Project name: ef888c71e7b2c0f [mutate: RG5A, YF10A, HR13A]

Status: done

Started: 2025-04-25 14:37:25
Chain sequence(s) A: DAEFRHDSGYEVHHQKRGGRLCYCRRRFCVCVGR
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
Mutated residues RG5A,YF10A,HR13A
Energy difference between WT (input) and mutated protein (by FoldX) -0.927492 kcal/mol
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]       FoldX:    Building mutant model                                                       (00:00:34)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:15)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/ef888c71e7b2c0f/tmp/folded.pdb                (00:01:15)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:33)
Show buried residues
Minimal score value
-4.2542
Maximal score value
1.3051
Average score
-1.8063
Total score value
-61.4149
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 D A -2.0290
2 A A -1.4903
3 E A -2.3928
4 F A -1.4262
5 G A -1.6847 mutated: RG5A
6 H A -2.0987
7 D A -2.7742
8 S A -1.3455
9 G A -1.1011
10 F A -1.5224 mutated: YF10A
11 E A -2.3718
12 V A -1.8511
13 R A -2.4140 mutated: HR13A
14 H A -2.7488
15 Q A -3.0333
16 K A -4.2542
17 R A -3.7972
18 G A -2.8190
19 G A -3.0204
20 R A -3.8813
21 L A -2.8022
22 C A 0.0000
23 Y A -0.5616
24 C A -0.5587
25 R A -1.6900
26 R A -2.2784
27 R A -1.7997
28 F A 0.5749
29 C A 0.7568
30 V A 1.3051
31 C A -0.2237
32 V A -0.9712
33 G A -2.3699
34 R A -2.7403
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 -2.1874 2.3292 View CSV PDB
4.5 -2.3044 2.3292 View CSV PDB
5.0 -2.4336 2.3292 View CSV PDB
5.5 -2.5455 2.3292 View CSV PDB
6.0 -2.6165 2.3292 View CSV PDB
6.5 -2.646 2.3292 View CSV PDB
7.0 -2.6541 2.3292 View CSV PDB
7.5 -2.6572 2.3292 View CSV PDB
8.0 -2.6564 2.3292 View CSV PDB
8.5 -2.6455 2.3292 View CSV PDB
9.0 -2.6207 2.3291 View CSV PDB