Project name: AB05-PrD

Status: done

Started: 2025-04-25 15:46:58
Chain sequence(s) A: GYSQRGGPGSARGVRGARGGAQQQRGRGVRGARGGRGGNVGGKRKADGYNQPDSKRRQTNNQNWGSQPIAQQPLQGGDHSGNYGY
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 partially or entirely disordered. Average 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                                          (00:00:58)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/b94600f7a0ad1c6/tmp/folded.pdb                (00:00:58)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:20)
Show buried residues
Minimal score value
-4.6549
Maximal score value
1.5734
Average score
-2.0002
Total score value
-170.0211
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 -0.0136
2 Y A 0.5015
3 S A -0.7835
4 Q A -2.1120
5 R A -2.6771
6 G A -2.0677
7 G A -1.5110
8 P A -1.1190
9 G A -1.6371
10 S A -1.2122
11 A A -1.4862
12 R A -2.5559
13 G A -1.7286
14 V A -0.9822
15 R A -2.9686
16 G A -2.2702
17 A A -1.9273
18 R A -2.9966
19 G A -2.5861
20 G A -2.4881
21 A A -2.7335
22 Q A -3.6901
23 Q A -3.4143
24 Q A -3.5271
25 R A -3.5906
26 G A 0.0000
27 R A -3.5604
28 G A -2.1338
29 V A -1.3614
30 R A -3.5668
31 G A -2.6534
32 A A -2.5009
33 R A -2.9706
34 G A -2.4766
35 G A -2.5531
36 R A -3.0099
37 G A -2.0325
38 G A -1.5294
39 N A -1.5965
40 V A -0.4205
41 G A -0.9913
42 G A -1.9741
43 K A -3.2672
44 R A -3.8569
45 K A -3.6307
46 A A -2.8949
47 D A -2.9199
48 G A -1.6329
49 Y A -0.9049
50 N A -2.3799
51 Q A -2.4518
52 P A -2.3276
53 D A -2.6089
54 S A -3.0181
55 K A -4.2376
56 R A -4.6549
57 R A -4.5571
58 Q A -3.6044
59 T A -3.6452
60 N A -3.9809
61 N A -3.3704
62 Q A -2.9974
63 N A -3.3054
64 W A -1.3516
65 G A -1.5955
66 S A -0.7523
67 Q A -0.9798
68 P A 0.0352
69 I A 1.5734
70 A A 0.6554
71 Q A 0.0080
72 Q A -0.3883
73 P A -0.8249
74 L A 0.3995
75 Q A -1.1465
76 G A -1.5399
77 G A -1.7783
78 D A -2.7472
79 H A -2.4031
80 S A -1.7548
81 G A -1.6655
82 N A -1.4717
83 Y A -0.2743
84 G A 0.1530
85 Y A 0.9834
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 partially or entirely disordered. Average score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -2.067 3.2432 View CSV PDB
4.5 -2.0939 3.2432 View CSV PDB
5.0 -2.1218 3.2432 View CSV PDB
5.5 -2.1445 3.2432 View CSV PDB
6.0 -2.1542 3.2432 View CSV PDB
6.5 -2.1473 3.2432 View CSV PDB
7.0 -2.1292 3.2432 View CSV PDB
7.5 -2.1072 3.2432 View CSV PDB
8.0 -2.0833 3.2432 View CSV PDB
8.5 -2.0557 3.2432 View CSV PDB
9.0 -2.0213 3.2432 View CSV PDB