Project name: VL_AL55

Status: done

Started: 2025-05-05 05:09:09
Chain sequence(s) A: NFMLTQPHSVSESPGKTLTISCTGSSASIASHYVQWYQQRRPGGAPTTLIYENDQRPSEVPDRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDGNNHWVFGGGTKLTVL
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                                          (00:00:43)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/48cb81b57744eb1/tmp/folded.pdb                (00:00:43)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:13)
Show buried residues
Minimal score value
-2.674
Maximal score value
1.805
Average score
-0.7235
Total score value
-80.3051
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 -1.2664
2 F A 0.0000
3 M A 0.8007
4 L A 0.0000
5 T A 0.0290
6 Q A -0.5195
7 P A -0.9102
8 H A -1.5340
9 S A -1.0744
10 V A -0.3593
11 S A -0.2518
12 E A -0.7226
13 S A -0.5949
14 P A -1.2967
15 G A -1.7322
16 K A -2.1564
17 T A -1.2940
18 L A 0.0000
19 T A -0.1636
20 I A 0.0000
21 S A -0.2208
22 C A 0.0000
23 T A -0.2787
24 G A 0.0000
25 S A -0.2630
26 S A -0.6099
27 A A -0.5114
28 S A -0.5479
29 I A 0.0000
30 A A -0.1749
31 S A -0.2153
32 H A -0.2690
33 Y A 0.4670
34 V A 0.0000
35 Q A 0.0000
36 W A 0.0000
37 Y A -0.0630
38 Q A -0.7670
39 Q A -1.5323
40 R A -2.2546
41 P A -1.4439
42 G A -1.2017
43 G A -1.0993
44 A A -0.6831
45 P A -0.8092
46 T A -0.4108
47 T A -0.2092
48 L A 0.0000
49 I A 0.0000
50 Y A -0.6669
51 E A -1.2772
52 N A -1.2883
53 D A -2.3698
54 Q A -2.2264
55 R A -2.2091
56 P A -1.4575
57 S A -1.5955
58 E A -2.2031
59 V A -1.5070
60 P A -1.6446
61 D A -2.3850
62 R A -1.3033
63 F A 0.0000
64 S A -1.3527
65 G A -1.1966
66 S A -1.0603
67 I A -0.5118
68 D A -1.2561
69 S A -0.9521
70 S A -0.8074
71 S A -0.7693
72 N A -0.8355
73 S A 0.0000
74 A A 0.0000
75 S A -0.4959
76 L A 0.0000
77 T A -0.2325
78 I A 0.0000
79 S A -1.2913
80 G A -1.5318
81 L A 0.0000
82 K A -2.3884
83 T A -1.6420
84 E A -2.6740
85 D A 0.0000
86 E A -2.1490
87 A A 0.0000
88 D A -1.7997
89 Y A 0.0000
90 Y A 0.1739
91 C A 0.0000
92 Q A 0.0000
93 S A 0.0000
94 Y A -0.1217
95 D A -1.3266
96 G A -1.9309
97 N A -2.3151
98 N A -2.2772
99 H A -1.5147
100 W A 0.5481
101 V A 0.0000
102 F A 1.8050
103 G A 0.0000
104 G A -0.3988
105 G A -0.6808
106 T A 0.0000
107 K A -1.8665
108 L A 0.0000
109 T A -0.3671
110 V A 0.0000
111 L A 1.1917
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 -0.5018 4.1979 View CSV PDB
4.5 -0.5604 4.1908 View CSV PDB
5.0 -0.6294 4.1836 View CSV PDB
5.5 -0.698 4.1763 View CSV PDB
6.0 -0.7546 4.169 View CSV PDB
6.5 -0.7929 4.1618 View CSV PDB
7.0 -0.8154 4.1548 View CSV PDB
7.5 -0.8288 4.1484 View CSV PDB
8.0 -0.836 4.1432 View CSV PDB
8.5 -0.8356 4.1399 View CSV PDB
9.0 -0.8265 4.1383 View CSV PDB