Project name: 87u

Status: done

Started: 2026-05-10 13:59:01
Chain sequence(s) A: SVADAKDVLAKLKAKLAETENQDNKDILEIEIAHIEKVLAAAEENPDSDAVKDQLDFVVAHSESILAKIA
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage No
Dynamic mode No
Automated mutations No
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)
[WARNING]    PDB-Info: The input structure is likely a peptide. Results may be inaccurate.         (00:00:01)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:32)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/d951f9a78c17dcd/tmp/folded.pdb                (00:01:32)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:09)
Show buried residues
Minimal score value
-3.5677
Maximal score value
0.894
Average score
-1.6784
Total score value
-117.4859
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 S A -1.5604
2 V A -1.1609
3 A A -1.5240
4 D A -2.9577
5 A A 0.0000
6 K A -3.1710
7 D A -3.2993
8 V A 0.0000
9 L A -2.3652
10 A A -2.0703
11 K A -2.3273
12 L A 0.0000
13 K A -2.2678
14 A A -1.5278
15 K A -1.7450
16 L A -2.2541
17 A A -1.6499
18 E A -2.5980
19 T A -2.5180
20 E A -3.2840
21 N A -3.3451
22 Q A -3.4162
23 D A -3.5677
24 N A -2.8882
25 K A -3.1827
26 D A -2.4558
27 I A -0.6770
28 L A 0.0000
29 E A -1.6056
30 I A 0.8940
31 E A 0.0000
32 I A -0.8086
33 A A -0.8128
34 H A -1.0754
35 I A 0.0000
36 E A -2.5991
37 K A -2.6787
38 V A 0.0000
39 L A -1.9673
40 A A -2.0816
41 A A -2.0334
42 A A 0.0000
43 E A -3.1473
44 E A -3.1743
45 N A -2.8329
46 P A -2.6524
47 D A -3.0389
48 S A -2.6313
49 D A -3.0615
50 A A -2.1720
51 V A -2.2697
52 K A -2.7549
53 D A -2.8610
54 Q A -1.5683
55 L A 0.0000
56 D A -1.9497
57 F A 0.1361
58 V A 0.0000
59 V A -1.3997
60 A A -0.6954
61 H A -0.5135
62 S A 0.0000
63 E A -1.9610
64 S A -1.3632
65 I A 0.0000
66 L A -1.0896
67 A A -1.1017
68 K A -1.7506
69 I A -0.7489
70 A A -0.3023
Download PDB file
View in 3Dmol

Calculations for various pH values

This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is likely a peptide. Results may be inaccurate. The input structure is globular. Max score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -0.6022 3.887 View CSV PDB
4.5 -0.8094 3.6279 View CSV PDB
5.0 -1.0748 3.311 View CSV PDB
5.5 -1.3604 2.973 View CSV PDB
6.0 -1.6238 2.6338 View CSV PDB
6.5 -1.8334 2.3004 View CSV PDB
7.0 -1.9759 1.9783 View CSV PDB
7.5 -2.0579 1.671 View CSV PDB
8.0 -2.0979 1.3812 View CSV PDB
8.5 -2.1031 1.1229 View CSV PDB
9.0 -2.067 0.9563 View CSV PDB