Project name: ag-h1-1(2)

Status: done

Started: 2025-03-10 09:13:56
Chain sequence(s) A: QLQLVESGGKLVQAGGSLRLSCAASGRSVNNYFMGWFRQAPGKEREFVARITWNGAGTYYADSVKGRFTISVDNAKNTVNLQMNSLKPEDTALYYCAARRTDSRRPLFEYDYRGQGTQVTVSS
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                                          (00:01:23)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/2f8b3842f88600d/tmp/folded.pdb                (00:01:23)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:54)
Show buried residues
Minimal score value
-3.6218
Maximal score value
0.9573
Average score
-0.9994
Total score value
-122.9253
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 -2.0167
2 L A 0.0000
3 Q A -1.8683
4 L A 0.0000
5 V A 0.6026
6 E A 0.0000
7 S A -0.7374
8 G A -1.6221
9 G A -1.6035
10 K A -1.6375
11 L A 0.2212
12 V A 0.0000
13 Q A -1.3156
14 A A -1.4270
15 G A -1.2986
16 G A -1.1044
17 S A -1.4524
18 L A 0.0000
19 R A -2.6836
20 L A 0.0000
21 S A -0.5960
22 C A 0.0000
23 A A -0.1644
24 A A 0.0000
25 S A -1.3296
26 G A -2.0751
27 R A -2.9606
28 S A -2.0088
29 V A 0.0000
30 N A -2.0885
31 N A -2.5124
32 Y A 0.0000
33 F A -0.4220
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 -2.2275
40 A A -2.0361
41 P A -1.4525
42 G A -1.9804
43 K A -3.3793
44 E A -3.6218
45 R A -2.9432
46 E A -1.9724
47 F A 0.0000
48 V A 0.0000
49 A A 0.0000
50 R A 0.3288
51 I A 0.0000
52 T A -0.3899
53 W A -0.9345
54 N A -1.5770
55 G A -0.8968
56 A A -0.4703
57 G A -0.1802
58 T A 0.3607
59 Y A 0.5475
60 Y A -0.4503
61 A A -1.2194
62 D A -2.3915
63 S A -1.7589
64 V A 0.0000
65 K A -2.5011
66 G A -1.7779
67 R A -1.6376
68 F A 0.0000
69 T A -0.9915
70 I A 0.0000
71 S A -0.5536
72 V A -0.7799
73 D A -1.3770
74 N A -1.7401
75 A A -1.2511
76 K A -2.0896
77 N A -1.7772
78 T A -0.8351
79 V A 0.0000
80 N A -0.9642
81 L A 0.0000
82 Q A -1.8796
83 M A 0.0000
84 N A -1.5535
85 S A -1.1617
86 L A 0.0000
87 K A -2.1097
88 P A -1.7826
89 E A -2.2353
90 D A 0.0000
91 T A -1.0831
92 A A 0.0000
93 L A -0.7242
94 Y A 0.0000
95 Y A 0.0000
96 C A 0.0000
97 A A 0.0000
98 A A 0.0000
99 R A -1.7522
100 R A -2.6741
101 T A -1.8933
102 D A -2.5793
103 S A -2.5799
104 R A -3.0400
105 R A -2.6671
106 P A -0.6797
107 L A 0.9573
108 F A 0.8276
109 E A -0.8986
110 Y A -1.0209
111 D A -1.7925
112 Y A -1.4565
113 R A -1.8491
114 G A -1.1168
115 Q A -1.3677
116 G A -0.9291
117 T A -1.0301
118 Q A -1.4819
119 V A 0.0000
120 T A -0.7207
121 V A 0.0000
122 S A -0.7948
123 S A -0.8346
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 -1.0158 2.6327 View CSV PDB
4.5 -1.0636 2.5246 View CSV PDB
5.0 -1.1163 2.393 View CSV PDB
5.5 -1.1647 2.2592 View CSV PDB
6.0 -1.1987 2.1441 View CSV PDB
6.5 -1.2112 2.0663 View CSV PDB
7.0 -1.2034 2.0272 View CSV PDB
7.5 -1.182 2.0119 View CSV PDB
8.0 -1.1522 2.0066 View CSV PDB
8.5 -1.1146 2.0049 View CSV PDB
9.0 -1.0699 2.0043 View CSV PDB