Project name: 64r

Status: done

Started: 2026-05-10 13:29:36
Chain sequence(s) A: AFIKDQAQSSIDIAQKYIDKAKENPNADKDIIKQAENKLAEAKKLFDAEKYVEAVEKAQEATILALDSIS
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.         (00:00:00)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:58)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/41a38385f188a2f/tmp/folded.pdb                (00:01:58)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:30)
Show buried residues
Minimal score value
-3.8175
Maximal score value
1.2548
Average score
-1.5661
Total score value
-109.6295
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 A A 0.4460
2 F A 1.2548
3 I A 0.6245
4 K A -1.3503
5 D A -1.6843
6 Q A -0.9482
7 A A 0.0000
8 Q A -1.8086
9 S A -1.5567
10 S A 0.0000
11 I A 0.0000
12 D A -2.0360
13 I A -0.8403
14 A A 0.0000
15 Q A -2.1185
16 K A -2.2596
17 Y A -1.3539
18 I A 0.0000
19 D A -3.6266
20 K A -3.4468
21 A A 0.0000
22 K A -3.5076
23 E A -3.5155
24 N A -2.7547
25 P A -1.9730
26 N A -2.1683
27 A A -2.3656
28 D A -2.8263
29 K A -3.6455
30 D A -3.3715
31 I A -2.1625
32 I A 0.0000
33 K A -3.8175
34 Q A -2.9923
35 A A 0.0000
36 E A -3.2994
37 N A -3.2039
38 K A -3.4800
39 L A 0.0000
40 A A -2.3844
41 E A -3.2043
42 A A 0.0000
43 K A -3.2742
44 K A -3.6060
45 L A -2.8890
46 F A -3.0520
47 D A -3.4773
48 A A -2.5115
49 E A -3.1585
50 K A -2.5160
51 Y A -1.5500
52 V A 0.1942
53 E A -1.9317
54 A A 0.0000
55 V A -1.4036
56 E A -2.6900
57 K A -2.9655
58 A A 0.0000
59 Q A -1.9893
60 E A -2.0605
61 A A 0.0000
62 T A 0.0000
63 I A 0.8185
64 L A -0.3758
65 A A 0.0000
66 L A 0.6803
67 D A -0.2669
68 S A 0.0000
69 I A -0.2300
70 S A 0.0021
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 -1.1216 4.3404 View CSV PDB
4.5 -1.3172 4.1993 View CSV PDB
5.0 -1.5531 4.05 View CSV PDB
5.5 -1.7889 3.9045 View CSV PDB
6.0 -1.9787 3.7747 View CSV PDB
6.5 -2.0839 3.6682 View CSV PDB
7.0 -2.0995 3.5816 View CSV PDB
7.5 -2.0535 3.5084 View CSV PDB
8.0 -1.9725 3.4503 View CSV PDB
8.5 -1.8636 3.4201 View CSV PDB
9.0 -1.7225 3.4318 View CSV PDB