Project name: R6mu_5

Status: done

Started: 2026-02-28 23:19:18
Chain sequence(s) A: SMLESLVTMILNLLTMIRLTGQNIDDLYADLVAGIKAGTLGQIETYRNQFMQLLAQLLMLLDELLRLIRELMRFIKENNVSENLLIILEEMLTALDEYKWIFQQANALFTQLLIGLATGTLTQEQLDAIIAQLEALRKLGEQVSTKIDSLMNKIKEELYE
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.  (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:04:37)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/ffb67133e597ade/tmp/folded.pdb                (00:04:37)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:43)
Show buried residues
Minimal score value
-3.9441
Maximal score value
1.585
Average score
-1.0579
Total score value
-169.2647
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 -0.0312
2 M A 0.6876
3 L A 0.1833
4 E A -0.6110
5 S A -0.1236
6 L A 0.0000
7 V A 0.0000
8 T A -0.3219
9 M A -0.1284
10 I A 0.0000
11 L A -0.4410
12 N A -1.0714
13 L A 0.0000
14 L A 0.0000
15 T A -0.3538
16 M A 0.0172
17 I A 0.0000
18 R A -1.4144
19 L A 0.1969
20 T A 0.0000
21 G A 0.0000
22 Q A -2.2283
23 N A -2.2363
24 I A 0.0000
25 D A -2.5013
26 D A -2.8554
27 L A -1.7715
28 Y A 0.0000
29 A A -1.1400
30 D A -1.7138
31 L A 0.0000
32 V A -0.5864
33 A A -0.9428
34 G A 0.0000
35 I A 0.0000
36 K A -1.8631
37 A A -0.9596
38 G A -0.9522
39 T A -0.6731
40 L A -0.1763
41 G A -0.9212
42 Q A -1.3273
43 I A 0.0000
44 E A -1.4490
45 T A -1.3977
46 Y A -1.2400
47 R A -1.7569
48 N A -2.2453
49 Q A -1.7997
50 F A 0.0000
51 M A -1.2334
52 Q A -1.7536
53 L A -0.9402
54 L A 0.0000
55 A A -0.2015
56 Q A -0.2612
57 L A 0.0000
58 L A -0.0854
59 M A 0.1534
60 L A 0.0000
61 L A 0.0000
62 D A -2.5322
63 E A -2.0320
64 L A 0.0000
65 L A 0.0000
66 R A -3.4401
67 L A -2.3314
68 I A 0.0000
69 R A -3.5760
70 E A -3.0782
71 L A 0.0000
72 M A 0.0000
73 R A -3.9057
74 F A -2.4865
75 I A 0.0000
76 K A -3.9441
77 E A -3.7460
78 N A -2.9050
79 N A -2.9332
80 V A -1.1382
81 S A -1.4046
82 E A -2.1331
83 N A -1.3945
84 L A 0.0000
85 L A -1.0578
86 I A 0.3629
87 I A 0.0000
88 L A 0.0000
89 E A -1.8495
90 E A -1.6548
91 M A 0.0000
92 L A -1.7296
93 T A -1.7409
94 A A 0.0000
95 L A 0.0000
96 D A -2.3264
97 E A -1.6539
98 Y A 0.0000
99 K A -1.3779
100 W A -0.6244
101 I A 0.0000
102 F A 0.0000
103 Q A -1.0999
104 Q A -0.8853
105 A A 0.0000
106 N A -0.8726
107 A A -0.7089
108 L A -0.5389
109 F A 0.0000
110 T A -0.0364
111 Q A -0.1566
112 L A 0.0000
113 L A 0.0000
114 I A 1.5850
115 G A 0.0000
116 L A 0.6336
117 A A 0.6709
118 T A 0.3818
119 G A -0.0378
120 T A -0.0398
121 L A -0.6687
122 T A -1.6180
123 Q A -2.6316
124 E A -3.2037
125 Q A -2.3991
126 L A -2.0162
127 D A -2.5137
128 A A -1.6810
129 I A -1.0998
130 I A -0.8674
131 A A -1.0658
132 Q A -1.2549
133 L A 0.0000
134 E A -2.0146
135 A A -1.5840
136 L A 0.0000
137 R A -3.3620
138 K A -3.3948
139 L A -2.1201
140 G A -2.5305
141 E A -3.5556
142 Q A -2.7987
143 V A 0.0000
144 S A -2.1351
145 T A -1.6490
146 K A -1.7196
147 I A 0.0000
148 D A -1.3836
149 S A -1.2443
150 L A 0.0000
151 M A -1.4668
152 N A -2.6200
153 K A -3.0193
154 I A 0.0000
155 K A -2.5734
156 E A -3.6068
157 E A -2.7755
158 L A -1.2130
159 Y A -0.7888
160 E A -2.4805
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 -0.6777 2.9892 View CSV PDB
4.5 -0.7714 2.9746 View CSV PDB
5.0 -0.8946 2.9532 View CSV PDB
5.5 -1.0278 2.9284 View CSV PDB
6.0 -1.1492 2.9042 View CSV PDB
6.5 -1.2403 2.8845 View CSV PDB
7.0 -1.2938 2.8723 View CSV PDB
7.5 -1.3165 2.8667 View CSV PDB
8.0 -1.3209 2.8646 View CSV PDB
8.5 -1.3145 2.8639 View CSV PDB
9.0 -1.2976 2.8636 View CSV PDB