Project name: a-syn

Status: done

Started: 2025-05-13 19:14:44
Chain sequence(s) A: MDVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGAGSIAAATGFVKKDQLGKNEEGAPQEGILEDMPVDPDNEAYEMPSEEGYQDYEPEA
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 partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:04)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/36d3fbc3d76a127/tmp/folded.pdb                (00:03:04)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:08)
Show buried residues
Minimal score value
-3.8897
Maximal score value
3.399
Average score
-0.7165
Total score value
-100.3119
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 1.1630
2 D A -0.0547
3 V A 1.7106
4 F A 2.0976
5 M A 0.6940
6 K A -1.2084
7 G A -0.8376
8 L A -0.7368
9 S A -1.7874
10 K A -2.7396
11 A A -1.7230
12 K A -2.2591
13 E A -2.1993
14 G A -0.9243
15 V A 0.6465
16 V A 0.5228
17 A A -0.6960
18 A A -0.8159
19 A A -1.1466
20 E A -2.7156
21 K A -2.9009
22 T A -2.2771
23 K A -3.2343
24 Q A -3.1775
25 G A -1.9252
26 V A -0.4788
27 A A -1.3783
28 E A -2.5286
29 A A -1.5479
30 A A -1.3778
31 G A -2.0414
32 K A -2.5826
33 T A -1.4594
34 K A -1.4803
35 E A -0.9339
36 G A 0.3905
37 V A 1.9671
38 L A 1.8763
39 Y A 1.9799
40 V A 1.8163
41 G A 0.7551
42 S A -0.3854
43 K A -1.3309
44 T A -0.9791
45 K A -1.7169
46 E A -2.1921
47 G A -1.0884
48 V A 0.9788
49 V A 0.7976
50 H A -0.4643
51 G A 0.6695
52 V A 1.9875
53 A A 0.5779
54 T A -0.0487
55 V A 0.6375
56 A A -0.9131
57 E A -3.0711
58 K A -3.0637
59 T A -1.9991
60 K A -3.3794
61 E A -3.8028
62 Q A -2.5082
63 V A -0.3041
64 T A -1.1056
65 N A -1.0309
66 V A 1.0762
67 G A 1.0079
68 G A 1.0482
69 A A 1.7487
70 V A 3.3990
71 V A 3.2276
72 T A 2.0904
73 G A 2.3575
74 V A 3.0692
75 T A 1.5736
76 A A 1.0306
77 V A 1.8869
78 A A 0.6136
79 Q A -0.6995
80 K A -1.4706
81 T A -0.2440
82 V A 0.3882
83 E A -1.5715
84 G A -0.5743
85 A A 0.1021
86 G A -0.2206
87 S A 0.0585
88 I A 1.9002
89 A A 1.4220
90 A A 1.0702
91 A A 1.0258
92 T A 1.3215
93 G A 0.8752
94 F A 1.8434
95 V A 1.0057
96 K A -1.9007
97 K A -2.5905
98 D A -2.8705
99 Q A -2.3216
100 L A -0.7563
101 G A -1.4346
102 K A -3.0580
103 N A -3.5106
104 E A -3.8897
105 E A -3.3870
106 G A -1.9043
107 A A -0.9173
108 P A -1.2712
109 Q A -2.3803
110 E A -2.3110
111 G A -0.5004
112 I A 1.5422
113 L A 1.2394
114 E A -1.2205
115 D A -1.4479
116 M A 0.0180
117 P A 0.1660
118 V A 0.3800
119 D A -1.8353
120 P A -2.2498
121 D A -3.4591
122 N A -2.9110
123 E A -2.9604
124 A A -1.3421
125 Y A -0.0477
126 E A -0.9806
127 M A 0.0560
128 P A -0.8512
129 S A -1.8878
130 E A -2.7448
131 E A -2.9405
132 G A -1.9113
133 Y A -0.5544
134 Q A -1.9606
135 D A -1.9326
136 Y A -0.8126
137 E A -2.4560
138 P A -1.8999
139 E A -2.2665
140 A A -1.1150
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 -0.2195 4.1024 View CSV PDB
4.5 -0.3623 3.9779 View CSV PDB
5.0 -0.545 3.8551 View CSV PDB
5.5 -0.7247 3.8341 View CSV PDB
6.0 -0.8542 3.8894 View CSV PDB
6.5 -0.8988 4.0137 View CSV PDB
7.0 -0.8568 4.1884 View CSV PDB
7.5 -0.7549 4.3872 View CSV PDB
8.0 -0.6224 4.5959 View CSV PDB
8.5 -0.4745 4.8103 View CSV PDB
9.0 -0.3153 5.0311 View CSV PDB