Project name: Q62959

Status: done

Started: 2025-03-04 13:03:19
Chain sequence(s) A: KDSFQTVQCNCSVRECECHVPVPRAK
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 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                                          (00:00:12)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/8f71ae2d39c3048/tmp/folded.pdb                (00:00:12)
[INFO]       Main:     Simulation completed successfully.                                          (00:00:31)
Show buried residues
Minimal score value
-2.9843
Maximal score value
1.3375
Average score
-0.9031
Total score value
-23.4804
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 K A -2.9843
2 D A -2.7419
3 S A -1.7334
4 F A 0.2128
5 Q A -0.0170
6 T A 0.6544
7 V A 1.3375
8 Q A -0.3895
9 C A -0.2293
10 N A -1.5705
11 C A -0.4490
12 S A -0.4665
13 V A 0.5439
14 R A -1.6839
15 E A -2.3663
16 C A -1.1085
17 E A -2.1385
18 C A -0.4977
19 H A -0.4391
20 V A 1.0201
21 P A 0.2760
22 V A 0.2770
23 P A -0.9456
24 R A -2.6860
25 A A -2.4028
26 K A -2.9523
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 -0.5184 2.7669 View CSV PDB
4.5 -0.6375 2.652 View CSV PDB
5.0 -0.7833 2.5246 View CSV PDB
5.5 -0.9241 2.3965 View CSV PDB
6.0 -1.0256 2.2779 View CSV PDB
6.5 -1.0642 2.1766 View CSV PDB
7.0 -1.0475 2.0922 View CSV PDB
7.5 -1.0049 2.0191 View CSV PDB
8.0 -0.9545 1.9786 View CSV PDB
8.5 -0.8978 1.9844 View CSV PDB
9.0 -0.8301 1.9863 View CSV PDB