Project name: PbrR

Status: done

Started: 2026-05-04 18:26:50
Chain sequence(s) A: MNIQIGELAKRTACPVVTIRFYEQEGLLPPPGRSRGNFRLYGEEHVERLQFIRHCRSLDMPLSDVRTLLSYRKRPDQDCGEVNMLLDEHIRQVESRIGALLELKHHLVELREACSGARPAQSCGILQGLSDCVCDTRGTTAHPSD
B: MNIQIGELAKRTACPVVTIRFYEQEGLLPPPGRSRGNFRLYGEEHVERLQFIRHCRSLDMPLSDVRTLLSYRKRPDQDCGEVNMLLDEHIRQVESRIGALLELKHHLVELREACSGARPAQSCGILQGLSDCVCDTRGTTAHPSD
input PDB
Selected Chain(s) A,B
Distance of aggregation 5 Å
FoldX usage Yes
pH calculations No
alphaCutter usage Used: no changes made
Dynamic mode No
Automated mutations Yes
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with all chain(s) selected           (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       PDB:      Running AlphaCutter                                                         (00:00:02)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:35)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:35)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:04:18)
[INFO]       AutoMutEv:Residue number 133 from chain A and a score of 1.872 (valine) selected for  
                       automated mutation                                                          (00:04:19)
[INFO]       AutoMutEv:Residue number 17 from chain A and a score of 1.865 (valine) selected for   
                       automated mutation                                                          (00:04:19)
[INFO]       AutoMutEv:Residue number 133 from chain B and a score of 1.865 (valine) selected for  
                       automated mutation                                                          (00:04:19)
[INFO]       AutoMutEv:Residue number 17 from chain B and a score of 1.862 (valine) selected for   
                       automated mutation                                                          (00:04:19)
[INFO]       AutoMutEv:Residue number 38 from chain A and a score of 1.516 (phenylalanine)         
                       selected for automated mutation                                             (00:04:19)
[INFO]       AutoMutEv:Residue number 38 from chain B and a score of 1.467 (phenylalanine)         
                       selected for automated mutation                                             (00:04:19)
[INFO]       AutoMutEv:Mutating residue number 133 from chain A (valine) into threonine            (00:04:19)
[INFO]       AutoMutEv:Mutating residue number 133 from chain A (valine) into methionine           (00:04:19)
[INFO]       AutoMutEv:Mutating residue number 17 from chain A (valine) into alanine               (00:04:19)
[INFO]       AutoMutEv:Mutating residue number 133 from chain A (valine) into alanine              (00:04:25)
[INFO]       AutoMutEv:Mutating residue number 17 from chain A (valine) into methionine            (00:04:26)
[INFO]       AutoMutEv:Mutating residue number 17 from chain A (valine) into threonine             (00:04:27)
[INFO]       AutoMutEv:Mutating residue number 133 from chain B (valine) into threonine            (00:04:31)
[INFO]       AutoMutEv:Mutating residue number 133 from chain B (valine) into methionine           (00:04:37)
[INFO]       AutoMutEv:Mutating residue number 133 from chain B (valine) into alanine              (00:04:37)
[INFO]       AutoMutEv:Mutating residue number 17 from chain B (valine) into alanine               (00:04:38)
[INFO]       AutoMutEv:Mutating residue number 38 from chain A (phenylalanine) into methionine     (00:04:43)
[INFO]       AutoMutEv:Mutating residue number 17 from chain B (valine) into methionine            (00:04:44)
[INFO]       AutoMutEv:Mutating residue number 17 from chain B (valine) into threonine             (00:04:45)
[INFO]       AutoMutEv:Mutating residue number 38 from chain A (phenylalanine) into tryptophan     (00:04:52)
