Project name: 511_0_0

Status: done

Started: 2026-05-13 09:35:00
Chain sequence(s) D: DNATLLIAALRAGDTAEAEKHLAELLPEVEALVSGLTPEEKQLLADLVQTSTTLSDEQKQAVLKELQKAGVPV
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                                          (00:00:56)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/4dbcdca0dc81f72/tmp/folded.pdb                (00:00:56)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:22)
Show buried residues
Minimal score value
-3.4337
Maximal score value
0.606
Average score
-1.2043
Total score value
-87.9167
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 D -1.7611
2 N D -1.4330
3 A D -0.8346
4 T D -0.2063
5 L D -0.1765
6 L D 0.0000
7 I D 0.0133
8 A D -0.5347
9 A D 0.0000
10 L D 0.0000
11 R D -2.0868
12 A D -1.5250
13 G D -1.5735
14 D D -2.0851
15 T D -1.5775
16 A D -1.3298
17 E D -1.8422
18 A D 0.0000
19 E D 0.0000
20 K D -2.4399
21 H D -1.8524
22 L D 0.0000
23 A D -1.5892
24 E D -2.4975
25 L D 0.0000
26 L D -1.4047
27 P D -1.6364
28 E D -2.5657
29 V D 0.0000
30 E D -2.9437
31 A D -1.5883
32 L D 0.0000
33 V D 0.0000
34 S D -1.1709
35 G D -0.8157
36 L D 0.0000
37 T D -0.9781
38 P D -1.3879
39 E D -2.2185
40 E D 0.0000
41 K D -1.4096
42 Q D -1.2076
43 L D -0.8261
44 L D 0.0000
45 A D 0.0000
46 D D -1.7936
47 L D 0.0000
48 V D 0.0000
49 Q D -2.0175
50 T D -1.1579
51 S D 0.0000
52 T D -0.4845
53 T D -0.6909
54 L D 0.0000
55 S D -1.9894
56 D D -3.4337
57 E D -3.4186
58 Q D -2.5848
59 K D -2.7458
60 Q D -3.1864
61 A D -2.3311
62 V D 0.0000
63 L D -2.0990
64 K D -2.9702
65 E D -2.7620
66 L D 0.0000
67 Q D -2.4784
68 K D -3.1944
69 A D -2.1495
70 G D -1.4187
71 V D 0.0000
72 P D -0.1313
73 V D 0.6060
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 -0.6162 1.7759 View CSV PDB
4.5 -0.7352 1.7768 View CSV PDB
5.0 -0.8814 1.7798 View CSV PDB
5.5 -1.0315 1.7881 View CSV PDB
6.0 -1.1609 1.8085 View CSV PDB
6.5 -1.2488 1.8464 View CSV PDB
7.0 -1.29 1.8993 View CSV PDB
7.5 -1.2973 1.9602 View CSV PDB
8.0 -1.2848 2.0241 View CSV PDB
8.5 -1.2566 2.089 View CSV PDB
9.0 -1.2117 2.1537 View CSV PDB