Project name: 3eak/A 10A [mutate: KR79A]

Status: done

Started: 2025-04-01 11:59:25
Chain sequence(s) A: QVQLVESGGGLVQPGGSLRLSCAASGGSEYSYSTFSLGWFRQAPGQGLEAVAAIASMGGLTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAAVRGYFMRLPSSHNFRYWGQGTLVTVS
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage Used: no changes made
Dynamic mode Yes
Automated mutations No
Mutated residues KR79A
Energy difference between WT (input) and mutated protein (by FoldX) 0.104221 kcal/mol
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 A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       PDB:      Running AlphaCutter                                                         (00:00:01)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:28)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:28)
[INFO]       FoldX:    Building mutant model                                                       (00:01:43)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:00)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:19:00)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:19:01)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:19:01)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:19:01)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:19:02)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:19:02)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:19:02)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:19:03)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:19:03)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:19:03)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:19:04)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:19:04)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:19:05)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:19:09)
[INFO]       Main:     Simulation completed successfully.                                          (00:19:10)
Show buried residues
Minimal score value
-2.5917
Maximal score value
1.6382
Average score
-0.3354
Total score value
-42.592
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 Q A -1.8131
2 V A 0.0000
3 Q A -1.0255
4 L A 0.0000
5 V A 0.8871
6 E A 0.0000
7 S A -0.2604
8 G A -0.3440
9 G A -0.0807
10 G A 0.3621
11 L A 1.4279
12 V A 0.0000
13 Q A -0.2476
14 P A -0.3134
15 G A -0.5931
16 G A -0.5316
17 S A -0.7292
18 L A -0.8707
19 R A -2.0889
20 L A 0.0000
21 S A -0.3448
22 C A 0.0000
23 A A -0.2273
24 A A -0.5995
25 S A -1.0862
26 G A -1.3237
27 G A -1.1864
28 S A -0.6635
29 E A -0.3684
30 Y A 0.4668
31 S A 0.0000
32 Y A 0.0000
33 S A -0.5137
34 T A -0.4418
35 F A 0.0000
36 S A 0.0000
37 L A 0.0000
38 G A 0.0000
39 W A 0.0000
40 F A 0.0000
41 R A 0.0000
42 Q A -0.4266
43 A A 0.0000
44 P A -0.6209
45 G A -1.1332
46 Q A -1.1442
47 G A -0.0832
48 L A 0.7137
49 E A -0.1591
50 A A 0.0000
51 V A 0.0000
52 A A 0.0000
53 A A 0.0000
54 I A 0.0000
55 A A 0.0000
56 S A -0.1851
57 M A 0.2705
58 G A 0.1709
59 G A 0.6049
60 L A 1.6382
61 T A 1.0215
62 Y A 0.9887
63 Y A 0.7901
64 A A -0.1252
65 D A -1.5087
66 S A 0.0000
67 V A 1.1273
68 K A 0.1354
69 G A -0.4042
70 R A -0.8604
71 F A 0.0000
72 T A -0.4773
73 I A 0.0000
74 S A -0.4972
75 R A -1.5323
76 D A -2.3138
77 N A -2.1131
78 S A -1.7723
79 R A -2.5917 mutated: KR79A
80 N A -1.8590
81 T A 0.0000
82 L A 0.0000
83 Y A -0.3533
84 L A 0.0000
85 Q A -1.1373
86 M A 0.0000
87 N A -1.0965
88 S A -0.5238
89 L A 0.1582
90 R A 0.0000
91 A A -0.9106
92 E A -1.8705
93 D A -1.8086
94 T A -0.7298
95 A A 0.0000
96 V A 0.2599
97 Y A 0.0000
98 Y A -0.0687
99 C A 0.0000
100 A A 0.0000
101 A A 0.0000
102 V A -1.3351
103 R A -1.9348
104 G A -0.5240
105 Y A 1.0263
106 F A 0.9027
107 M A 0.7747
108 R A -1.0540
109 L A 0.0000
110 P A 0.0000
111 S A -1.2410
112 S A -0.9870
113 H A -1.1020
114 N A -1.3973
115 F A 0.0000
116 R A -2.0291
117 Y A -0.8224
118 W A 0.2868
119 G A -0.1634
120 Q A -0.5865
121 G A -0.5265
122 T A 0.0000
123 L A 1.1563
124 V A 0.0000
125 T A 0.3267
126 V A -0.0713
127 S A -0.3542
Download PDB file
View in 3Dmol

CABS-flex predictions of flexibility of input structure

In dynamic mode, A4D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A4D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A4D score, -0.3354 in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

Model
Average A4D Score
model_8 -0.3354 View CSV PDB
model_10 -0.3548 View CSV PDB
model_6 -0.374 View CSV PDB
model_9 -0.3779 View CSV PDB
model_5 -0.3795 View CSV PDB
model_2 -0.3905 View CSV PDB
CABS_average -0.4242 View CSV PDB
model_1 -0.4329 View CSV PDB
model_3 -0.4337 View CSV PDB
model_11 -0.4759 View CSV PDB
model_7 -0.4795 View CSV PDB
model_4 -0.5173 View CSV PDB
model_0 -0.5386 View CSV PDB
input -0.6138 View CSV PDB