Project name: abc9

Status: done

Started: 2025-04-25 18:43:30
Chain sequence(s) A: QVQLQESGGGLVQAGGSLRLSCAASGRTFSSYAMGWFRQAPGKEREFVAAISSSGGTYYADSVKGRFTISRDDARNTVYLQMNSLKPEDTAVYYCATGMIASRMVEFDYWGQGTQVTVSS
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]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:00)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:00:46)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/c3f94d2369a640/tmp/folded.pdb                 (00:00:46)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:14)
Show buried residues
Minimal score value
-3.5677
Maximal score value
2.1185
Average score
-0.732
Total score value
-87.8457
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 -2.0194
2 V A 0.0000
3 Q A -2.0319
4 L A 0.0000
5 Q A -1.7684
6 E A 0.0000
7 S A -1.1634
8 G A -1.1693
9 G A -0.8217
10 G A -0.0472
11 L A 1.0473
12 V A 0.0304
13 Q A -1.2256
14 A A -1.4014
15 G A -1.3325
16 G A -0.9094
17 S A -1.1191
18 L A -0.9540
19 R A -2.0801
20 L A 0.0000
21 S A -0.7041
22 C A 0.0000
23 A A -0.9414
24 A A -1.5255
25 S A -1.4574
26 G A -1.6997
27 R A -2.2851
28 T A -1.3676
29 F A 0.0000
30 S A -1.0419
31 S A -0.3891
32 Y A 0.5422
33 A A 0.2899
34 M 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 -2.0444
40 A A -1.9490
41 P A -1.3861
42 G A -1.9409
43 K A -3.3382
44 E A -3.5677
45 R A -2.5406
46 E A -2.2685
47 F A -0.5051
48 V A 0.0000
49 A A 0.0000
50 A A 0.0000
51 I A 0.0000
52 S A 0.0512
53 S A -0.2086
54 S A -0.7527
55 G A -0.9242
56 G A -0.2909
57 T A 0.3328
58 Y A 0.9252
59 Y A -0.0602
60 A A -0.9443
61 D A -2.1966
62 S A -1.7652
63 V A 0.0000
64 K A -2.4057
65 G A -1.7690
66 R A -1.5400
67 F A 0.0000
68 T A -0.6965
69 I A 0.0000
70 S A -0.4332
71 R A -0.9994
72 D A -1.5478
73 D A -1.9635
74 A A -1.6049
75 R A -2.2698
76 N A -1.8049
77 T A -1.1043
78 V A 0.0000
79 Y A -0.2634
80 L A 0.0000
81 Q A -1.1967
82 M A 0.0000
83 N A -1.6004
84 S A -1.2673
85 L A 0.0000
86 K A -2.1669
87 P A -1.7761
88 E A -2.2411
89 D A 0.0000
90 T A -0.8503
91 A A 0.0000
92 V A -0.4631
93 Y A 0.0000
94 Y A -0.5211
95 C A 0.0000
96 A A 0.0000
97 T A 0.0000
98 G A 0.0000
99 M A 1.6169
100 I A 2.1185
101 A A 0.8345
102 S A 0.1346
103 R A -1.0235
104 M A -0.1112
105 V A 1.0280
106 E A 0.1117
107 F A 0.0000
108 D A -1.0551
109 Y A -0.8988
110 W A -0.6893
111 G A -1.0638
112 Q A -1.5211
113 G A -1.0674
114 T A 0.0000
115 Q A -0.9978
116 V A 0.0000
117 T A -0.2484
118 V A 0.0000
119 S A -0.8150
120 S A -0.7937
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 -0.7054 3.1651 View CSV PDB
4.5 -0.7446 3.1376 View CSV PDB
5.0 -0.7949 3.0872 View CSV PDB
5.5 -0.8492 3.0168 View CSV PDB
6.0 -0.8985 2.9363 View CSV PDB
6.5 -0.9356 2.8544 View CSV PDB
7.0 -0.9572 2.7779 View CSV PDB
7.5 -0.9654 2.7126 View CSV PDB
8.0 -0.964 2.6584 View CSV PDB
8.5 -0.9551 2.6113 View CSV PDB
9.0 -0.9398 2.5693 View CSV PDB