Project name: 399ee801133793f

Status: done

Started: 2025-12-26 07:21:46
Chain sequence(s) A: HMGPADLDAIMTVLQAHQGRLLIDVLIKNVSLNLGKSRLTEAGKRRILESIYALQSQGKIRLENGMAILVK
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]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[WARNING]    PDB-Info: The input structure is likely a peptide. Results may be inaccurate.         (00:00:02)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:56)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/399ee801133793f/tmp/folded.pdb                (00:01:56)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:08)
Show buried residues
Minimal score value
-3.7502
Maximal score value
0.0107
Average score
-1.1439
Total score value
-81.2157
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 H A -0.9025
2 M A -0.4854
3 G A -0.5233
4 P A -0.6259
5 A A -0.6060
6 D A 0.0000
7 L A -0.7758
8 D A -1.6821
9 A A -0.9911
10 I A 0.0000
11 M A -0.8253
12 T A -1.0534
13 V A 0.0000
14 L A 0.0000
15 Q A -1.8623
16 A A -1.2631
17 H A -1.7366
18 Q A -2.2104
19 G A 0.0000
20 R A -2.0494
21 L A -0.6201
22 L A 0.0107
23 I A -0.4749
24 D A -1.3584
25 V A -0.0525
26 L A 0.0000
27 I A 0.0000
28 K A -1.4342
29 N A -0.6637
30 V A 0.0000
31 S A 0.0000
32 L A -0.2900
33 N A -1.0824
34 L A -0.5858
35 G A -1.3225
36 K A -2.3216
37 S A -1.6771
38 R A -2.4473
39 L A -1.7474
40 T A -2.1005
41 E A -2.9095
42 A A -2.0484
43 G A -2.7293
44 K A -3.1980
45 R A -3.7502
46 R A -3.4003
47 I A 0.0000
48 L A -1.8739
49 E A -2.3434
50 S A 0.0000
51 I A 0.0000
52 Y A -0.2920
53 A A -0.5452
54 L A 0.0000
55 Q A -1.4343
56 S A -1.2555
57 Q A -1.9488
58 G A -1.8606
59 K A -1.8027
60 I A 0.0000
61 R A -2.2493
62 L A -1.4915
63 E A -2.2035
64 N A -1.8108
65 G A -1.0626
66 M A -0.9407
67 A A 0.0000
68 I A -1.3960
69 L A -1.0965
70 V A -0.5503
71 K A -1.2621
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 -1.3638 1.9604 View CSV PDB
4.5 -1.4236 1.8754 View CSV PDB
5.0 -1.4973 1.7792 View CSV PDB
5.5 -1.5682 1.6864 View CSV PDB
6.0 -1.6194 1.604 View CSV PDB
6.5 -1.6413 1.5248 View CSV PDB
7.0 -1.6359 1.4365 View CSV PDB
7.5 -1.6123 1.337 View CSV PDB
8.0 -1.5785 1.2341 View CSV PDB
8.5 -1.538 1.1385 View CSV PDB
9.0 -1.4892 1.0637 View CSV PDB