Project name: des9

Status: done

Started: 2026-08-08 07:24:47
Chain sequence(s) A: GYSEKICQIDRLDHVTSWLRNHTQFQGYVGQRGGRSQVSYYPAENSYSRWSGLLSPCDADWLGMLVVKKAKDSDMIVPGPSYKGKVFFERPTFDGYVAWGCSSGKSRTESGEFCSSDSAVSSGLLPSDRVLWIGDVACQP
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                                          (00:01:22)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/517d722852517e3/tmp/folded.pdb                (00:01:22)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:57)
Show buried residues
Minimal score value
-3.295
Maximal score value
1.273
Average score
-0.6259
Total score value
-87.632
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 G A -0.5723
2 Y A 0.3844
3 S A -0.5820
4 E A -1.9320
5 K A -1.4769
6 I A -0.8781
7 C A -1.3829
8 Q A -2.0637
9 I A 0.0000
10 D A -2.9299
11 R A -3.2950
12 L A 0.0000
13 D A -1.8089
14 H A 0.0000
15 V A 0.0000
16 T A 0.0000
17 S A -0.9717
18 W A 0.0000
19 L A 0.0000
20 R A -2.1222
21 N A -2.2832
22 H A -1.9013
23 T A -1.6892
24 Q A -2.0795
25 F A 0.0000
26 Q A -1.5844
27 G A 0.0000
28 Y A 0.5137
29 V A 0.0000
30 G A 0.0000
31 Q A -1.4985
32 R A -2.3857
33 G A -2.4103
34 G A -2.7922
35 R A 0.0000
36 S A -1.7868
37 Q A -2.1222
38 V A 0.0000
39 S A -0.9022
40 Y A -0.5183
41 Y A -0.0863
42 P A -0.5794
43 A A -0.7671
44 E A -1.9825
45 N A 0.0000
46 S A -0.7590
47 Y A -0.1564
48 S A -0.9092
49 R A -1.4672
50 W A 0.2063
51 S A -0.4396
52 G A -0.4429
53 L A 0.0717
54 L A 0.1300
55 S A 0.0000
56 P A 0.0000
57 C A 0.0000
58 D A 0.0000
59 A A 0.0000
60 D A 0.3893
61 W A 0.3555
62 L A 0.5645
63 G A 0.2784
64 M A 0.5300
65 L A 1.0080
66 V A 1.2730
67 V A 0.0000
68 K A -1.9330
69 K A -2.4814
70 A A -2.1748
71 K A -3.1281
72 D A -2.9388
73 S A -1.5251
74 D A -1.1496
75 M A 0.2051
76 I A 0.1193
77 V A 0.4224
78 P A -0.1830
79 G A -0.4701
80 P A 0.0000
81 S A -1.2004
82 Y A 0.0000
83 K A -2.6318
84 G A -1.7292
85 K A 0.0000
86 V A 0.0000
87 F A 0.0000
88 F A 0.0000
89 E A 0.0000
90 R A -0.0091
91 P A -0.0376
92 T A 0.3610
93 F A 1.0480
94 D A -0.8723
95 G A -0.3015
96 Y A -0.1759
97 V A 0.0000
98 A A 0.0000
99 W A 0.0000
100 G A -0.3491
101 C A 0.0000
102 S A -1.2035
103 S A -1.1877
104 G A -1.1215
105 K A -0.8064
106 S A 0.0000
107 R A 0.0000
108 T A -1.5967
109 E A -2.6977
110 S A -1.6376
111 G A 0.0000
112 E A -1.3751
113 F A 0.5790
114 C A 0.0023
115 S A -0.3806
116 S A -0.8086
117 D A -0.8728
118 S A -0.6642
119 A A -0.2556
120 V A 0.0000
121 S A -0.4511
122 S A 0.1912
123 G A 0.3359
124 L A 1.2655
125 L A 0.0000
126 P A -0.9900
127 S A 0.0000
128 D A -2.3302
129 R A -1.5352
130 V A 0.0000
131 L A 0.0000
132 W A 0.0000
133 I A 0.0000
134 G A -0.2741
135 D A -0.8253
136 V A -0.0996
137 A A 0.0130
138 C A 0.0000
139 Q A -1.1749
140 P A -0.7413
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 -0.4499 4.4984 View CSV PDB
4.5 -0.5175 4.3673 View CSV PDB
5.0 -0.5978 4.1902 View CSV PDB
5.5 -0.6789 3.9902 View CSV PDB
6.0 -0.7478 3.7817 View CSV PDB
6.5 -0.7946 3.5703 View CSV PDB
7.0 -0.8185 3.3583 View CSV PDB
7.5 -0.827 3.1471 View CSV PDB
8.0 -0.8259 2.9391 View CSV PDB
8.5 -0.8151 2.7408 View CSV PDB
9.0 -0.7927 2.5679 View CSV PDB