Project name: 887

Status: done

Started: 2026-06-23 10:28:29
Chain sequence(s) A: AKPKKNAARRTPSAGMANPSPPGGPLLGGQGVNIMEFCKAFNAKTDSIEKGLKIPVVITVYADRSFTFVTQPPSASELLRKAAGIEKGAGNPKKDKVGKISRAQLQEIAQTLAADRRGRDIRRAAEGEAGLARSMGLVVED
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage Used: no changes made
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:      Running AlphaCutter                                                         (00:00:01)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:09)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:10)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:10)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:57)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/6b74098fbb94ec4/tmp/folded.pdb                (00:03:57)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:35)
Show buried residues
Minimal score value
-4.0293
Maximal score value
1.5606
Average score
-1.4963
Total score value
-210.9755
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 A A -0.9417
2 K A -2.3858
3 P A -2.4399
4 K A -3.3038
5 K A -3.4730
6 N A -2.2385
7 A A -1.3368
8 A A 0.0000
9 R A -1.8345
10 R A -1.6604
11 T A -1.1758
12 P A -0.9051
13 S A -1.1961
14 A A 0.0000
15 G A -1.9198
16 M A -0.6375
17 A A 0.0000
18 N A -1.3702
19 P A -0.9406
20 S A -0.8928
21 P A -0.6641
22 P A -0.5028
23 G A -0.5080
24 G A 0.0000
25 P A -0.1917
26 L A 0.5409
27 L A 0.0000
28 G A -0.4637
29 G A -0.5461
30 Q A -1.1155
31 G A -1.1800
32 V A 0.0000
33 N A -1.4643
34 I A -0.7931
35 M A -0.9670
36 E A -2.2061
37 F A 0.0000
38 C A 0.0000
39 K A -2.5008
40 A A -1.6457
41 F A 0.0000
42 N A -2.2707
43 A A -1.9409
44 K A -2.4870
45 T A 0.0000
46 D A -2.8579
47 S A -1.7911
48 I A -1.6526
49 E A -2.8839
50 K A -2.9230
51 G A -1.5188
52 L A 0.0000
53 K A -1.6257
54 I A 0.0000
55 P A -0.8981
56 V A 0.0000
57 V A -0.0418
58 I A 0.0000
59 T A -0.6044
60 V A 0.0000
61 Y A -2.6828
62 A A -2.6527
63 D A -3.1818
64 R A -2.9323
65 S A -1.7321
66 F A -0.9980
67 T A 0.7500
68 F A 1.0365
69 V A 1.5606
70 T A 0.2783
71 Q A -0.4968
72 P A -0.7436
73 P A -0.6221
74 S A -0.4875
75 A A -0.3102
76 S A -0.5843
77 E A -1.3572
78 L A -1.0628
79 L A 0.0000
80 R A -2.0019
81 K A -2.4295
82 A A -1.5004
83 A A -1.4499
84 G A -1.7837
85 I A -2.0375
86 E A -2.9857
87 K A -2.8592
88 G A -2.1062
89 A A -2.2939
90 G A -1.9291
91 N A -2.6111
92 P A -3.0945
93 K A -3.8671
94 K A -3.9677
95 D A -4.0293
96 K A -3.5380
97 V A -1.7631
98 G A -1.3860
99 K A -2.2350
100 I A 0.0000
101 S A -2.3110
102 R A -3.0627
103 A A -2.0213
104 Q A -1.8241
105 L A 0.0000
106 Q A -2.9444
107 E A -2.8682
108 I A 0.0000
109 A A 0.0000
110 Q A -2.5210
111 T A -1.6398
112 L A 0.0000
113 A A -2.5144
114 A A -2.1051
115 D A -3.2500
116 R A -3.4268
117 R A -3.5759
118 G A -2.6907
119 R A -3.6349
120 D A -2.6840
121 I A -2.4517
122 R A -3.5714
123 R A -3.7673
124 A A 0.0000
125 A A 0.0000
126 E A -3.3273
127 G A -1.9482
128 E A -1.8130
129 A A -1.7213
130 G A -1.3623
131 L A -0.6956
132 A A 0.0000
133 R A -2.3873
134 S A -1.3621
135 M A -1.5983
136 G A 0.0000
137 L A 0.0000
138 V A -1.4265
139 V A -1.9588
140 E A -3.1190
141 D A -2.9473
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 -1.6366 3.2787 View CSV PDB
4.5 -1.7107 3.2787 View CSV PDB
5.0 -1.8003 3.2787 View CSV PDB
5.5 -1.8854 3.2787 View CSV PDB
6.0 -1.9408 3.2787 View CSV PDB
6.5 -1.9472 3.2787 View CSV PDB
7.0 -1.9046 3.2787 View CSV PDB
7.5 -1.8279 3.2787 View CSV PDB
8.0 -1.7319 3.2787 View CSV PDB
8.5 -1.6239 3.2787 View CSV PDB
9.0 -1.5059 3.2787 View CSV PDB