A and a score of 0.624 (glycine) selected for  
                       automated muatation                                                         (00:02:07)
[INFO]       Auto_mut: Residue number 93 from chain A and a score of 0.594 (isoleucine) selected   
                       for automated muatation                                                     (00:02:07)
[INFO]       Auto_mut: Residue number 32 from chain B and a score of 0.529 (phenylalanine)         
                       selected for automated muatation                                            (00:02:07)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (leucine) into glutamic acid        (00:02:07)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (leucine) into aspartic acid        (00:02:07)
[INFO]       Auto_mut: Mutating residue number 30 from chain B (tyrosine) into glutamic acid       (00:02:07)
[INFO]       Auto_mut: Mutating residue number 30 from chain B (tyrosine) into lysine              (00:03:08)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (leucine) into arginine             (00:03:12)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (leucine) into lysine               (00:03:15)
[INFO]       Auto_mut: Mutating residue number 30 from chain B (tyrosine) into aspartic acid       (00:04:25)
[INFO]       Auto_mut: Mutating residue number 117 from chain A (leucine) into glutamic acid       (00:04:28)
[INFO]       Auto_mut: Mutating residue number 117 from chain A (leucine) into aspartic acid       (00:04:32)
[INFO]       Auto_mut: Mutating residue number 30 from chain B (tyrosine) into arginine            (00:05:25)
[INFO]       Auto_mut: Mutating residue number 117 from chain A (leucine) into lysine              (00:05:28)
[INFO]       Auto_mut: Mutating residue number 117 from chain A (leucine) into arginine            (00:05:34)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (glycine) into glutamic acid        (00:06:37)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (glycine) into aspartic acid        (00:06:38)
[INFO]       Auto_mut: Mutating residue number 93 from chain A (isoleucine) into glutamic acid     (00:06:41)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (glycine) into arginine             (00:07:54)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (glycine) into lysine               (00:07:55)
[INFO]       Auto_mut: Mutating residue number 93 from chain A (isoleucine) into lysine            (00:08:00)
[INFO]       Auto_mut: Mutating residue number 93 from chain A (isoleucine) into aspartic acid     (00:09:04)
[INFO]       Auto_mut: Mutating residue number 32 from chain B (phenylalanine) into glutamic acid  
                       Mutating residue number 32 from chain B (phenylalanine) into glutamic acid  (00:09:05)
[INFO]       Auto_mut: Mutating residue number 32 from chain B (phenylalanine) into aspartic acid  
                       Mutating residue number 32 from chain B (phenylalanine) into aspartic acid  (00:09:07)
[INFO]       Auto_mut: Mutating residue number 93 from chain A (isoleucine) into arginine          (00:10:01)
[INFO]       Auto_mut: Mutating residue number 32 from chain B (phenylalanine) into arginine       (00:10:03)
[INFO]       Auto_mut: Mutating residue number 32 from chain B (phenylalanine) into lysine         (00:10:06)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into glutamic   
                       acid: Energy difference: 0.9590 kcal/mol, Difference in average score from  
                       the base case: -0.0410                                                      (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into lysine:    
                       Energy difference: 0.3457 kcal/mol, Difference in average score from the    
                       base case: -0.0390                                                          (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into aspartic   
                       acid: Energy difference: 0.9802 kcal/mol, Difference in average score from  
                       the base case: -0.0401                                                      (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into arginine:  
                       Energy difference: 0.4392 kcal/mol, Difference in average score from the    
                       base case: -0.0417                                                          (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 30 from chain B (tyrosine) into glutamic  
                       acid: Energy difference: -0.1017 kcal/mol, Difference in average score from 
                       the base case: -0.0510                                                      (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 30 from chain B (tyrosine) into lysine:   
