Project name: 349

Status: done

Started: 2026-05-09 18:56:14
Chain sequence(s) A: VNLTLIGADVSDLSAAGKAKVLEILKQLEGKTGVVDNVYVDDNNQLCVDINFDDFPYISPYIVPADQQDLAKQYLTKGAKVKVDEVRQENDKILVDISVL
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]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (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                                          (00:01:21)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/4ec83306d68be56/tmp/folded.pdb                (00:01:21)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:55)
Show buried residues
Minimal score value
-3.0535
Maximal score value
1.5499
Average score
-0.9885
Total score value
-98.848
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 V A 1.1188
2 N A -0.7259
3 L A 0.0000
4 T A -0.5407
5 L A 0.0000
6 I A -0.2010
7 G A -0.3566
8 A A -1.0533
9 D A -2.7357
10 V A 0.0000
11 S A -2.1307
12 D A -2.0867
13 L A -0.9087
14 S A -0.5357
15 A A -0.4309
16 A A -0.3609
17 G A -0.9484
18 K A -1.5755
19 A A -1.1689
20 K A -2.0354
21 V A -1.1677
22 L A -1.5097
23 E A -2.4278
24 I A -0.9247
25 L A -1.2664
26 K A -2.4157
27 Q A -2.0205
28 L A 0.0000
29 E A -2.5978
30 G A -2.0085
31 K A -2.1537
32 T A -1.4749
33 G A 0.0000
34 V A -0.7465
35 V A 0.0000
36 D A -1.5750
37 N A -1.3767
38 V A -0.0385
39 Y A 0.7350
40 V A 0.7904
41 D A -1.2001
42 D A -2.6919
43 N A -2.7447
44 N A -2.2382
45 Q A -1.2477
46 L A 0.0000
47 C A 0.0000
48 V A 0.0000
49 D A -0.4480
50 I A 0.0000
51 N A -0.5883
52 F A 0.0000
53 D A -2.1462
54 D A -2.4034
55 F A -0.8653
56 P A 0.1214
57 Y A 1.4512
58 I A 1.5499
59 S A 0.6301
60 P A 0.1190
61 Y A 0.0000
62 I A 0.4644
63 V A 0.0000
64 P A -0.8002
65 A A -1.2955
66 D A -2.2192
67 Q A -1.9605
68 Q A -2.2477
69 D A -2.8356
70 L A -1.4101
71 A A 0.0000
72 K A -2.4817
73 Q A -2.0140
74 Y A -0.4122
75 L A 0.0000
76 T A -1.6113
77 K A -2.2386
78 G A -1.7044
79 A A -0.7800
80 K A -0.8472
81 V A 0.0000
82 K A -1.5926
83 V A 0.0000
84 D A -2.5906
85 E A -2.4649
86 V A 0.0000
87 R A -1.7850
88 Q A -2.2670
89 E A -2.6772
90 N A -2.7882
91 D A -3.0535
92 K A -2.6347
93 I A 0.0000
94 L A -1.1459
95 V A 0.0000
96 D A -1.4891
97 I A 0.0000
98 S A -0.4957
99 V A 0.8004
100 L A 1.2869
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 -0.4132 3.5096 View CSV PDB
4.5 -0.5342 3.4461 View CSV PDB
5.0 -0.6787 3.3662 View CSV PDB
5.5 -0.8282 3.2776 View CSV PDB
6.0 -0.9622 3.1856 View CSV PDB
6.5 -1.0636 3.0925 View CSV PDB
7.0 -1.1288 2.9994 View CSV PDB
7.5 -1.1666 2.9072 View CSV PDB
8.0 -1.1843 2.818 View CSV PDB
8.5 -1.1814 2.7363 View CSV PDB
9.0 -1.1539 2.6679 View CSV PDB