Project name: a3d_pea_WT [mutate: VT53A]

Status: done

Started: 2026-08-15 09:52:21
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 VT53A
Energy difference between WT (input) and mutated protein (by FoldX) 0.147518 kcal/mol
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       PDB:      Running AlphaCutter                                                         (00:00:02)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:13)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:13)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:13)
[INFO]       FoldX:    Building mutant model                                                       (00:02:58)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:02)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/af0831e45dc6010/tmp/folded.pdb                (00:03:02)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:29)
Show buried residues
Minimal score value
-3.6158
Maximal score value
1.1027
Average score
-0.9697
Total score value
-141.5708
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 -1.0986
4 T A -1.7195
5 E A -2.9566
6 K A -2.9724
7 Q A 0.0000
8 E A -1.7800
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 -1.5207
23 S A -0.8404
24 Y A -0.8723
25 S A 0.0000
26 V A -0.2158
27 L A -0.0748
28 F A 0.0000
29 Y A 0.0000
30 T A -0.5569
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 -1.5005
41 G A -1.4816
42 M A -1.0049
43 F A 0.0000
44 S A -1.3685
45 F A -1.4317
46 L A 0.0000
47 K A -2.9459
48 D A -2.9055
49 S A -1.8914
50 A A -1.5051
51 E A -2.2992
52 V A -1.2650
53 T A -1.1823 mutated: VT53A
54 D A -2.0927
55 S A -1.5234
56 P A -1.5647
57 K A -2.3001
58 L A 0.0000
59 Q A -2.0034
60 A A -1.6461
61 H A -1.5914
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 -0.8665
69 V A 0.0000
70 H A -0.9449
71 D A -1.2813
72 S A 0.0000
73 A A 0.0000
74 I A -1.1000
75 Q A -1.0590
76 L A -1.3161
77 R A -2.5487
78 A A -1.2949
79 S A -1.1748
80 G A -1.7205
81 E A -1.8222
82 V A -0.5079
83 V A 1.1027
84 L A 0.5216
85 G A -0.2294
86 D A -0.6458
87 A A -0.0177
88 T A 0.0103
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 -1.4957
136 G A -0.9426
137 L A 0.0000
138 A A 0.0000
139 S A -1.0310
140 A A 0.0000
141 I A 0.0000
142 K A -1.7390
143 K A -2.3716
144 A A -1.1139
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 -0.7191 2.3194 View CSV PDB
4.5 -0.8129 2.1635 View CSV PDB
5.0 -0.9298 1.9933 View CSV PDB
5.5 -1.0478 1.8623 View CSV PDB
6.0 -1.1397 1.9076 View CSV PDB
6.5 -1.1813 1.99 View CSV PDB
7.0 -1.1678 2.098 View CSV PDB
7.5 -1.115 2.2175 View CSV PDB
8.0 -1.0406 2.3413 View CSV PDB
8.5 -0.9531 2.4663 View CSV PDB
9.0 -0.8547 2.5906 View CSV PDB