Project name: 3ee

Status: done

Started: 2026-05-10 14:23:27
Chain sequence(s) A: GAAAAAAAQKAKELSAQAGELLVEGKYNEAIDLCTQAIALDATYIPAYFNRSTAYTMLGNADLAQQDKDTALAIMDAINA
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.  (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:00:49)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/3be89de2809bd20/tmp/folded.pdb                (00:00:49)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:15)
Show buried residues
Minimal score value
-3.3232
Maximal score value
1.1503
Average score
-0.7359
Total score value
-58.8732
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 -0.3764
2 A A -0.0823
3 A A -0.0779
4 A A -0.2566
5 A A -0.4113
6 A A -0.7712
7 A A -1.0334
8 A A -1.3479
9 Q A -2.5228
10 K A -3.1250
11 A A 0.0000
12 K A -2.9697
13 E A -3.3232
14 L A -2.2711
15 S A 0.0000
16 A A -1.7775
17 Q A -1.9150
18 A A 0.0000
19 G A -1.0672
20 E A -1.8878
21 L A -1.7052
22 L A -0.8159
23 V A 0.1746
24 E A -1.6765
25 G A -1.2978
26 K A -2.2049
27 Y A -1.2703
28 N A -2.3951
29 E A -3.2061
30 A A 0.0000
31 I A -1.8243
32 D A -2.6676
33 L A -1.6967
34 C A 0.0000
35 T A -0.9228
36 Q A -1.0085
37 A A 0.0000
38 I A -0.0985
39 A A 0.1561
40 L A -0.1989
41 D A -0.4286
42 A A 0.1997
43 T A 0.5003
44 Y A 0.1415
45 I A 0.5646
46 P A 0.0308
47 A A 0.0000
48 Y A 0.0000
49 F A 0.4505
50 N A 0.1738
51 R A -0.4104
52 S A -0.4385
53 T A 0.3152
54 A A 0.0000
55 Y A 0.1270
56 T A 0.1403
57 M A 0.9101
58 L A 0.8923
59 G A -0.1534
60 N A -0.8285
61 A A -1.1333
62 D A -2.2895
63 L A -1.3836
64 A A 0.0000
65 Q A -2.1584
66 Q A -2.1416
67 D A 0.0000
68 K A -1.6165
69 D A -1.6383
70 T A -0.8556
71 A A 0.0000
72 L A 0.4019
73 A A -0.1537
74 I A 0.3511
75 M A 0.2358
76 D A -1.0209
77 A A 0.1298
78 I A 1.1503
79 N A -0.7464
80 A A -0.3163
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 0.2374 3.5729 View CSV PDB
4.5 0.1305 3.4881 View CSV PDB
5.0 -0.0036 3.3735 View CSV PDB
5.5 -0.1432 3.2442 View CSV PDB
6.0 -0.2657 3.1092 View CSV PDB
6.5 -0.3532 2.9725 View CSV PDB
7.0 -0.4026 2.8354 View CSV PDB
7.5 -0.4249 2.6987 View CSV PDB
8.0 -0.4315 2.5642 View CSV PDB
8.5 -0.4258 2.436 View CSV PDB
9.0 -0.4041 2.3241 View CSV PDB