Project name: prot920_agg

Status: done

Started: 2025-02-27 22:39:44
Chain sequence(s) D: STYRVRSSGLTCSTCPPGTHKERDCSLNTETICKACGEGEYTAHNNSLPKCLACKSCFNATEIETKSCDPTSDTICACREGYSINNLGECN
input PDB
Selected Chain(s) D
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 D 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/a2651e12b96ec99/tmp/folded.pdb                (00:00:43)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:12)
Show buried residues
Minimal score value
-2.5029
Maximal score value
0.8307
Average score
-0.8559
Total score value
-77.8889
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 S D -0.5682
2 T D -0.6985
3 Y D -1.0388
4 R D -2.2780
5 V D -1.7438
6 R D -2.4001
7 S D -1.3793
8 S D -0.9562
9 G D -1.2023
10 L D -0.5095
11 T D -0.7879
12 C D 0.0000
13 S D -0.7938
14 T D -0.8624
15 C D 0.0000
16 P D -1.2331
17 P D -1.0179
18 G D 0.0000
19 T D -1.1290
20 H D 0.0000
21 K D -1.5792
22 E D -2.3327
23 R D -2.5029
24 D D -1.7474
25 C D -1.1147
26 S D -0.5082
27 L D 0.6074
28 N D -0.9660
29 T D -0.9812
30 E D -1.7587
31 T D -1.0974
32 I D -0.1203
33 C D -0.7013
34 K D -1.7589
35 A D -1.3063
36 C D -1.3104
37 G D -1.9988
38 E D -2.4132
39 G D -1.7681
40 E D -1.6336
41 Y D -0.7973
42 T D 0.0000
43 A D -0.7955
44 H D -1.7256
45 N D -1.9425
46 N D -1.1819
47 S D -1.1988
48 L D -0.3879
49 P D -1.5730
50 K D -1.9505
51 C D 0.0000
52 L D 0.2334
53 A D -0.6551
54 C D -0.9974
55 K D -1.3267
56 S D -0.6647
57 C D 0.0686
58 F D 0.8307
59 N D -0.3922
60 A D -0.0184
61 T D -0.3630
62 E D -0.1329
63 I D 0.0641
64 E D -1.0750
65 T D -0.5472
66 K D -0.8672
67 S D -1.0313
68 C D -1.2116
69 D D -1.2921
70 P D -0.9219
71 T D -0.5974
72 S D -0.3601
73 D D -0.5400
74 T D 0.0000
75 I D 0.5234
76 C D -0.1589
77 A D 0.1892
78 C D -0.5147
79 R D -1.4937
80 E D -2.0645
81 G D -1.4132
82 Y D -0.6863
83 S D -0.3776
84 I D 0.8298
85 N D -0.5075
86 N D -0.7827
87 L D 0.4133
88 G D -0.5278
89 E D -1.0447
90 C D 0.0000
91 N D -1.3319
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 -0.4997 3.453 View CSV PDB
4.5 -0.5863 3.3781 View CSV PDB
5.0 -0.6972 3.273 View CSV PDB
5.5 -0.812 3.1553 View CSV PDB
6.0 -0.9061 3.0488 View CSV PDB
6.5 -0.9553 2.9785 View CSV PDB
7.0 -0.954 2.9572 View CSV PDB
7.5 -0.919 2.976 View CSV PDB
8.0 -0.8672 3.0167 View CSV PDB
8.5 -0.8066 3.0665 View CSV PDB
9.0 -0.7409 3.1193 View CSV PDB