Project name: dcb44c33e19e1e0

Status: done

Started: 2026-07-26 07:54:58
Chain sequence(s) A: GRKKRRQRRREAAAKEAAAKCGNLSTCVLGKTLSQELHKLQTYPRTNAIGVTP
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]                                                (00:00:00)
[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 A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[WARNING]    PDB-Info: The input structure is likely a peptide. Results may be inaccurate.         (00:00:01)
[INFO]       PDB-Info: The input structure is partially or entirely disordered. Average 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                                          (00:01:17)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/dcb44c33e19e1e0/tmp/folded.pdb                (00:01:17)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:36)
Show buried residues
Minimal score value
-6.677
Maximal score value
2.4569
Average score
-1.8217
Total score value
-96.5476
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 G A -3.0997
2 R A -4.8510
3 K A -5.4932
4 K A -5.9695
5 R A -6.5574
6 R A -6.6770
7 Q A -6.2173
8 R A -6.3883
9 R A -6.0364
10 R A -5.5754
11 E A -4.9928
12 A A -3.8301
13 A A -3.0666
14 A A -2.7529
15 K A -3.4160
16 E A -3.3766
17 A A -1.9097
18 A A -1.5263
19 A A -1.9177
20 K A -2.2819
21 C A -0.8136
22 G A -0.9705
23 N A -0.9036
24 L A 1.0644
25 S A 0.7232
26 T A 0.8100
27 C A 1.3483
28 V A 2.4569
29 L A 2.0747
30 G A 0.2017
31 K A -1.4487
32 T A -0.8370
33 L A -0.2920
34 S A -1.0220
35 Q A -2.3868
36 E A -2.4073
37 L A -1.4848
38 H A -2.1598
39 K A -2.0631
40 L A -0.6990
41 Q A -1.7094
42 T A -0.9792
43 Y A 0.0684
44 P A -0.8803
45 R A -1.9393
46 T A -1.1425
47 N A -1.3042
48 A A 0.1543
49 I A 1.7545
50 G A 1.1385
51 V A 2.0497
52 T A 0.8251
53 P A 0.1616
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 partially or entirely disordered. Average score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -2.8759 3.0979 View CSV PDB
4.5 -2.9243 3.0979 View CSV PDB
5.0 -2.9814 3.0979 View CSV PDB
5.5 -3.015 3.0979 View CSV PDB
6.0 -2.994 3.0979 View CSV PDB
6.5 -2.9077 3.0979 View CSV PDB
7.0 -2.7655 3.0979 View CSV PDB
7.5 -2.5884 3.0979 View CSV PDB
8.0 -2.3954 3.0979 View CSV PDB
8.5 -2.1975 3.0979 View CSV PDB
9.0 -2.001 3.0979 View CSV PDB