                       Energy difference: -0.2556 kcal/mol, Difference in average score from the   
                       base case: -0.0494                                                          (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 30 from chain B (tyrosine) into aspartic  
                       acid: Energy difference: -0.7420 kcal/mol, Difference in average score from 
                       the base case: -0.0468                                                      (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 30 from chain B (tyrosine) into arginine: 
                       Energy difference: -0.1126 kcal/mol, Difference in average score from the   
                       base case: -0.0391                                                          (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 117 from chain A (leucine) into glutamic  
                       acid: Energy difference: 1.1231 kcal/mol, Difference in average score from  
                       the base case: -0.0423                                                      (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 117 from chain A (leucine) into lysine:   
                       Energy difference: 0.5280 kcal/mol, Difference in average score from the    
                       base case: -0.0343                                                          (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 117 from chain A (leucine) into aspartic  
                       acid: Energy difference: 2.0468 kcal/mol, Difference in average score from  
                       the base case: -0.0401                                                      (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 117 from chain A (leucine) into arginine: 
                       Energy difference: 0.3596 kcal/mol, Difference in average score from the    
                       base case: -0.0406                                                          (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (glycine) into glutamic   
                       acid: Energy difference: 1.1780 kcal/mol, Difference in average score from  
                       the base case: -0.0269                                                      (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (glycine) into lysine:    
                       Energy difference: 0.7938 kcal/mol, Difference in average score from the    
                       base case: -0.0319                                                          (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (glycine) into aspartic   
                       acid: Energy difference: 0.9047 kcal/mol, Difference in average score from  
                       the base case: -0.0271                                                      (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (glycine) into arginine:  
                       Energy difference: 0.6563 kcal/mol, Difference in average score from the    
                       base case: -0.0333                                                          (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 93 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 2.6835 kcal/mol, Difference in average    
                       score from the base case: -0.0158                                           (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 93 from chain A (isoleucine) into lysine: 
                       Energy difference: 1.6938 kcal/mol, Difference in average score from the    
                       base case: -0.0151                                                          (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 93 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 3.5154 kcal/mol, Difference in average    
                       score from the base case: -0.0176                                           (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 93 from chain A (isoleucine) into         
                       arginine: Energy difference: 2.0048 kcal/mol, Difference in average score   
                       from the base case: -0.0241                                                 (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 32 from chain B (phenylalanine) into      
                       glutamic acid: Energy difference: 0.8798 kcal/mol, Difference in average    
                       score from the base case: -0.0044                                           (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 32 from chain B (phenylalanine) into      
                       lysine: Energy difference: 0.1965 kcal/mol, Difference in average score     
                       from the base case: -0.0016                                                 (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 32 from chain B (phenylalanine) into      
