Project name: 38b544f02971f81

Status: done

Started: 2025-02-22 14:47:02
Chain sequence(s) A: MADNKQSFQAGQAAGRAEEKGNVLMDKVKDAATAAGASAQTAGQKITEAAGGAVNLVKEKTGMNK
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                                          (00:01:18)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/38b544f02971f81/tmp/folded.pdb                (00:01:18)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:40)
Show buried residues
Minimal score value
-4.1316
Maximal score value
0.1654
Average score
-1.641
Total score value
-106.6673
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 A 0.1437
2 A A -1.2830
3 D A -2.4989
4 N A -2.2167
5 K A -2.7324
6 Q A -2.8899
7 S A -1.7368
8 F A -0.5956
9 Q A -1.8493
10 A A -1.4693
11 G A -1.4488
12 Q A -2.2176
13 A A -1.9132
14 A A -2.1162
15 G A -3.2278
16 R A -4.1316
17 A A -3.2476
18 E A -4.0123
19 E A -4.0637
20 K A -3.4487
21 G A -2.5416
22 N A -2.2229
23 V A -0.9676
24 L A -0.2557
25 M A -0.8178
26 D A -2.5336
27 K A -2.1027
28 V A -0.3438
29 K A -2.3986
30 D A -2.9048
31 A A -1.3871
32 A A -1.1227
33 T A -1.1408
34 A A -0.7530
35 A A -0.7571
36 G A -0.8780
37 A A -0.6384
38 S A -0.7728
39 A A -1.1113
40 Q A -1.6901
41 T A -1.2832
42 A A -1.0869
43 G A -1.2300
44 Q A -2.1425
45 K A -2.0781
46 I A 0.0409
47 T A -0.9040
48 E A -2.1321
49 A A -0.9365
50 A A -0.1740
51 G A -0.7036
52 G A -0.4987
53 A A 0.1654
54 V A -0.0894
55 N A -1.1753
56 L A -0.0611
57 V A -0.3206
58 K A -2.0728
59 E A -3.0114
60 K A -2.4554
61 T A -1.5593
62 G A -1.9707
63 M A -1.4134
64 N A -2.8535
65 K A -2.4250
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 -0.9249 1.6892 View CSV PDB
4.5 -1.0398 1.6364 View CSV PDB
5.0 -1.1846 1.5489 View CSV PDB
5.5 -1.3273 1.4627 View CSV PDB
6.0 -1.4269 1.4558 View CSV PDB
6.5 -1.4527 1.4963 View CSV PDB
7.0 -1.4034 1.5776 View CSV PDB
7.5 -1.3009 1.6838 View CSV PDB
8.0 -1.1676 1.8085 View CSV PDB
8.5 -1.0147 1.9519 View CSV PDB
9.0 -0.8454 2.1097 View CSV PDB