Project name: a3d_spi_WT

Status: done

Started: 2026-08-15 09:51:10
Chain sequence(s) A: MGTVLETKLETTTTFTQEQEALVVRSWNAIKKNSAELALKFFLKIFEIAPSAQKLFSFLKDSNVPLDQNPKLKPHALSVFLMTCESAVQLRKAGKVTVRESTLKKIGATHFRYGVVDEHFEVTKFALLETIKEAVPEMWSPAMKNAWGEAYDQLVNAIKSEMKPAS
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
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.                                                               (00:00:12)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:12)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:12)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:50)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/a801e433d68d7cb/tmp/folded.pdb                (00:02:50)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:25)
Show buried residues
Minimal score value
-3.3658
Maximal score value
1.9501
Average score
-1.0428
Total score value
-173.0987
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 1.0123
2 G A 0.6754
3 T A 1.0125
4 V A 1.9501
5 L A 1.2070
6 E A -0.8518
7 T A -0.9191
8 K A -1.8224
9 L A -0.4766
10 E A -1.6293
11 T A -0.7879
12 T A -0.5594
13 T A -0.4908
14 T A -0.9905
15 F A 0.0000
16 T A -1.7380
17 Q A -2.4932
18 E A -2.4855
19 Q A -1.7590
20 E A 0.0000
21 A A -1.3724
22 L A -1.2603
23 V A 0.0000
24 V A -1.1284
25 R A -1.9224
26 S A 0.0000
27 W A 0.0000
28 N A -2.2423
29 A A -1.6310
30 I A 0.0000
31 K A -2.5841
32 K A -3.0416
33 N A -2.5414
34 S A -2.0755
35 A A -1.7892
36 E A -2.7681
37 L A 0.0000
38 A A 0.0000
39 L A -1.8504
40 K A -2.2280
41 F A 0.0000
42 F A 0.0000
43 L A -1.0500
44 K A -1.1303
45 I A 0.0000
46 F A 0.0000
47 E A -1.6579
48 I A -0.0181
49 A A -0.6072
50 P A -1.0316
51 S A -0.9674
52 A A 0.0000
53 Q A -1.5063
54 K A -2.1650
55 L A -0.7818
56 F A -0.7130
57 S A -0.8830
58 F A -0.9204
59 L A -1.6569
60 K A -3.0544
61 D A -2.8713
62 S A -1.6191
63 N A -1.4943
64 V A -0.5375
65 P A -0.8909
66 L A -1.1289
67 D A -2.5672
68 Q A -2.1546
69 N A 0.0000
70 P A -1.7302
71 K A -2.3051
72 L A 0.0000
73 K A -2.4922
74 P A -1.4388
75 H A -1.3896
76 A A 0.0000
77 L A -0.2705
78 S A 0.0836
79 V A 0.2510
80 F A 0.0000
81 L A 0.5872
82 M A 0.2504
83 T A 0.0000
84 C A 0.0000
85 E A -1.1656
86 S A 0.0000
87 A A 0.0000
88 V A -1.2510
89 Q A 0.0000
90 L A 0.0000
91 R A -2.5413
92 K A -2.5581
93 A A -1.7520
94 G A -1.9513
95 K A -2.2977
96 V A -1.6614
97 T A -1.4541
98 V A -1.5138
99 R A -2.8355
100 E A -3.3658
101 S A -2.5316
102 T A -2.2128
103 L A -2.3350
104 K A -3.3403
105 K A -2.4990
106 I A -1.4202
107 G A 0.0000
108 A A -1.4919
109 T A -0.9066
110 H A -0.2063
111 F A -0.0465
112 R A -1.1023
113 Y A 0.3355
114 G A 0.3544
115 V A 0.1173
116 V A -0.3043
117 D A -2.6337
118 E A -2.9853
119 H A -1.6756
120 F A 0.0000
121 E A -2.6512
122 V A -1.0687
123 T A -0.7727
124 K A -0.8638
125 F A 0.3714
126 A A 0.0000
127 L A 0.0000
128 L A 0.0000
129 E A -1.2514
130 T A 0.0000
131 I A 0.0000
132 K A -2.0698
133 E A -2.6564
134 A A -1.6163
135 V A 0.0000
136 P A -1.7728
137 E A -2.0306
138 M A -0.8519
139 W A -0.9130
140 S A -0.7467
141 P A -0.8654
142 A A -1.0309
143 M A 0.0000
144 K A -1.7736
145 N A -1.9191
146 A A 0.0000
147 W A 0.0000
148 G A 0.0000
149 E A -1.5026
150 A A 0.0000
151 Y A 0.0000
152 D A -1.8237
153 Q A -1.8411
154 L A 0.0000
155 V A 0.0000
156 N A -2.0387
157 A A -1.6940
158 I A 0.0000
159 K A -1.8208
160 S A -1.4891
161 E A -2.0132
162 M A -1.3737
163 K A -1.7742
164 P A -1.1264
165 A A -1.0044
166 S A -0.4395
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 -1.053 2.4123 View CSV PDB
4.5 -1.1318 2.3196 View CSV PDB
5.0 -1.2287 2.198 View CSV PDB
5.5 -1.3189 2.0679 View CSV PDB
6.0 -1.3751 1.9491 View CSV PDB
6.5 -1.3773 1.8618 View CSV PDB
7.0 -1.3252 1.8142 View CSV PDB
7.5 -1.2357 1.7944 View CSV PDB
8.0 -1.1269 1.7875 View CSV PDB
8.5 -1.0078 1.7852 View CSV PDB
9.0 -0.8815 1.7845 View CSV PDB