Project name: 872c813590aa48b

Status: done

Started: 2025-11-07 08:41:13
Chain sequence(s) B: MFTFEDYKKLSKEEQEKLKEELVEKYYVGDPDSITEEEEEVYKKIMEEEN
input PDB
Selected Chain(s) B
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]                                                (00:00:03)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:03)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with B chain(s) selected             (00:00:03)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:03)
[WARNING]    PDB-Info: The input structure is likely a peptide. Results may be inaccurate.         (00:00:04)
[INFO]       PDB-Info: The input structure is partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:04)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:04)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:09)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/872c813590aa48b/tmp/folded.pdb                (00:03:09)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:12)
Show buried residues
Minimal score value
-5.0288
Maximal score value
1.3936
Average score
-2.3222
Total score value
-116.111
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 B 1.0766
2 F B 0.3664
3 T B -1.4704
4 F B -2.3507
5 E B -2.8396
6 D B -2.4099
7 Y B 0.0000
8 K B -3.5863
9 K B -3.4288
10 L B -2.7915
11 S B -3.0052
12 K B -4.1990
13 E B -4.4667
14 E B -4.5778
15 Q B -4.3571
16 E B -5.0288
17 K B -4.9423
18 L B -3.1898
19 K B -3.4976
20 E B -4.2843
21 E B -3.9228
22 L B 0.0000
23 V B -0.9262
24 E B -1.7704
25 K B -1.7016
26 Y B -0.4408
27 Y B 1.3936
28 V B 1.2130
29 G B -0.8124
30 D B -2.2584
31 P B -1.6554
32 D B -2.9093
33 S B -1.7764
34 I B 0.0000
35 T B -2.2740
36 E B -3.3671
37 E B -2.5914
38 E B -2.5797
39 E B -2.8041
40 E B -3.4702
41 V B 0.0000
42 Y B 0.0000
43 K B -2.7939
44 K B -3.1530
45 I B 0.0000
46 M B -2.8218
47 E B -4.0946
48 E B -4.2409
49 E B -4.0091
50 N B -3.3613
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 -1.6905 2.1414 View CSV PDB
4.5 -1.9872 2.0121 View CSV PDB
5.0 -2.3882 1.835 View CSV PDB
5.5 -2.817 1.7342 View CSV PDB
6.0 -3.1879 1.6755 View CSV PDB
6.5 -3.428 1.6264 View CSV PDB
7.0 -3.51 1.5891 View CSV PDB
7.5 -3.4708 1.5604 View CSV PDB
8.0 -3.3683 1.5365 View CSV PDB
8.5 -3.2368 1.5167 View CSV PDB
9.0 -3.0875 1.5025 View CSV PDB