[INFO]       AutoMutEv:Mutating residue number 38 from chain A (phenylalanine) into tyrosine       (00:04:53)
[INFO]       AutoMutEv:Mutating residue number 38 from chain B (phenylalanine) into tryptophan     (00:04:55)
[INFO]       AutoMutEv:Mutating residue number 38 from chain B (phenylalanine) into methionine     (00:05:00)
[INFO]       AutoMutEv:Mutating residue number 38 from chain B (phenylalanine) into tyrosine       (00:05:03)
[INFO]       AutoMutEv:Effect of mutation residue number 133 from chain A (valine) into threonine: 
                       Energy difference: -0.1214 kcal/mol, Difference in average score from the   
                       base case: -0.0089                                                          (00:05:11)
[INFO]       AutoMutEv:Effect of mutation residue number 133 from chain A (valine) into alanine:   
                       Energy difference: -0.0841 kcal/mol, Difference in average score from the   
                       base case: -0.0083                                                          (00:05:11)
[INFO]       AutoMutEv:Effect of mutation residue number 133 from chain A (valine) into            
                       methionine: Energy difference: 0.0559 kcal/mol, Difference in average score 
                       from the base case: -0.0035                                                 (00:05:11)
[INFO]       AutoMutEv:Effect of mutation residue number 17 from chain A (valine) into threonine:  
                       Energy difference: -0.2304 kcal/mol, Difference in average score from the   
                       base case: -0.0077                                                          (00:05:11)
[INFO]       AutoMutEv:Effect of mutation residue number 17 from chain A (valine) into alanine:    
                       Energy difference: -0.0214 kcal/mol, Difference in average score from the   
                       base case: -0.0069                                                          (00:05:11)
[INFO]       AutoMutEv:Effect of mutation residue number 17 from chain A (valine) into methionine: 
                       Energy difference: -1.1016 kcal/mol, Difference in average score from the   
                       base case: -0.0033                                                          (00:05:11)
[INFO]       AutoMutEv:Effect of mutation residue number 133 from chain B (valine) into threonine: 
                       Energy difference: -0.1506 kcal/mol, Difference in average score from the   
                       base case: -0.0088                                                          (00:05:11)
[INFO]       AutoMutEv:Effect of mutation residue number 133 from chain B (valine) into alanine:   
                       Energy difference: -0.1610 kcal/mol, Difference in average score from the   
                       base case: -0.0083                                                          (00:05:11)
[INFO]       AutoMutEv:Effect of mutation residue number 133 from chain B (valine) into            
                       methionine: Energy difference: -0.1752 kcal/mol, Difference in average      
                       score from the base case: -0.0035                                           (00:05:11)
[INFO]       AutoMutEv:Effect of mutation residue number 17 from chain B (valine) into threonine:  
                       Energy difference: -0.3733 kcal/mol, Difference in average score from the   
                       base case: -0.0004                                                          (00:05:11)
[INFO]       AutoMutEv:Effect of mutation residue number 17 from chain B (valine) into alanine:    
                       Energy difference: -0.0854 kcal/mol, Difference in average score from the   
