Project name: Vg-vWF

Status: done

Started: 2025-04-29 12:32:32
Chain sequence(s) A: NNVFYEDETSCMLDKTRAQTFDGKDYPLRLGPCWHAVMTTYPRINPDNHNEKLHIPKDKSVSVLSRENEAGQKEVKVLLGSDKIKFVPGTTSQPEVFVNGEKIVVSRNKAYQKVEENEIIFEIYKMGDRFIGLTSDKFDVSLALDGERVMLKASEDYRYSVRGLCGNFDHDSTNDFVGPKNCLFRKPEHFVASYALISNQCEGDS
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]                                                (00:00:10)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:10)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:10)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:10)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:10)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:10)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:32)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/3e4a598c959fa3d/tmp/folded.pdb                (00:03:32)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:20)
Show buried residues
Minimal score value
-3.7386
Maximal score value
1.9225
Average score
-1.0706
Total score value
-219.4818
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 N A -1.1759
2 N A -0.2764
3 V A 1.9225
4 F A 1.8693
5 Y A 0.6778
6 E A -1.7671
7 D A -3.0216
8 E A -2.9934
9 T A -2.1771
10 S A -1.0738
11 C A 0.0000
12 M A -0.9139
13 L A 0.0000
14 D A -2.3840
15 K A -3.1673
16 T A -2.5779
17 R A -3.4095
18 A A 0.0000
19 Q A -1.9292
20 T A 0.0000
21 F A 0.0000
22 D A -1.4975
23 G A -1.4877
24 K A -1.7714
25 D A -2.7225
26 Y A 0.0000
27 P A -2.4141
28 L A 0.0000
29 R A -2.9494
30 L A 0.0000
31 G A -1.6349
32 P A -1.4765
33 C A 0.0000
34 W A 0.5376
35 H A 0.0000
36 A A 0.0000
37 V A 0.0000
38 M A 0.0000
39 T A -0.0254
40 T A -0.0528
41 Y A -0.0890
42 P A -0.8201
43 R A -1.2429
44 I A -2.0078
45 N A -2.6526
46 P A -2.2279
47 D A -2.9655
48 N A -3.4395
49 H A -3.2977
50 N A -3.2514
51 E A -3.7386
52 K A -3.0323
53 L A -1.3556
54 H A -1.3861
55 I A -0.9075
56 P A -1.4978
57 K A -2.6828
58 D A -2.9467
59 K A -2.2257
60 S A -1.1980
61 V A 0.0000
62 S A -0.0762
63 V A 0.0000
64 L A 0.1061
65 S A 0.0000
66 R A -0.7365
67 E A 0.0000
68 N A -1.3644
69 E A -2.0702
70 A A -1.0929
71 G A -1.7162
72 Q A -1.5013
73 K A 0.0000
74 E A 0.0000
75 V A 0.0000
76 K A -0.4473
77 V A 0.0000
78 L A -0.2693
79 L A 0.0000
80 G A -1.4125
81 S A -1.0227
82 D A 0.0000
83 K A -1.4626
84 I A 0.0000
85 K A -1.3375
86 F A 0.0000
87 V A -0.1886
88 P A -0.4473
89 G A -0.5286
90 T A -0.3454
91 T A -0.5305
92 S A -1.3136
93 Q A -1.3269
94 P A -0.8794
95 E A -0.7612
96 V A 0.0000
97 F A -1.6624
98 V A 0.0000
99 N A -2.5273
100 G A -2.4671
101 E A -3.2677
102 K A -2.5288
103 I A 0.0000
104 V A 1.0470
105 V A 0.0000
106 S A -1.8763
107 R A -3.3116
108 N A -2.9995
109 K A -2.5541
110 A A -1.2895
111 Y A -0.2646
112 Q A -1.1514
113 K A -0.7284
114 V A -1.0434
115 E A -2.8455
116 E A -3.3699
117 N A -3.0315
118 E A -3.2069
119 I A -1.3500
120 I A 0.0000
121 F A 0.0000
122 E A -0.6515
123 I A 0.0000
124 Y A -0.5675
125 K A -1.6715
126 M A -0.9034
127 G A -1.8876
128 D A -3.0548
129 R A -2.4529
130 F A -0.9367
131 I A 0.0000
132 G A 0.0000
133 L A 0.0000
134 T A -1.0525
135 S A 0.0000
136 D A -3.0446
137 K A -2.9819
138 F A 0.0000
139 D A -3.4102
140 V A 0.0000
141 S A -0.8874
142 L A 0.0000
143 A A 0.0710
144 L A 0.0000
145 D A 0.0000
146 G A 0.0000
147 E A -1.8968
148 R A -1.7862
149 V A 0.0000
150 M A -0.0846
151 L A 0.0000
152 K A -1.4829
153 A A 0.0000
154 S A -3.0715
155 E A -3.6195
156 D A -3.0605
157 Y A 0.0000
158 R A -1.6966
159 Y A -0.0328
160 S A 0.0000
161 V A 0.0000
162 R A -0.3287
163 G A 0.0000
164 L A 0.0000
165 C A 0.0000
166 G A 0.0000
167 N A 0.0000
168 F A 0.0000
169 D A -1.1604
170 H A -1.6720
171 D A -1.6536
172 S A -1.4510
173 T A -0.6009
174 N A -0.6083
175 D A 0.0000
176 F A 0.0000
177 V A 0.0000
178 G A 0.0000
179 P A -1.1434
180 K A -2.0618
181 N A -1.4695
182 C A -0.2872
183 L A 0.4642
184 F A -0.9989
185 R A -2.6176
186 K A -3.2403
187 P A -2.6622
188 E A -3.3669
189 H A -2.5334
190 F A 0.0000
191 V A 0.0000
192 A A -0.9421
193 S A -0.4157
194 Y A 0.0000
195 A A 0.9042
196 L A 1.5638
197 I A 1.4555
198 S A -0.3392
199 N A -1.8636
200 Q A -1.9985
201 C A 0.0000
202 E A -2.5020
203 G A -1.8134
204 D A -2.4623
205 S A -1.5022
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 globular. Max score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -0.9435 4.916 View CSV PDB
4.5 -1.0335 4.7389 View CSV PDB
5.0 -1.1421 4.5046 View CSV PDB
5.5 -1.2497 4.2478 View CSV PDB
6.0 -1.3356 4.002 View CSV PDB
6.5 -1.3863 3.7977 View CSV PDB
7.0 -1.403 3.651 View CSV PDB
7.5 -1.3973 3.5506 View CSV PDB
8.0 -1.3782 3.4751 View CSV PDB
8.5 -1.3477 3.4129 View CSV PDB
9.0 -1.304 3.3633 View CSV PDB