Project name: two

Status: done

Started: 2026-05-10 05:53:28
Chain sequence(s) A: TRPIDGLTDEDIREILTRYKKIALVGASPKPERDANIVMKYLLEHGYDVYPVNPKYEEVLGRKCYPSVLDIPDKIEVVDLFVKPKLTMEYVEQAIKKGAKVVWFQYNTYNREASKKADEAGLIIVANRCMMREHERLLGEK
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                                          (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:40)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/8151c4fe7d9d5f5/tmp/folded.pdb                (00:02:40)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:24)
Show buried residues
Minimal score value
-3.7825
Maximal score value
0.8039
Average score
-1.1653
Total score value
-164.3042
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
4 T A -0.9417
5 R A -1.5929
6 P A -0.4294
7 I A 0.8039
8 D A 0.1910
9 G A -0.2652
10 L A -0.4739
11 T A -1.7326
12 D A -2.7511
13 E A -3.3513
14 D A -2.8195
15 I A 0.0000
16 R A -2.8895
17 E A -3.4360
18 I A 0.0000
19 L A 0.0000
20 T A -1.8583
21 R A -2.5577
22 Y A -1.7049
23 K A -1.5804
24 K A -1.5646
25 I A 0.0000
26 A A 0.0000
27 L A 0.0000
28 V A 0.0000
29 G A -0.7647
30 A A 0.0000
31 S A 0.0000
32 P A -1.4027
33 K A -2.5116
34 P A -2.4396
35 E A -3.4356
36 R A -3.7825
37 D A -2.9963
38 A A 0.0000
39 N A 0.0000
40 I A -1.0722
41 V A 0.0000
42 M A 0.0000
43 K A -1.2333
44 Y A -1.1647
45 L A 0.0000
46 L A -1.3697
47 E A -2.2972
48 H A -1.8590
49 G A -1.4729
50 Y A 0.0000
51 D A -1.3625
52 V A 0.0000
53 Y A 0.0000
54 P A 0.0000
55 V A 0.0000
56 N A 0.0000
57 P A -1.4275
58 K A -2.3333
59 Y A -2.3349
60 E A -3.4881
61 E A -3.5704
62 V A 0.0000
63 L A -0.9589
64 G A -1.5092
65 R A -2.1756
66 K A -2.8102
67 C A 0.0000
68 Y A -1.6726
69 P A -1.1209
70 S A -0.6649
71 V A 0.0000
72 L A -0.8740
73 D A -1.6241
74 I A 0.0000
75 P A -1.4314
76 D A -2.2428
77 K A -2.2990
78 I A 0.0000
79 E A 0.0000
80 V A 0.0000
81 V A 0.0000
82 D A 0.0000
83 L A 0.0000
84 F A -0.6260
85 V A -0.7873
86 K A -2.1237
87 P A -2.1095
88 K A -2.3650
89 L A -1.1581
90 T A 0.0000
91 M A -2.0157
92 E A -2.0262
93 Y A 0.0000
94 V A 0.0000
95 E A -1.7157
96 Q A 0.0000
97 A A 0.0000
98 I A -1.1626
99 K A -1.6963
100 K A -1.7202
101 G A -1.3472
102 A A 0.0000
103 K A -0.9916
104 V A 0.0000
105 V A 0.0000
106 W A 0.0000
107 F A 0.0000
108 Q A 0.0000
109 Y A -0.7537
110 N A -1.4256
111 T A 0.0000
112 Y A -1.0561
113 N A -2.3242
114 R A -3.1183
115 E A -3.6092
116 A A 0.0000
117 S A 0.0000
118 K A -3.6360
119 K A -3.2819
120 A A 0.0000
121 D A -3.3216
122 E A -3.2889
123 A A -2.2417
124 G A -1.7878
125 L A 0.0000
126 I A -0.2063
127 I A 0.0152
128 V A 0.0000
129 A A 0.0000
130 N A -0.3523
131 R A 0.0000
132 C A 0.0000
133 M A 0.0000
134 M A -1.4391
135 R A -2.3620
136 E A 0.0000
137 H A -1.6795
138 E A -3.1158
139 R A -3.1414
140 L A 0.0000
141 L A -1.2189
142 G A -2.3793
143 E A -3.1412
144 K A -2.9371
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 -1.0491 1.4206 View CSV PDB
4.5 -1.1406 1.356 View CSV PDB
5.0 -1.2593 1.3276 View CSV PDB
5.5 -1.3838 1.2992 View CSV PDB
6.0 -1.4875 1.271 View CSV PDB
6.5 -1.5475 1.2434 View CSV PDB
7.0 -1.5565 1.2178 View CSV PDB
7.5 -1.5272 1.1966 View CSV PDB
8.0 -1.4767 1.1828 View CSV PDB
8.5 -1.4141 1.2409 View CSV PDB
9.0 -1.3414 1.4832 View CSV PDB