Project name: 24A12

Status: done

Started: 2025-05-13 02:40:16
Chain sequence(s) A: VEQDPGPFNVPEGATVAFNCTYSNSASQSFFWYRQDCRKEPKLLMSVYSSGNEDGRFTAQLNRASQYISLLIRDSKLSDSATYLCVVQPGGYQKVTFGTGTKLQV
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                                          (00:01:31)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/c6774c878ed7b16/tmp/folded.pdb                (00:01:31)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:11)
Show buried residues
Minimal score value
-3.1397
Maximal score value
1.3223
Average score
-0.7089
Total score value
-74.4378
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 V A -0.1477
2 E A -1.5995
3 Q A -1.1444
4 D A -1.3361
5 P A -1.1564
6 G A -1.3171
7 P A -1.3193
8 F A -0.9279
9 N A -1.5563
10 V A -0.7294
11 P A -1.2883
12 E A -2.2778
13 G A -2.1679
14 A A -1.6623
15 T A -1.1261
16 V A 0.0000
17 A A -0.0043
18 F A 0.0000
19 N A -0.7965
20 C A 0.0000
21 T A -0.8800
22 Y A 0.0000
23 S A -0.7279
24 N A -0.9967
25 S A -1.0252
26 A A -0.7387
27 S A 0.0000
28 Q A -1.4838
29 S A -0.2766
30 F A 0.0000
31 F A 0.9894
32 W A 0.0000
33 Y A 0.2826
34 R A -0.8173
35 Q A -1.7919
36 D A -1.6763
37 C A -1.0216
38 R A -2.5437
39 K A -3.0302
40 E A -3.1397
41 P A -1.8321
42 K A -1.2456
43 L A 0.8916
44 L A 0.4768
45 M A 0.0000
46 S A 0.3618
47 V A 0.0000
48 Y A 0.2876
49 S A -0.4184
50 S A -0.4935
51 G A -0.9084
52 N A -1.5867
53 E A -3.0040
54 D A -3.0003
55 G A -2.0675
56 R A -2.0309
57 F A -1.5915
58 T A 0.0000
59 A A 0.0000
60 Q A -1.3351
61 L A 0.0000
62 N A -1.4279
63 R A -1.7018
64 A A -0.8585
65 S A -0.8017
66 Q A -0.9441
67 Y A -0.6467
68 I A 0.0000
69 S A 0.0000
70 L A 0.0000
71 L A -0.2549
72 I A 0.0000
73 R A -2.0065
74 D A -3.0090
75 S A 0.0000
76 K A -1.2952
77 L A 0.6619
78 S A 0.0381
79 D A 0.0000
80 S A -0.2517
81 A A 0.0000
82 T A -0.8148
83 Y A 0.0000
84 L A 0.0000
85 C A 0.0000
86 V A 0.0000
87 V A 0.0000
88 Q A -0.3087
89 P A 0.0000
90 G A -0.7335
91 G A -0.5698
92 Y A 0.4310
93 Q A -0.8663
94 K A -0.9914
95 V A 0.9610
96 T A 0.9144
97 F A 1.3223
98 G A 0.0000
99 T A -0.3714
100 G A -0.6883
101 T A 0.0000
102 K A -1.8477
103 L A 0.0000
104 Q A -1.1894
105 V A -0.2561
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 -0.4241 2.7921 View CSV PDB
4.5 -0.4827 2.7567 View CSV PDB
5.0 -0.5567 2.7058 View CSV PDB
5.5 -0.6337 2.6503 View CSV PDB
6.0 -0.6994 2.6043 View CSV PDB
6.5 -0.7394 2.5832 View CSV PDB
7.0 -0.7486 2.5946 View CSV PDB
7.5 -0.7361 2.6306 View CSV PDB
8.0 -0.7125 2.6787 View CSV PDB
8.5 -0.6822 2.7313 View CSV PDB
9.0 -0.6452 2.7852 View CSV PDB