Project name: 354

Status: done

Started: 2026-05-09 18:58:31
Chain sequence(s) A: SDLAEACALLNEALDLILAEMPQPDADGVSVVTFDSKTKLLTELYGHVSKALTLTQQEKYDEAIDEINNALDVLSLLDIPSKDKIEDCLLKAKDILISLS
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                                          (00:00:00)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:23)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/58294a11a42c239/tmp/folded.pdb                (00:01:23)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:55)
Show buried residues
Minimal score value
-3.8233
Maximal score value
2.9599
Average score
-1.087
Total score value
-108.6973
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 S A -1.1130
2 D A -1.5876
3 L A -1.2019
4 A A -1.2122
5 E A -2.3111
6 A A 0.0000
7 C A -1.1974
8 A A -1.3419
9 L A -1.7311
10 L A 0.0000
11 N A -2.4420
12 E A -2.8540
13 A A 0.0000
14 L A 0.0000
15 D A -2.2458
16 L A -1.3521
17 I A 0.0000
18 L A -0.1645
19 A A -0.3432
20 E A -0.5329
21 M A 0.1699
22 P A -0.0997
23 Q A -0.9841
24 P A -1.2775
25 D A -2.1649
26 A A -1.6917
27 D A -2.0778
28 G A -1.3369
29 V A 0.6972
30 S A 0.7737
31 V A 2.6366
32 V A 2.9599
33 T A 1.3130
34 F A 1.1817
35 D A -1.0336
36 S A -1.4094
37 K A -1.8747
38 T A -1.1395
39 K A -2.1355
40 L A -1.1793
41 L A 0.0000
42 T A -1.1703
43 E A -2.4024
44 L A 0.0000
45 Y A -0.8168
46 G A -1.2430
47 H A -1.6182
48 V A 0.0000
49 S A -1.0251
50 K A -1.7677
51 A A 0.0000
52 L A -1.1334
53 T A -1.4211
54 L A -2.1833
55 T A 0.0000
56 Q A -2.4622
57 Q A -2.8169
58 E A -3.3960
59 K A -2.9792
60 Y A -2.2859
61 D A -2.9291
62 E A -3.2271
63 A A 0.0000
64 I A -1.9849
65 D A -3.1280
66 E A 0.0000
67 I A 0.0000
68 N A -2.0984
69 N A -2.3993
70 A A 0.0000
71 L A -1.2981
72 D A -1.8758
73 V A 0.0000
74 L A 0.0000
75 S A -0.4924
76 L A 0.6507
77 L A 0.0000
78 D A -1.9859
79 I A 0.0000
80 P A -1.3737
81 S A -1.9983
82 K A -2.8761
83 D A -3.8233
84 K A -3.6631
85 I A 0.0000
86 E A -2.9488
87 D A -3.2230
88 C A 0.0000
89 L A 0.0000
90 L A -1.4686
91 K A -2.4253
92 A A 0.0000
93 K A -1.5899
94 D A -1.7316
95 I A -1.0674
96 L A 0.0000
97 I A 0.1529
98 S A -0.0302
99 L A -0.3191
100 S A -0.5187
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 -0.3213 3.5309 View CSV PDB
4.5 -0.4852 3.4861 View CSV PDB
5.0 -0.6844 3.4407 View CSV PDB
5.5 -0.8934 3.3951 View CSV PDB
6.0 -1.0853 3.3497 View CSV PDB
6.5 -1.2409 3.305 View CSV PDB
7.0 -1.3544 3.2623 View CSV PDB
7.5 -1.4313 3.225 View CSV PDB
8.0 -1.4793 3.1981 View CSV PDB
8.5 -1.4985 3.1835 View CSV PDB
9.0 -1.4856 3.1776 View CSV PDB