                       base case: -0.0080                                                          (00:05:11)
[INFO]       AutoMutEv:Effect of mutation residue number 17 from chain B (valine) into methionine: 
                       Energy difference: -0.0935 kcal/mol, Difference in average score from the   
                       base case: -0.0027                                                          (00:05:11)
[INFO]       AutoMutEv:Effect of mutation residue number 38 from chain A (phenylalanine) into      
                       methionine: Energy difference: -0.2361 kcal/mol, Difference in average      
                       score from the base case: -0.0063                                           (00:05:11)
[INFO]       AutoMutEv:Effect of mutation residue number 38 from chain A (phenylalanine) into      
                       tryptophan: Energy difference: 0.6281 kcal/mol, Difference in average score 
                       from the base case: -0.0037                                                 (00:05:11)
[INFO]       AutoMutEv:Effect of mutation residue number 38 from chain A (phenylalanine) into      
                       tyrosine: Energy difference: 0.1672 kcal/mol, Difference in average score   
                       from the base case: -0.0026                                                 (00:05:11)
[INFO]       AutoMutEv:Effect of mutation residue number 38 from chain B (phenylalanine) into      
                       methionine: Energy difference: -0.4980 kcal/mol, Difference in average      
                       score from the base case: -0.0062                                           (00:05:11)
[INFO]       AutoMutEv:Effect of mutation residue number 38 from chain B (phenylalanine) into      
                       tryptophan: Energy difference: 0.4872 kcal/mol, Difference in average score 
                       from the base case: -0.0047                                                 (00:05:11)
[INFO]       AutoMutEv:Effect of mutation residue number 38 from chain B (phenylalanine) into      
                       tyrosine: Energy difference: -0.0089 kcal/mol, Difference in average score  
                       from the base case: -0.0032                                                 (00:05:11)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:14)
Show buried residues
Minimal score value
-2.1833
Maximal score value
1.8724
Average score
-0.5108
Total score value
-148.1225
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
1 M A 0.7498
2 N A -1.0964
3 I A 0.0000
4 Q A -0.5304
5 I A 0.1581
6 G A -0.1610
7 E A -0.6755
8 L A 0.0000
9 A A -0.3005
10 K A -1.9987
11 R A -1.9825
12 T A 0.0000
13 A A 0.0302
14 C A 0.0000
15 P A -0.1624
16 V A 0.7880
17 V A 1.8653
18 T A 0.0000
19 I A 0.0000
20 R A -1.7874
21 F A 0.1131
22 Y A 0.0000
23 E A -0.6467
24 Q A -1.3690
25 E A -1.0127
26 G A -0.5937
27 L A 0.0000
28 L A 0.0000
29 P A -0.1099
30 P A -0.2730
31 P A -0.1450
32 G A -0.6560
33 R A -2.0317
34 S A -0.7328
35 R A -1.9387
36 G A -1.0235
37 N A -1.0056
38 F A 1.5158
39 R A -0.8890
40 L A 0.0143
41 Y A 0.0000
42 G A -0.3272
43 E A -1.8353
44 E A -1.7878
45 H A 0.0000
46 V A -0.1084
47 E A -1.8192
48 R A -0.7848
49 L A 0.0000
50 Q A -0.2729
51 F A 0.0000
52 I A 0.0000
53 R A -0.2600
54 H A 0.0000
55 C A 0.0000
56 R A -0.4592
57 S A -0.1704
58 L A 0.0000
59 D A -1.8155
60 M A 0.0000
61 P A -0.0757
62 L A 0.0000
63 S A -0.2684
64 D A -0.3462
65 V A 0.0000
66 R A -1.3875
67 T A -0.2955
68 L A 0.0000
69 L A 0.1587
70 S A -0.0220
71 Y A 0.0000
72 R A -1.3040
73 K A -2.0373
74 R A -1.2272
75 P A -0.7748
76 D A -1.8956
77 Q A -1.0240
78 D A -1.8430
79 C A 0.0000
80 G A -0.4093
81 E A -1.1914
82 V A 0.0000
83 N A 0.0000
84 M A 0.7598
85 L A 0.0000
86 L A 0.0000
87 D A -0.6573
88 E A -1.9142
