Project name: parental VHH

Status: done

Started: 2025-04-01 13:02:59
Chain sequence(s) A: QVQLVESGGGLVQPGGSLRLSCAASGGSEYSYSTFSLGWFRQAPGQGLEAVAAIASMGGLTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAAVRGYFMRLPSSHNFRYWGQGTLVTVS
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 globular. Max score is recommended for pH analysis.  (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:11)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/899ddf1e45c85a5/tmp/folded.pdb                (00:01:11)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:58)
Show buried residues
Minimal score value
-2.5929
Maximal score value
1.6205
Average score
-0.6099
Total score value
-77.4554
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 Q A -1.5509
2 V A -1.3151
3 Q A -1.3700
4 L A 0.0000
5 V A 0.6817
6 E A 0.0000
7 S A -0.3384
8 G A -0.7355
9 G A 0.0637
10 G A 0.8532
11 L A 1.3626
12 V A -0.0461
13 Q A -1.2938
14 P A -1.6163
15 G A -1.4049
16 G A -1.1086
17 S A -1.3363
18 L A -1.1632
19 R A -2.3599
20 L A 0.0000
21 S A -0.6255
22 C A 0.0000
23 A A -0.3122
24 A A -0.5603
25 S A -1.0336
26 G A -1.4112
27 G A -1.3441
28 S A -1.2529
29 E A -1.7761
30 Y A -0.8986
31 S A -0.7556
32 Y A -1.0925
33 S A -0.6025
34 T A -0.1473
35 F A 0.0000
36 S A 0.0000
37 L A 0.0000
38 G A 0.0000
39 W A 0.0000
40 F A 0.0000
41 R A 0.0000
42 Q A -0.7684
43 A A -1.0534
44 P A -1.1205
45 G A -1.3585
46 Q A -1.8422
47 G A -1.2170
48 L A -0.3346
49 E A -0.9751
50 A A -0.4663
51 V A 0.0000
52 A A 0.0000
53 A A 0.0000
54 I A 0.0000
55 A A 0.0000
56 S A 0.0000
57 M A 1.0633
58 G A 0.3341
59 G A 0.3134
60 L A 0.8778
61 T A 0.2856
62 Y A -0.2454
63 Y A -1.0164
64 A A -1.3783
65 D A -2.3548
66 S A -1.8397
67 V A 0.0000
68 K A -2.5215
69 G A -1.7288
70 R A -1.4050
71 F A 0.0000
72 T A -1.0139
73 I A 0.0000
74 S A -0.6492
75 R A -1.2981
76 D A -1.9306
77 N A -2.1689
78 S A -1.8441
79 K A -2.5929
80 N A -2.0200
81 T A 0.0000
82 L A 0.0000
83 Y A 0.0000
84 L A 0.0000
85 Q A -1.7566
86 M A 0.0000
87 N A -1.4644
88 S A -1.1722
89 L A 0.0000
90 R A -2.3135
91 A A -1.7308
92 E A -2.2803
93 D A 0.0000
94 T A -0.4502
95 A A 0.0000
96 V A 0.7949
97 Y A 0.0000
98 Y A 0.3102
99 C A 0.0000
100 A A 0.0000
101 A A 0.0000
102 V A -1.2383
103 R A -1.9150
104 G A -0.6120
105 Y A 0.9529
106 F A 0.0000
107 M A 0.6713
108 R A -0.8652
109 L A -0.5289
110 P A 0.0000
111 S A -0.8768
112 S A -1.0196
113 H A -1.7074
114 N A -1.6108
115 F A 0.0000
116 R A -2.3281
117 Y A 0.0000
118 W A -0.3187
119 G A -0.2497
120 Q A -0.9414
121 G A 0.0157
122 T A 0.5248
123 L A 1.6205
124 V A 0.0000
125 T A 0.3702
126 V A 0.0000
127 S A -0.5764
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 -0.6939 2.1525 View CSV PDB
4.5 -0.722 2.1525 View CSV PDB
5.0 -0.7527 2.1525 View CSV PDB
5.5 -0.7797 2.1525 View CSV PDB
6.0 -0.7983 2.1525 View CSV PDB
6.5 -0.8061 2.1525 View CSV PDB
7.0 -0.8043 2.1525 View CSV PDB
7.5 -0.7961 2.1525 View CSV PDB
8.0 -0.7836 2.1525 View CSV PDB
8.5 -0.7673 2.1525 View CSV PDB
9.0 -0.7477 2.1525 View CSV PDB