Project name: 3me

Status: done

Started: 2026-05-10 14:50:34
Chain sequence(s) A: SAADEMEQVKQAVEDLKSTDENVVLNAIDTLKNLALTSSDATVQDYAVTALSLTAIKGTGNVKAAAIAALKEISEKAANADVRKQASMAYKVASQIQAEA
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                                          (00:02:07)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/10c46194a1d45f0/tmp/folded.pdb                (00:02:07)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:57)
Show buried residues
Minimal score value
-3.4473
Maximal score value
0.7365
Average score
-1.1347
Total score value
-113.4712
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 -1.1076
2 A A -1.1281
3 A A -1.4679
4 D A -2.7958
5 E A -2.2402
6 M A -1.9699
7 E A -3.3705
8 Q A -2.8362
9 V A 0.0000
10 K A -2.9489
11 Q A -2.9982
12 A A 0.0000
13 V A -1.8394
14 E A -3.0422
15 D A -2.2979
16 L A -1.8224
17 K A -2.5395
18 S A -2.0255
19 T A -1.6983
20 D A -2.5955
21 E A -3.2302
22 N A -2.3928
23 V A -1.6607
24 V A 0.0000
25 L A -1.7165
26 N A -2.0717
27 A A 0.0000
28 I A 0.0000
29 D A -2.2503
30 T A -1.6595
31 L A 0.0000
32 K A -1.5024
33 N A -1.5785
34 L A -0.8820
35 A A 0.0000
36 L A -0.9095
37 T A -0.4844
38 S A 0.0000
39 S A -0.4377
40 D A -0.6932
41 A A -0.7779
42 T A -0.4611
43 V A 0.0000
44 Q A 0.0000
45 D A -1.4410
46 Y A -0.1302
47 A A 0.0000
48 V A 0.0000
49 T A 0.0287
50 A A 0.0000
51 L A 0.0000
52 S A 0.6743
53 L A 0.7365
54 T A 0.0000
55 A A 0.0000
56 I A 0.4801
57 K A -1.0930
58 G A -0.7765
59 T A -0.9906
60 G A -1.1812
61 N A -1.6364
62 V A -1.1960
63 K A -0.6916
64 A A -0.5755
65 A A -0.7121
66 A A 0.0000
67 I A -0.3151
68 A A -0.3487
69 A A 0.0000
70 L A 0.0000
71 K A -2.1439
72 E A -2.3641
73 I A 0.0000
74 S A -2.8588
75 E A -3.4473
76 K A -3.0028
77 A A 0.0000
78 A A -1.0864
79 N A -1.5901
80 A A -1.8968
81 D A -2.9551
82 V A 0.0000
83 R A -3.1221
84 K A -2.7799
85 Q A -1.6899
86 A A 0.0000
87 S A -1.5105
88 M A -0.0627
89 A A 0.0000
90 Y A -0.5739
91 K A -1.2587
92 V A 0.0730
93 A A 0.0000
94 S A -0.9858
95 Q A -1.6262
96 I A -0.5141
97 Q A -1.2302
98 A A -1.2422
99 E A -2.0057
100 A A -0.9963
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 -0.8478 0.5583 View CSV PDB
4.5 -0.9603 0.5556 View CSV PDB
5.0 -1.0967 0.5597 View CSV PDB
5.5 -1.2338 0.5713 View CSV PDB
6.0 -1.3446 0.5984 View CSV PDB
6.5 -1.4085 0.6708 View CSV PDB
7.0 -1.4238 0.7935 View CSV PDB
7.5 -1.4047 0.9313 View CSV PDB
8.0 -1.365 1.0746 View CSV PDB
8.5 -1.3088 1.2903 View CSV PDB
9.0 -1.235 1.5425 View CSV PDB