89 H A -0.3906
90 I A -0.1330
91 R A -2.1833
92 Q A -1.5251
93 V A 0.0000
94 E A -1.8147
95 S A -0.7528
96 R A -1.4221
97 I A -0.0852
98 G A -0.1529
99 A A 0.0557
100 L A 0.2918
101 L A 0.0835
102 E A -1.7128
103 L A -0.1919
104 K A -0.4623
105 H A -1.2332
106 H A -1.1687
107 L A 0.0000
108 V A 0.2496
109 E A -1.6835
110 L A -0.2377
111 R A -0.5655
112 E A -1.8700
113 A A -0.2857
114 C A 0.0000
115 S A -0.2574
116 G A -0.2775
117 A A -0.3502
118 R A -1.8566
119 P A -0.8260
120 A A 0.0000
121 Q A -1.2506
122 S A -0.4256
123 C A 0.0000
124 G A -0.1648
125 I A 0.0000
126 L A 0.0000
127 Q A -0.8125
128 G A -0.2386
129 L A 0.0000
130 S A -0.3799
131 D A -1.7297
132 C A 0.3867
133 V A 1.8724
134 C A 0.1506
135 D A -1.7744
136 T A -0.7290
137 R A -1.9428
138 G A -0.8191
139 T A -0.1697
140 T A -0.0749
141 A A -0.1472
142 H A -1.0265
143 P A -0.4700
144 S A -0.5808
145 D A -1.8277
1 M B 0.3376
2 N B -1.1337
3 I B -0.1808
4 Q B -0.7559
5 I B 0.1141
6 G B -0.3342
7 E B -1.5215
8 L B 0.0000
9 A B -0.3003
10 K B -2.0279
11 R B -2.1474
12 T B 0.0000
13 A B 0.0233
14 C B 0.0000
15 P B -0.1645
16 V B 0.7790
17 V B 1.8620
18 T B 0.3657
19 I B 0.0000
20 R B -1.7658
21 F B 0.2210
22 Y B 0.0000
23 E B -0.6336
24 Q B -1.3693
25 E B -1.0283
26 G B -0.5969
27 L B 0.0000
28 L B 0.0000
29 P B -0.1086
30 P B -0.2741
31 P B -0.1497
32 G B -0.6465
33 R B -2.0587
34 S B -0.7351
35 R B -1.9389
36 G B -1.0235
37 N B -1.0086
38 F B 1.4671
39 R B -1.1741
40 L B -0.0966
41 Y B 0.0000
42 G B 0.0000
43 E B -1.6738
44 E B -1.5286
45 H B 0.0000
46 V B 0.0000
47 E B -1.7416
48 R B -0.9056
49 L B 0.0000
50 Q B -0.2715
51 F B 0.0000
52 I B 0.0000
53 R B -0.2739
54 H B 0.0000
55 C B 0.0000
56 R B -0.4216
57 S B -0.1845
58 L B 0.0000
59 D B -1.4340
60 M B 0.0000
61 P B -0.0883
62 L B 0.1113
63 S B -0.2379
64 D B -0.3462
65 V B 0.0000
66 R B -1.4093
67 T B -0.3008
68 L B 0.0000
69 L B 0.1623
70 S B -0.0214
71 Y B 0.0000
72 R B -1.6800
73 K B -2.1022
74 R B -1.2083
75 P B -0.7422
76 D B -1.8941
77 Q B -1.0348
78 D B -1.8282
79 C B 0.0000
80 G B -0.3990
81 E B -1.1261
82 V B 0.0000
83 N B 0.0000
84 M B 0.7250
85 L B 0.0000
86 L B 0.0000
87 D B -0.6533
88 E B -1.9123
89 H B -0.3893
90 I B -0.1401
91 R B -2.1181
92 Q B -1.4020
93 V B 0.0000
94 E B -1.3767
95 S B -0.7066
96 R B -1.6024
97 I B -0.1403
98 G B -0.2983
99 A B 0.0287
100 L B 0.2976
101 L B 0.1518
102 E B -1.7034
103 L B -0.1976
104 K B -0.4251
105 H B -1.1789
106 H B -0.9021
107 L B 0.0000
108 V B 0.3492
109 E B -1.6662
110 L B -0.2286
111 R B -0.5136
112 E B -1.8625
113 A B -0.2840
114 C B 0.0000
115 S B -0.2532
116 G B -0.2513
117 A B -0.2380
118 R B -1.3098
119 P B -0.7207
120 A B 0.0000
121 Q B -1.2323
122 S B -0.3030
123 C B 0.0000
124 G B -0.1865
125 I B 0.0000
126 L B 0.0000
127 Q B -1.2200
128 G B -0.2956
129 L B 0.0000
130 S B -0.3977
131 D B -1.7379
132 C B 0.3648
133 V B 1.8645
134 C B 0.1301
135 D B -1.7776
136 T B -0.7295
137 R B -1.9429
138 G B -0.8197
139 T B -0.1703
140 T B -0.0782
141 A B -0.1654
142 H B -1.0059
143 P B -0.3356
144 S B -0.5540
145 D B -1.8274
Download PDB file
View in 3Dmol

Automated mutations analysis - evolutionary conserved mutations

In the automated mutations mode, the server selects aggregation prone resides and each selected residue is mutated based off an evolutionary approach. 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
FM38B -0.498 -0.0062 View CSV PDB
VT133B -0.1506 -0.0088 View CSV PDB
VT17A -0.2304 -0.0077 View CSV PDB
VT133A -0.1214 -0.0089 View CSV PDB
VA133B -0.161 -0.0083 View CSV PDB
VM17A -1.1016 -0.0033 View CSV PDB
VA133A -0.0841 -0.0083 View CSV PDB
VA17B -0.0854 -0.008 View CSV PDB
FM38A -0.2361 -0.0063 View CSV PDB
FY38B -0.0089 -0.0032 View CSV PDB
VM17B -0.0935 -0.0027 View CSV PDB
FY38A 0.1672 -0.0026 View CSV PDB