Project name: a3d_pea_WT [mutate: VT83A]

Status: done

Started: 2026-08-15 09:56:06
Chain sequence(s) A: MGFTEKQEALVNSSWELFKQNPSYSVLFYTIILKKAPAAKGMFSFLKDSAEVVDSPKLQAHAEKVFGMVHDSAIQLRASGEVVLGDATLGAIHIQKGVVDPHFVVVKEALLETIKEASGEKWSEELSTAWEVAYEGLASAIKKAMN
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage Used: no changes made
Dynamic mode No
Automated mutations No
Mutated residues VT83A
Energy difference between WT (input) and mutated protein (by FoldX) 0.00559008 kcal/mol
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:      Running AlphaCutter                                                         (00:00:01)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:08)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:08)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:09)
[INFO]       FoldX:    Building mutant model                                                       (00:03:03)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:07)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/5b8a9d05e81a194/tmp/folded.pdb                (00:03:07)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:24)
Show buried residues
Minimal score value
-3.6158
Maximal score value
1.0515
Average score
-0.9969
Total score value
-145.5529
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 M A 0.8144
2 G A -0.6071
3 F A -1.0991
4 T A -1.7195
5 E A -2.9566
6 K A -2.9724
7 Q A 0.0000
8 E A -1.7805
9 A A -1.1582
10 L A -1.1701
11 V A 0.0000
12 N A -1.1412
13 S A -1.0291
14 S A 0.0000
15 W A 0.0000
16 E A -2.6647
17 L A -1.8519
18 F A 0.0000
19 K A -2.9731
20 Q A -2.5459
21 N A -1.8619
22 P A -1.5434
23 S A -0.7794
24 Y A -0.8871
25 S A 0.0000
26 V A -0.0663
27 L A -0.0904
28 F A 0.0000
29 Y A 0.0000
30 T A -0.4545
31 I A -0.9549
32 I A 0.0000
33 L A -1.3461
34 K A -2.2939
35 K A -2.2016
36 A A -1.2195
37 P A -1.1195
38 A A -0.5911
39 A A 0.0000
40 K A -1.5006
41 G A -1.4819
42 M A -1.0053
43 F A 0.0000
44 S A -1.3699
45 F A -1.3391
46 L A 0.0000
47 K A -2.9459
48 D A -2.9046
49 S A -1.7045
50 A A -1.3762
51 E A -2.0689
52 V A -0.8860
53 V A -0.4036
54 D A -1.8196
55 S A -1.3746
56 P A -1.5935
57 K A -2.3209
58 L A 0.0000
59 Q A -2.0316
60 A A -1.6458
61 H A -1.5917
62 A A 0.0000
63 E A -2.2462
64 K A -1.8906
65 V A -0.7667
66 F A 0.0000
67 G A -1.3583
68 M A -0.8670
69 V A 0.0000
70 H A -0.9455
71 D A -1.4753
72 S A 0.0000
73 A A 0.0000
74 I A -1.1015
75 Q A -1.3893
76 L A -1.5289
77 R A -2.5497
78 A A -1.2960
79 S A -1.3720
80 G A -1.7207
81 E A -2.2623
82 V A -1.4027
83 T A -0.7415 mutated: VT83A
84 L A -0.3773
85 G A -0.6977
86 D A -0.8927
87 A A -0.2434
88 T A 0.0099
89 L A 0.0000
90 G A 0.0000
91 A A 0.5051
92 I A 0.8985
93 H A 0.5097
94 I A 0.9237
95 Q A -0.6208
96 K A -0.9429
97 G A -0.2981
98 V A 0.0349
99 V A 0.2720
100 D A -1.1699
101 P A -0.2024
102 H A -0.0560
103 F A 0.0000
104 V A 1.0515
105 V A 0.0421
106 V A 0.2151
107 K A -0.4972
108 E A -1.0223
109 A A 0.0000
110 L A 0.0000
111 L A -1.7431
112 E A -2.8288
113 T A 0.0000
114 I A 0.0000
115 K A -3.6158
116 E A -3.3359
117 A A 0.0000
118 S A 0.0000
119 G A -2.6702
120 E A -3.1551
121 K A -2.9528
122 W A -2.5575
123 S A -2.3180
124 E A -2.8237
125 E A -2.9069
126 L A 0.0000
127 S A -1.7366
128 T A -1.1743
129 A A 0.0000
130 W A 0.0000
131 E A -1.1111
132 V A -0.1153
133 A A 0.0000
134 Y A 0.0000
135 E A -1.4953
136 G A -1.1751
137 L A 0.0000
138 A A 0.0000
139 S A -1.2200
140 A A 0.0000
141 I A 0.0000
142 K A -1.7390
143 K A -2.3716
144 A A -1.1144
145 M A -0.6525
146 N A -1.6387
Download PDB file
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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 -0.7301 2.3127 View CSV PDB
4.5 -0.8241 2.1558 View CSV PDB
5.0 -0.9417 1.9852 View CSV PDB
5.5 -1.0605 1.8619 View CSV PDB
6.0 -1.1534 1.9075 View CSV PDB
6.5 -1.1962 1.9905 View CSV PDB
7.0 -1.1838 2.0987 View CSV PDB
7.5 -1.132 2.2183 View CSV PDB
8.0 -1.0589 2.3422 View CSV PDB
8.5 -0.973 2.4672 View CSV PDB
9.0 -0.8764 2.5914 View CSV PDB