Project name: P48356

Status: done

Started: 2025-03-04 13:00:22
Chain sequence(s) A: KDSFQTVQCNCSLRGCECHVPVPRAK
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/7ef7435ea6fe1b3/tmp/folded.pdb                (00:00:12)
[INFO]       Main:     Simulation completed successfully.                                          (00:00:31)
Show buried residues
Minimal score value
-3.1993
Maximal score value
1.8559
Average score
-0.6159
Total score value
-16.0137
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 -2.9781
2 D A -3.1993
3 S A -1.1893
4 F A 0.7772
5 Q A 0.1144
6 T A 0.5174
7 V A 1.1159
8 Q A -0.7714
9 C A -0.2721
10 N A -1.3837
11 C A -0.1271
12 S A -0.0731
13 L A 0.7090
14 R A -1.0642
15 G A -0.8431
16 C A -0.3354
17 E A -1.8076
18 C A -0.5373
19 H A -0.4432
20 V A 1.8559
21 P A 1.1766
22 V A 1.3055
23 P A -0.6259
24 R A -2.8127
25 A A -2.3631
26 K A -2.7590
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 -0.1244 3.3612 View CSV PDB
4.5 -0.2045 3.2731 View CSV PDB
5.0 -0.2996 3.1762 View CSV PDB
5.5 -0.386 3.0828 View CSV PDB
6.0 -0.4364 3.0025 View CSV PDB
6.5 -0.437 2.9375 View CSV PDB
7.0 -0.4024 2.8829 View CSV PDB
7.5 -0.3567 2.834 View CSV PDB
8.0 -0.3102 2.7914 View CSV PDB
8.5 -0.2595 2.7615 View CSV PDB
9.0 -0.1977 2.7553 View CSV PDB