Project name: b66639a99dacb9b

Status: done

Started: 2025-12-26 04:58:10
Chain sequence(s) A: HMDKVSVPGVVGEKESSAKSTLEAAGLKVSVKTKYSTDVAKGKVISQSPGSGNQVAKNSTVVITVSKGE
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                                          (00:01:41)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/b66639a99dacb9b/tmp/folded.pdb                (00:01:41)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:31)
Show buried residues
Minimal score value
-3.2712
Maximal score value
0.788
Average score
-1.3078
Total score value
-90.2358
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 -1.2301
2 M A -0.9200
3 D A -2.9001
4 K A -3.2712
5 V A -2.0853
6 S A -1.6416
7 V A 0.0000
8 P A -0.7800
9 G A -0.5508
10 V A 0.0000
11 V A 0.7880
12 G A -0.3782
13 E A -1.6729
14 K A -2.6996
15 E A -1.9292
16 S A -1.5290
17 S A -1.6501
18 A A 0.0000
19 K A -1.9114
20 S A -1.3056
21 T A -1.1351
22 L A 0.0000
23 E A -2.6553
24 A A -1.2139
25 A A -1.3073
26 G A -2.0266
27 L A 0.0000
28 K A -2.5735
29 V A -1.1531
30 S A -0.3114
31 V A -0.2012
32 K A -1.7704
33 T A -1.7300
34 K A -2.1074
35 Y A -0.8105
36 S A -1.4040
37 T A -1.7341
38 D A -1.9299
39 V A -1.3362
40 A A -1.7390
41 K A -2.9643
42 G A -2.1744
43 K A -2.1156
44 V A 0.0000
45 I A -0.5984
46 S A 0.0694
47 Q A 0.0566
48 S A -0.2885
49 P A -0.7899
50 G A -0.7991
51 S A -1.0346
52 G A -1.4747
53 N A -2.0946
54 Q A -2.5764
55 V A -1.8381
56 A A -2.0342
57 K A -3.0759
58 N A -2.9821
59 S A -1.7200
60 T A -1.2220
61 V A 0.0000
62 V A -0.1076
63 I A 0.0000
64 T A -0.7484
65 V A 0.0000
66 S A 0.0000
67 K A -2.2095
68 G A -2.3213
69 E A -2.3862
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 -1.7489 0.3321 View CSV PDB
4.5 -1.8017 0.242 View CSV PDB
5.0 -1.8693 0.1737 View CSV PDB
5.5 -1.927 0.11 View CSV PDB
6.0 -1.9424 0.0739 View CSV PDB
6.5 -1.8914 0.0838 View CSV PDB
7.0 -1.7771 0.1398 View CSV PDB
7.5 -1.6231 0.2249 View CSV PDB
8.0 -1.4503 0.3226 View CSV PDB
8.5 -1.2693 0.4245 View CSV PDB
9.0 -1.0831 0.5269 View CSV PDB