Project name: CD8 VHH

Status: done

Started: 2026-07-20 01:57:53
Chain sequence(s) A: EVQLVESGGGLVQPGGSLRLSCAASGFTFDEYAIGWFRQAPGKEREGVSCLRVSDGRTYYPDSVKGRFTISRDNSKNTVYLQMNSLRAEDTAVYYCASGSYYGCTVDDYDFWGQGTQVTVSSGGGGSGGGGSC
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                                          (00:00:45)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/2d9dd38dadeaebe/tmp/folded.pdb                (00:00:45)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:17)
Show buried residues
Minimal score value
-3.3952
Maximal score value
1.5738
Average score
-0.8308
Total score value
-110.4922
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 E A -1.9797
2 V A -1.1102
3 Q A -0.8853
4 L A 0.0000
5 V A 1.2696
6 E A 0.0000
7 S A -0.4860
8 G A -1.1552
9 G A -0.8324
10 G A -0.1183
11 L A 0.8650
12 V A 0.0000
13 Q A -1.4997
14 P A -1.6885
15 G A -1.4419
16 G A -1.0292
17 S A -1.3703
18 L A -1.0845
19 R A -2.1511
20 L A 0.0000
21 S A -0.3626
22 C A 0.0000
23 A A -0.0843
24 A A 0.0000
25 S A -0.8847
26 G A -1.1148
27 F A -0.8726
28 T A -1.0984
29 F A 0.0000
30 D A -2.9344
31 E A -2.4129
32 Y A -0.7077
33 A A 0.0000
34 I A 0.0000
35 G A 0.0000
36 W A 0.0000
37 F A 0.0000
38 R A 0.0000
39 Q A -1.8965
40 A A -1.8707
41 P A -1.3288
42 G A -1.8907
43 K A -3.2529
44 E A -3.3952
45 R A -2.3527
46 E A -2.0594
47 G A -0.5191
48 V A 0.0000
49 S A 0.0000
50 C A 0.0000
51 L A -0.4633
52 R A -0.8448
53 V A -1.0383
54 S A -1.2505
55 D A -1.8004
56 G A -1.9115
57 R A -2.1915
58 T A -0.8380
59 Y A -0.1943
60 Y A -0.6133
61 P A -1.4347
62 D A -2.5051
63 S A -1.7619
64 V A 0.0000
65 K A -2.5778
66 G A -1.7956
67 R A -1.5624
68 F A 0.0000
69 T A -0.7808
70 I A 0.0000
71 S A -0.5575
72 R A -1.4983
73 D A -2.2065
74 N A -2.8695
75 S A -2.0063
76 K A -2.6937
77 N A -2.3739
78 T A 0.0000
79 V A 0.0000
80 Y A -0.6261
81 L A 0.0000
82 Q A -1.2637
83 M A 0.0000
84 N A -1.5533
85 S A -1.2779
86 L A 0.0000
87 R A -2.3669
88 A A -1.7481
89 E A -2.2517
90 D A 0.0000
91 T A -0.8804
92 A A 0.0000
93 V A -0.4290
94 Y A 0.0000
95 Y A -0.1460
96 C A 0.0000
97 A A 0.0000
98 S A 0.0000
99 G A 0.0000
100 S A 0.1795
101 Y A 1.1379
102 Y A 1.5738
103 G A 0.7003
104 C A 0.3232
105 T A -0.3315
106 V A -0.8816
107 D A -1.7845
108 D A -0.6830
109 Y A 0.0000
110 D A -1.6077
111 F A -0.3533
112 W A 0.0308
113 G A 0.0775
114 Q A -0.7860
115 G A 0.0000
116 T A -0.6513
117 Q A -1.0052
118 V A 0.0000
119 T A -0.3576
120 V A 0.0000
121 S A -0.9855
122 S A -1.1352
123 G A -1.0912
124 G A -1.1762
125 G A -1.2255
126 G A -1.2316
127 S A -1.0941
128 G A -1.2032
129 G A -1.2108
130 G A -1.0565
131 G A -0.7995
132 S A -0.2675
133 C A 0.4524
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 -0.6008 1.6027 View CSV PDB
4.5 -0.6635 1.5649 View CSV PDB
5.0 -0.7397 1.4941 View CSV PDB
5.5 -0.8199 1.4538 View CSV PDB
6.0 -0.8927 1.4538 View CSV PDB
6.5 -0.9483 1.4538 View CSV PDB
7.0 -0.9842 1.4538 View CSV PDB
7.5 -1.0052 1.4538 View CSV PDB
8.0 -1.0166 1.4538 View CSV PDB
8.5 -1.0193 1.4538 View CSV PDB
9.0 -1.013 1.4538 View CSV PDB