                       aspartic acid: Energy difference: 2.2113 kcal/mol, Difference in average    
                       score from the base case: -0.0019                                           (00:11:16)
[INFO]       Auto_mut: Effect of mutation residue number 32 from chain B (phenylalanine) into      
                       arginine: Energy difference: 1.4179 kcal/mol, Difference in average score   
                       from the base case: -0.0082                                                 (00:11:16)
[INFO]       Main:     Simulation completed successfully.                                          (00:11:22)
Show buried residues
Minimal score value
-3.3581
Maximal score value
0.9986
Average score
-0.7456
Total score value
-169.9855
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 Q A -1.5500
2 V A -1.0738
3 Q A -1.8055
4 L A 0.0000
5 Q A -1.3040
6 E A 0.0000
7 S A -0.6074
8 G A -0.2296
9 P A 0.0591
10 G A 0.6238
11 L A 0.9986
12 V A 0.0000
13 K A -2.0668
14 P A -1.7336
15 S A -1.9456
16 E A -2.7267
17 T A -2.1648
18 L A 0.0000
19 S A -1.0183
20 L A 0.0000
21 T A -0.4743
22 C A 0.0000
23 T A -1.1693
24 A A 0.0000
25 S A -1.1770
26 G A -1.1204
27 Y A -0.4512
28 T A -0.2102
29 F A -0.7085
30 T A -0.8687
31 S A -0.4065
32 Y A 0.0202
33 G A 0.0000
34 I A 0.0000
35 S A 0.0000
36 W A 0.0000
37 V A 0.0000
38 R A 0.0000
39 Q A 0.0000
40 T A -0.6678
41 P A -0.7544
42 G A -1.4206
43 K A -2.3190
44 G A -1.5933
45 L A 0.0000
46 E A -0.9990
47 W A 0.0000
48 I A 0.0000
49 G A 0.0000
50 E A 0.0000
51 I A 0.0000
52 Y A 0.0000
53 P A -1.4502
54 R A -2.0576
55 S A -1.4893
56 G A -1.2973
57 N A -1.0990
58 T A -0.1773
59 Y A -0.2368
60 Y A -0.8749
61 N A -2.0650
62 E A -3.3581
63 K A -3.0334
64 F A 0.0000
65 K A -2.5363
66 G A -2.0592
67 R A -2.2457
68 A A 0.0000
69 T A -0.9486
70 L A 0.0000
71 S A -0.7158
72 A A -1.3496
73 D A -2.4269
74 K A -2.7435
75 S A -2.2343
76 K A -2.9156
77 N A -2.4325
78 Q A -1.9795
79 A A 0.0000
80 S A -0.5246
81 L A 0.0000
82 K A -1.3564
83 L A 0.0000
84 K A -2.7190
85 S A -2.0846
86 V A 0.0000
87 T A -0.9166
88 A A -0.2661
89 A A 0.0591
90 D A 0.0000
91 T A 0.3548
92 A A 0.0000
93 I A 0.5938
94 Y A 0.0000
95 F A 0.0000
96 C A 0.0000
97 A A 0.0000
98 R A 0.0000
99 E A 0.0000
100 S A -0.1993
101 I A -0.1295
102 S A -0.9445
103 R A -1.6400
104 R A -1.8114
105 L A 0.0824
106 G A 0.0000
107 W A 0.0000
108 N A -0.0445
109 F A 0.0000
110 D A -0.6078
111 V A -0.7047
112 W A 0.0000
113 G A 0.0000
114 R A -2.4436
115 G A -1.1019
116 T A -0.1262
117 L A 0.8599
118 V A 0.0000
119 T A 0.3800
120 V A 0.0000
121 S A -0.5508
1 D B -2.4980
2 I B -1.8845
3 Q B -2.1981
4 M B 0.0000
5 T B -1.1328
6 Q B 0.0000
7 T B -0.4631
8 P B -0.5398
9 S B -0.8632
10 S B -1.0110
11 L B -0.6253
12 S B -1.0227
13 A B 0.0000
14 S B -0.9802
15 V B -0.1979
16 G B -0.9265
17 D B -1.8945
18 R B -2.3772
19 V B 0.0000
20 T B -0.6080
21 I B 0.0000
22 T B -0.6230
23 C B 0.0000
24 R B -2.1290
25 A B 0.0000
26 S B -2.2369
27 E B -2.7902
28 N B -1.6428
29 I B 0.0000
30 Y B 0.9098
31 S B 0.2045
32 F B 0.5294
33 L B 0.0000
34 A B 0.0000
35 W B 0.0000
36 Y B 0.0000
37 Q B 0.0000
38 Q B -1.5450
39 K B -1.8277
40 P B -1.2022
41 G B -1.8515
42 E B -2.9873
43 A B -2.1638
44 P B 0.0000
45 K B -2.2639
46 R B -1.4293
47 V B 0.0000
48 V B 0.0000
49 Y B -0.0546
50 N B -0.4005
51 A B 0.0000
52 K B -1.7267
53 T B -0.7897
54 L B -0.4567
55 T B -1.1110
56 E B -1.9396
57 G B -1.2136
58 V B -0.8312
59 P B -0.5179
60 S B -0.3778
61 R B -0.7391
62 F B 0.0000
63 S B -0.6627
64 G B -0.9127
65 S B -1.2474
66 G B -1.1462
67 S B -0.8263
68 G B -0.8263
69 T B -1.6701
70 D B -2.1719
71 F B 0.0000
72 T B -0.8611
73 L B 0.0000
74 T B -0.6043
75 I B 0.0000
76 S B -1.3280
77 S B -1.2162
78 L B 0.0000
79 Q B -0.9896
80 P B -1.1130
81 E B -1.6991
82 D B 0.0000
83 F B -0.5863
84 A B 0.0000
85 T B -0.9482
86 Y B 0.0000
87 Y B 0.0000
88 C B 0.0000
89 Q B 0.0000
90 H B 0.0000
91 H B 0.0000
92 Y B 0.1802
93 G B -0.4857
94 P B -0.7768
95 P B -1.2031
96 L B 0.0000
97 T B -0.8739
98 F B 0.0000
99 G B 0.0000
100 Q B -1.7364
101 G B 0.0000
102 T B 0.0000
103 K B -1.7450
104 L B 0.0000
105 E B -1.3628
106 I B -0.7534
107 K B -1.5566
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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
YD30B -0.742 -0.0468 View CSV PDB
YK30B -0.2556 -0.0494 View CSV PDB
LR117A 0.3596 -0.0406 View CSV PDB
LK11A 0.3457 -0.039 View CSV PDB
LR11A 0.4392 -0.0417 View CSV PDB
LK117A 0.528 -0.0343 View CSV PDB
GR10A 0.6563 -0.0333 View CSV PDB
GK10A 0.7938 -0.0319 View CSV PDB
IR93A 2.0048 -0.0241 View CSV PDB
IK93A 1.6938 -0.0151 View CSV PDB
FK32B 0.1965 -0.0016 View CSV PDB
FR32B 1.4179 -0.0082 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018