Project name: 28u

Status: done

Started: 2026-05-10 15:05:37
Chain sequence(s) A: GAQVVADMCDLCHTHMLKVAAVAKDPETKKYCLEAADACLKGKQAAQAGDLAAAAAHCNEAADACLKGAAAADAAGEDGIKITCEACHTVMLRVAAAAKA
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]                                                (00:00:00)
[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)
[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                                          (00:01:45)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/4859284378704ec/tmp/folded.pdb                (00:01:45)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:20)
Show buried residues
Minimal score value
-3.1007
Maximal score value
0.8827
Average score
-0.8371
Total score value
-83.7062
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 G A -0.6547
2 A A -1.4160
3 Q A -1.3113
4 V A 0.2228
5 V A 0.0000
6 A A 0.0000
7 D A -1.1597
8 M A 0.1351
9 C A 0.0000
10 D A -0.6405
11 L A 0.7439
12 C A 0.0000
13 H A -0.5834
14 T A -0.2493
15 H A -0.5720
16 M A 0.0000
17 L A -0.1986
18 K A -0.9450
19 V A 0.0000
20 A A 0.0000
21 A A 0.1746
22 V A 0.8827
23 A A 0.0000
24 K A -1.8221
25 D A -1.9026
26 P A -2.0875
27 E A -2.5880
28 T A 0.0000
29 K A -1.8091
30 K A -2.3937
31 Y A -1.9492
32 C A 0.0000
33 L A -0.9465
34 E A -2.3032
35 A A 0.0000
36 A A 0.0000
37 D A -1.9930
38 A A 0.0000
39 C A 0.0000
40 L A -0.9942
41 K A -2.1346
42 G A 0.0000
43 K A -2.1653
44 Q A -2.4481
45 A A -1.8261
46 A A 0.0000
47 Q A -2.5317
48 A A -1.6025
49 G A -1.7659
50 D A -1.8725
51 L A -1.1065
52 A A -0.6671
53 A A -1.0332
54 A A 0.0000
55 A A 0.0000
56 A A -1.1194
57 H A -1.8630
58 C A 0.0000
59 N A -2.4065
60 E A -3.1007
61 A A 0.0000
62 A A 0.0000
63 D A -2.8242
64 A A 0.0000
65 C A 0.0000
66 L A -1.0570
67 K A -2.0416
68 G A 0.0000
69 A A 0.0000
70 A A -1.3019
71 A A -1.6055
72 A A 0.0000
73 D A -2.4842
74 A A -1.2724
75 A A -1.6522
76 G A -1.8503
77 E A -1.9153
78 D A -2.3183
79 G A -0.9914
80 I A 0.0000
81 K A -1.3476
82 I A 0.4067
83 T A -0.0515
84 C A 0.0000
85 E A -0.6691
86 A A 0.1403
87 C A 0.0000
88 H A -0.8264
89 T A -0.0489
90 V A 0.4301
91 M A 0.0000
92 L A -0.6217
93 R A -1.4436
94 V A 0.0000
95 A A 0.0000
96 A A -1.0062
97 A A -0.6628
98 A A 0.0000
99 K A -1.9111
100 A A -0.7765
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 globular. Max score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -0.4563 2.1866 View CSV PDB
4.5 -0.5448 1.9749 View CSV PDB
5.0 -0.6503 1.7174 View CSV PDB
5.5 -0.7564 1.4413 View CSV PDB
6.0 -0.8449 1.1756 View CSV PDB
6.5 -0.9009 0.9478 View CSV PDB
7.0 -0.9214 0.7726 View CSV PDB
7.5 -0.9151 0.8253 View CSV PDB
8.0 -0.8917 1.0898 View CSV PDB
8.5 -0.8531 1.3579 View CSV PDB
9.0 -0.7954 1.6255 View CSV PDB