Project name: 8ce78b59450633

Status: done

Started: 2025-12-26 12:00:08
Chain sequence(s) A: HMKRNTQQRRRSIVEQLNRTGEVAVDELAKLFSTSEVTIRKDFIELESNGLLLRKFGGAILLPT
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]                                                (00:00:03)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:03)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:03)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:03)
[WARNING]    PDB-Info: The input structure is likely a peptide. Results may be inaccurate.         (00:00:03)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:03)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:03)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:46)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/8ce78b59450633/tmp/folded.pdb                 (00:03:46)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:14)
Show buried residues
Minimal score value
-3.8915
Maximal score value
1.1453
Average score
-1.2965
Total score value
-82.9738
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 -1.5943
2 M A -1.3125
3 K A -3.2083
4 R A -3.8915
5 N A -3.2976
6 T A -3.0792
7 Q A -3.6405
8 Q A -3.6561
9 R A 0.0000
10 R A -2.5462
11 R A -2.9134
12 S A -1.9893
13 I A 0.0000
14 V A -1.6606
15 E A -2.5414
16 Q A -2.3156
17 L A 0.0000
18 N A -2.5366
19 R A -3.0725
20 T A -2.0409
21 G A -1.6707
22 E A -2.2005
23 V A -1.9054
24 A A -1.7354
25 V A 0.0000
26 D A -3.3179
27 E A -2.9778
28 L A 0.0000
29 A A 0.0000
30 K A -2.1863
31 L A 0.1130
32 F A -0.0216
33 S A -0.5209
34 T A -0.4235
35 S A -1.1118
36 E A -2.2494
37 V A -0.1789
38 T A -0.6489
39 I A 0.0000
40 R A -2.6606
41 K A -2.3185
42 D A 0.0000
43 F A 0.0000
44 I A -1.2013
45 E A -1.9894
46 L A 0.0000
47 E A -1.2627
48 S A -1.2393
49 N A -1.7707
50 G A -0.8408
51 L A -0.1373
52 L A 0.0000
53 L A -0.0797
54 R A -1.5385
55 K A -1.4531
56 F A 0.6230
57 G A -1.0764
58 G A -1.5108
59 A A 0.0000
60 I A -0.4191
61 L A 0.2869
62 L A 1.1453
63 P A 0.5894
64 T A 0.2123
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 -1.6219 2.9358 View CSV PDB
4.5 -1.7008 2.9358 View CSV PDB
5.0 -1.8013 2.9358 View CSV PDB
5.5 -1.9012 2.9358 View CSV PDB
6.0 -1.9761 2.9358 View CSV PDB
6.5 -2.0078 2.9358 View CSV PDB
7.0 -1.9919 2.9358 View CSV PDB
7.5 -1.9405 2.9358 View CSV PDB
8.0 -1.8701 2.9358 View CSV PDB
8.5 -1.7893 2.9358 View CSV PDB
9.0 -1.7015 3.1111 View CSV PDB