Project name: VHL_AlphaFoldDB

Status: done

Started: 2026-01-26 11:27:11
Chain sequence(s) A: MPRRAENWDEAEVGAEEAGVEEYGPEEDGGEESGAEESGPEESGPEELGAEEEMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD
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]                                                (00:00:03)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:03)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:03)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:03)
[INFO]       PDB-Info: The input structure is partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:03)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:03)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:43)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/ad4a1dfd5428b15/tmp/folded.pdb                (00:03:43)
[INFO]       Main:     Simulation completed successfully.                                          (00:07:01)
Show buried residues
Minimal score value
-3.8457
Maximal score value
1.9507
Average score
-1.2293
Total score value
-261.8404
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 0.3191
2 P A -1.0626
3 R A -2.7978
4 R A -3.2195
5 A A -2.3340
6 E A -2.9279
7 N A -2.4144
8 W A -1.2022
9 D A -2.8097
10 E A -2.7148
11 A A -1.5708
12 E A -1.6264
13 V A 0.5040
14 G A -0.6784
15 A A -1.3122
16 E A -2.8307
17 E A -2.6189
18 A A -1.2403
19 G A -0.8349
20 V A 0.1405
21 E A -1.6608
22 E A -1.7975
23 Y A -0.3436
24 G A -1.2429
25 P A -1.9101
26 E A -3.2244
27 E A -3.8457
28 D A -3.6717
29 G A -2.6002
30 G A -2.6680
31 E A -3.3295
32 E A -3.1021
33 S A -2.0127
34 G A -1.5962
35 A A -1.7270
36 E A -2.9146
37 E A -2.9533
38 S A -2.0369
39 G A -1.8987
40 P A -2.0938
41 E A -3.0609
42 E A -3.0703
43 S A -1.9184
44 G A -1.7783
45 P A -1.8535
46 E A -2.5825
47 E A -2.1199
48 L A -0.3607
49 G A -1.3399
50 A A -1.8761
51 E A -3.0594
52 E A -3.6686
53 E A -3.1651
54 M A -1.5287
55 E A -2.7956
56 A A -1.5274
57 G A -1.8709
58 R A -2.9599
59 P A -2.0583
60 R A -2.8943
61 P A -1.6186
62 V A -0.6374
63 L A 0.0000
64 R A -0.9697
65 S A 0.0000
66 V A 0.7490
67 N A -1.0014
68 S A -1.4360
69 R A -2.4456
70 E A -1.5829
71 P A -1.2062
72 S A 0.0000
73 Q A -0.9679
74 V A 0.0000
75 I A -0.4628
76 F A 0.0000
77 C A -1.0651
78 N A 0.0000
79 R A -2.1940
80 S A 0.0000
81 P A -0.6593
82 R A -0.2639
83 V A 0.6254
84 V A 0.0000
85 L A 0.1875
86 P A 0.0000
87 V A 0.0000
88 W A -0.3277
89 L A 0.0000
90 N A -0.9554
91 F A -0.3447
92 D A -2.1588
93 G A -1.8331
94 E A -2.6731
95 P A -1.6152
96 Q A -1.0856
97 P A -0.4990
98 Y A 0.1375
99 P A -0.0581
100 T A 0.0965
101 L A 0.0000
102 P A -0.3938
103 P A -0.7873
104 G A -1.2566
105 T A -0.9479
106 G A -1.3983
107 R A -1.6399
108 R A -2.1436
109 I A -1.3006
110 H A -1.3188
111 S A 0.0000
112 Y A -0.7195
113 R A -0.8319
114 G A 0.0828
115 H A 0.0000
116 L A 0.0000
117 W A 0.0000
118 L A 0.0000
119 F A 0.0000
120 R A 0.0000
121 D A -0.1819
122 A A -0.1582
123 G A -0.4632
124 T A -0.6921
125 H A -0.9417
126 D A 0.0000
127 G A -0.4075
128 L A 0.0000
129 L A -0.2540
130 V A 0.0000
131 N A -1.2829
132 Q A -1.5794
133 T A -0.9980
134 E A -0.7792
135 L A 0.1343
136 F A 0.0000
137 V A 1.5514
138 P A 0.0000
139 S A 0.6232
140 L A 0.8752
141 N A 0.0680
142 V A 0.6347
143 D A -1.4603
144 G A -1.2759
145 Q A -1.2714
146 P A -0.4575
147 I A 0.7604
148 F A 0.6230
149 A A 0.0000
150 N A -0.8393
151 I A 0.0000
152 T A -0.6197
153 L A 0.4350
154 P A 0.9061
155 V A 1.9507
156 Y A 0.6688
157 T A 0.0703
158 L A 0.4216
159 K A -1.6300
160 E A -1.4894
161 R A -0.8844
162 C A -0.2211
163 L A 0.0000
164 Q A 0.0000
165 V A 0.8989
166 V A 0.8523
167 R A 0.0308
168 S A 0.5493
169 L A 1.4283
170 V A -0.2807
171 K A -2.0559
172 P A -2.4752
173 E A -3.3445
174 N A -2.9533
175 Y A 0.0000
176 R A -3.7342
177 R A -3.3217
178 L A -1.7308
179 D A -1.9771
180 I A -0.2961
181 V A 0.4862
182 R A -1.7522
183 S A -1.0124
184 L A -1.1023
185 Y A 0.0000
186 E A -3.2367
187 D A -2.7626
188 L A 0.0000
189 E A -3.0213
190 D A -3.1633
191 H A -2.4030
192 P A -1.9565
193 N A -2.3064
194 V A 0.0000
195 Q A -2.9418
196 K A -3.3555
197 D A -2.6657
198 L A 0.0000
199 E A -3.6489
200 R A -3.1804
201 L A -2.3232
202 T A -2.3079
203 Q A -2.9465
204 E A -3.2049
205 R A -3.3938
206 I A -1.7243
207 A A -2.1186
208 H A -2.9634
209 Q A -3.2288
210 R A -2.9039
211 M A -1.1858
212 G A -2.0446
213 D A -2.6263
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 -0.696 2.8081 View CSV PDB
4.5 -0.8153 2.5085 View CSV PDB
5.0 -0.9757 2.4993 View CSV PDB
5.5 -1.15 2.4993 View CSV PDB
6.0 -1.3122 2.4993 View CSV PDB
6.5 -1.442 2.4993 View CSV PDB
7.0 -1.5278 2.4993 View CSV PDB
7.5 -1.5762 2.4993 View CSV PDB
8.0 -1.603 2.4992 View CSV PDB
8.5 -1.6179 2.4988 View CSV PDB
9.0 -1.6226 2.4978 View CSV PDB