Project name: R4mu_1

Status: done

Started: 2026-02-28 20:09:02
Chain sequence(s) A: SMLESLVGKISLLLTQVRLTGQNIDDLYADLVAGYEAGTLGQIETYRNQLIQLLRMLLMLLDELVVLIRELMRYVKENNVSENLLIILEEMLTALDEYKWIFQQANALFTQLLIGLATGTLTQEQLDAIIAQLEALRKLGEQVSTKIDSLMNKIKEELYE
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]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:04:20)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/6b3d77d22401671/tmp/folded.pdb                (00:04:20)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:32)
Show buried residues
Minimal score value
-3.9196
Maximal score value
0.9242
Average score
-1.0229
Total score value
-163.6583
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 S A -0.4114
2 M A 0.2289
3 L A -0.6012
4 E A -1.7994
5 S A -1.2163
6 L A 0.0000
7 V A 0.0000
8 G A -0.9954
9 K A -1.0812
10 I A 0.0000
11 S A -0.1291
12 L A 0.9242
13 L A 0.0000
14 L A 0.0000
15 T A 0.2334
16 Q A 0.1325
17 V A 0.0000
18 R A -0.9027
19 L A -0.0592
20 T A -0.7073
21 G A 0.0000
22 Q A -2.4602
23 N A -2.4021
24 I A 0.0000
25 D A -2.5502
26 D A -3.1280
27 L A -2.0136
28 Y A 0.0000
29 A A -1.7481
30 D A -2.2899
31 L A 0.0000
32 V A -1.1490
33 A A -1.0833
34 G A -1.0631
35 Y A -1.1299
36 E A -2.1063
37 A A -0.9566
38 G A -0.9723
39 T A -0.7376
40 L A -0.7372
41 G A -1.1735
42 Q A -1.8916
43 I A -1.3211
44 E A -2.5768
45 T A -1.8610
46 Y A -1.5490
47 R A -1.8719
48 N A -2.1480
49 Q A -1.7068
50 L A 0.0000
51 I A -0.8193
52 Q A -1.6785
53 L A 0.0000
54 L A 0.0000
55 R A -1.4369
56 M A -0.4811
57 L A 0.0000
58 L A -0.6738
59 M A -0.0738
60 L A -0.2369
61 L A 0.0000
62 D A -1.5362
63 E A -0.8490
64 L A 0.0000
65 V A -0.4187
66 V A 0.2882
67 L A 0.0000
68 I A 0.0000
69 R A -2.2011
70 E A -2.0535
71 L A 0.0000
72 M A -2.0745
73 R A -3.7865
74 Y A -2.3992
75 V A 0.0000
76 K A -3.9196
77 E A -3.6797
78 N A -2.8200
79 N A -2.8697
80 V A -1.1799
81 S A -1.3684
82 E A -2.1132
83 N A -1.4903
84 L A 0.0000
85 L A -1.1851
86 I A 0.2533
87 I A 0.0000
88 L A 0.0000
89 E A -2.1684
90 E A -2.3566
91 M A 0.0000
92 L A -1.3791
93 T A -1.9288
94 A A 0.0000
95 L A 0.0000
96 D A -2.4442
97 E A -1.5237
98 Y A 0.0000
99 K A -1.4493
100 W A -0.4083
101 I A 0.0000
102 F A 0.0000
103 Q A -0.7335
104 Q A -0.6582
105 A A 0.0000
106 N A -0.4006
107 A A -0.4499
108 L A -0.2171
109 F A 0.0000
110 T A -0.0114
111 Q A -0.0912
112 L A 0.0000
113 L A 0.0000
114 I A 0.9073
115 G A 0.0000
116 L A 0.4703
117 A A 0.2642
118 T A 0.2017
119 G A -0.2677
120 T A -0.1390
121 L A -0.7227
122 T A -1.5939
123 Q A -2.6152
124 E A -3.1226
125 Q A -2.2981
126 L A 0.0000
127 D A -2.5088
128 A A -1.6002
129 I A -1.0829
130 I A -0.7876
131 A A -0.8966
132 Q A -1.1454
133 L A 0.0000
134 E A -1.5482
135 A A -1.1719
136 L A 0.0000
137 R A -2.2536
138 K A -2.7450
139 L A -1.6062
140 G A 0.0000
141 E A -3.2965
142 Q A -2.6252
143 V A 0.0000
144 S A -1.8356
145 T A -1.6404
146 K A -2.0705
147 I A 0.0000
148 D A -1.4604
149 S A -1.4279
150 L A 0.0000
151 M A 0.0000
152 N A -2.7806
153 K A -2.8062
154 I A 0.0000
155 K A -2.4692
156 E A -3.1292
157 E A -2.2237
158 L A -1.0973
159 Y A -0.5803
160 E A -1.9182
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 -0.5765 2.1518 View CSV PDB
4.5 -0.6817 2.0103 View CSV PDB
5.0 -0.8208 1.9685 View CSV PDB
5.5 -0.9728 1.9229 View CSV PDB
6.0 -1.1134 1.8807 View CSV PDB
6.5 -1.2225 1.8488 View CSV PDB
7.0 -1.2911 1.8308 View CSV PDB
7.5 -1.3255 1.8232 View CSV PDB
8.0 -1.3384 1.8205 View CSV PDB
8.5 -1.3379 1.8196 View CSV PDB
9.0 -1.3249 1.8193 View CSV PDB