Project name: c5a511b25dc0f2a

Status: done

Started: 2025-12-26 13:59:06
Chain sequence(s) A: HMSQVDTANFHKGLRIIYEDEMWEIVDFQHRVMQQRSPVVKTKLKNIISGYVQERSFRSGDTFELP
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]                                                (00:00:02)
[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 A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[WARNING]    PDB-Info: The input structure is likely a peptide. Results may be inaccurate.         (00:00:03)
[INFO]       PDB-Info: The input structure is partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:03)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:03)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:34)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/c5a511b25dc0f2a/tmp/folded.pdb                (00:02:34)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:16)
Show buried residues
Minimal score value
-3.0486
Maximal score value
2.1862
Average score
-1.1289
Total score value
-74.506
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 H A -0.6812
2 M A -0.0061
3 S A -0.6937
4 Q A -1.4448
5 V A -1.4707
6 D A -1.8810
7 T A 0.0000
8 A A -1.3994
9 N A -1.6257
10 F A 0.0000
11 H A -2.2899
12 K A -2.6786
13 G A -1.9407
14 L A -1.6142
15 R A -1.4044
16 I A 0.0000
17 I A -1.3524
18 Y A -1.7339
19 E A -2.8657
20 D A -3.0486
21 E A -2.0278
22 M A -0.7782
23 W A 0.0000
24 E A -1.4112
25 I A 0.0000
26 V A -1.5898
27 D A -2.2687
28 F A -2.0210
29 Q A -1.9417
30 H A -1.9887
31 R A -2.0262
32 V A -0.1162
33 M A -1.0092
34 Q A -1.9077
35 Q A -2.3697
36 R A -2.5864
37 S A -1.7063
38 P A -1.4477
39 V A -1.8872
40 V A 0.0000
41 K A -2.8861
42 T A 0.0000
43 K A -2.5060
44 L A 0.0000
45 K A -0.3259
46 N A 0.0000
47 I A 1.3812
48 I A 2.1862
49 S A 1.2273
50 G A 1.1325
51 Y A 1.8243
52 V A 0.6893
53 Q A -0.8655
54 E A -2.8470
55 R A -2.3777
56 S A -2.2399
57 F A 0.0000
58 R A -2.7625
59 S A -1.6920
60 G A -1.6814
61 D A -1.9016
62 T A -1.6371
63 F A 0.0000
64 E A -1.0655
65 L A -0.4359
66 P A -0.5080
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 -1.4081 2.9178 View CSV PDB
4.5 -1.4808 2.8908 View CSV PDB
5.0 -1.5766 2.8501 View CSV PDB
5.5 -1.674 2.8036 View CSV PDB
6.0 -1.7538 2.761 View CSV PDB
6.5 -1.8067 2.7332 View CSV PDB
7.0 -1.8313 2.7271 View CSV PDB
7.5 -1.8328 2.7394 View CSV PDB
8.0 -1.8202 2.7613 View CSV PDB
8.5 -1.7981 2.7868 View CSV PDB
9.0 -1.7663 2.8132 View CSV PDB