Project name: 491_2_0

Status: done

Started: 2026-05-13 09:17:19
Chain sequence(s) D: SHPNLATTYFNLGSVYQELGQLDKAKEYFQKAVDIFQKLGINSPDLKRSQLLL
input PDB
Selected Chain(s) D
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 D 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 globular. Max 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                                          (00:01:16)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/4b08cf49592f460/tmp/folded.pdb                (00:01:16)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:40)
Show buried residues
Minimal score value
-2.9818
Maximal score value
0.6178
Average score
-1.0502
Total score value
-55.6586
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 S D -0.8255
2 H D -1.1904
3 P D -0.8184
4 N D -1.2287
5 L D -0.2940
6 A D 0.0000
7 T D -0.5450
8 T D -0.2517
9 Y D -0.1889
10 F D -0.6673
11 N D -0.4554
12 L D 0.1029
13 G D 0.0000
14 S D -0.2713
15 V D 0.4362
16 Y D -0.5829
17 Q D -1.2117
18 E D -1.1052
19 L D 0.4530
20 G D -0.8064
21 Q D -1.4673
22 L D -1.4186
23 D D -2.9818
24 K D -2.6192
25 A D 0.0000
26 K D -2.6683
27 E D -2.8867
28 Y D -1.7038
29 F D 0.0000
30 Q D -1.9256
31 K D -1.6706
32 A D 0.0000
33 V D -1.8471
34 D D -1.8835
35 I D -1.3984
36 F D 0.0000
37 Q D -2.2892
38 K D -2.1879
39 L D -1.0945
40 G D -1.2236
41 I D -0.7148
42 N D -1.6580
43 S D -1.5112
44 P D -1.8369
45 D D -1.9158
46 L D -2.1747
47 K D -2.9383
48 R D -2.3853
49 S D 0.0000
50 Q D -1.3480
51 L D 0.4780
52 L D 0.4454
53 L D 0.6178
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 globular. Max score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -0.9976 1.5899 View CSV PDB
4.5 -1.0632 1.5062 View CSV PDB
5.0 -1.1414 1.3555 View CSV PDB
5.5 -1.2162 1.1538 View CSV PDB
6.0 -1.2701 0.935 View CSV PDB
6.5 -1.2895 0.7326 View CSV PDB
7.0 -1.2691 0.5807 View CSV PDB
7.5 -1.2157 0.6105 View CSV PDB
8.0 -1.141 0.6943 View CSV PDB
8.5 -1.0506 0.7831 View CSV PDB
9.0 -0.9458 0.873 View CSV PDB