Project name: AB10-PrD

Status: done

Started: 2025-04-25 15:48:21
Chain sequence(s) A: QQKQQIMAALNSQTAVQFQQYAAQQYPGNYEQQQILIRQLQEQHYQQYMQQLYQVQLAQQQAALQKQQ
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 partially or entirely disordered. Average 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                                          (00:01:08)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/69dcba13b415bca/tmp/folded.pdb                (00:01:08)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:34)
Show buried residues
Minimal score value
-3.0727
Maximal score value
0.954
Average score
-1.1808
Total score value
-80.2919
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 Q A -2.7468
2 Q A -3.0727
3 K A -3.0092
4 Q A -2.8485
5 Q A -2.6765
6 I A -1.3961
7 M A 0.0000
8 A A -1.2014
9 A A -0.7334
10 L A 0.0000
11 N A -1.0813
12 S A -0.8500
13 Q A -1.3066
14 T A -0.8384
15 A A -0.3349
16 V A 0.4658
17 Q A -0.9191
18 F A -0.7800
19 Q A -0.9826
20 Q A -1.5421
21 Y A -0.6916
22 A A 0.0000
23 A A -1.2746
24 Q A -1.8184
25 Q A -1.5439
26 Y A -0.8369
27 P A -0.9533
28 G A -0.9772
29 N A -1.0966
30 Y A -0.0304
31 E A -1.3142
32 Q A -0.7902
33 Q A -0.7151
34 Q A -0.3251
35 I A 0.9540
36 L A -0.0285
37 I A -0.6054
38 R A -1.1113
39 Q A -1.6117
40 L A -1.0393
41 Q A 0.0000
42 E A -3.0318
43 Q A -2.9176
44 H A -2.2114
45 Y A -2.2576
46 Q A -2.6999
47 Q A -2.4226
48 Y A -1.0360
49 M A -0.5010
50 Q A -1.3813
51 Q A -1.0366
52 L A 0.4137
53 Y A 0.7154
54 Q A -0.3652
55 V A 0.6349
56 Q A -0.5901
57 L A -0.2689
58 A A -0.3715
59 Q A -1.6961
60 Q A -1.4076
61 Q A -1.5737
62 A A -2.0274
63 A A -1.5783
64 L A -0.5655
65 Q A -2.2763
66 K A -2.8400
67 Q A -2.9381
68 Q A -2.3979
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 -0.5881 2.0512 View CSV PDB
4.5 -0.6136 1.9684 View CSV PDB
5.0 -0.6473 1.8624 View CSV PDB
5.5 -0.6811 1.7508 View CSV PDB
6.0 -0.7039 1.661 View CSV PDB
6.5 -0.7058 1.661 View CSV PDB
7.0 -0.6862 1.6609 View CSV PDB
7.5 -0.6526 1.6608 View CSV PDB
8.0 -0.6127 1.6605 View CSV PDB
8.5 -0.5708 1.6596 View CSV PDB
9.0 -0.5292 1.6566 View CSV PDB