Project name: R3mu5

Status: done

Started: 2026-02-28 13:38:54
Chain sequence(s) A: SMLESLVGKISLLLTQVRLTGQNIDDLYADLVAGYEAGTLGQIETYRNQLIQLLAQLLMLLDELVVLIRELQLYVKENNVSENLLIILEEMLTALDEYKWIFQQANALFTQLLIGLATGRTTQEQLDAIIAQLEALRKLGEQVSTKIDSLMNKIKEELYE
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                                          (00:04:33)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/301c301cfa8976c/tmp/folded.pdb                (00:04:33)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:56)
Show buried residues
Minimal score value
-3.4558
Maximal score value
0.7748
Average score
-0.9727
Total score value
-155.6378
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 -0.4755
2 M A 0.1127
3 L A -0.6862
4 E A -1.9114
5 S A -1.2670
6 L A 0.0000
7 V A 0.0000
8 G A -0.9936
9 K A -1.1964
10 I A 0.0000
11 S A -0.0817
12 L A 0.7748
13 L A 0.0000
14 L A 0.0000
15 T A 0.0067
16 Q A -0.1208
17 V A 0.0000
18 R A -1.1338
19 L A -0.1547
20 T A 0.0000
21 G A 0.0000
22 Q A -2.3777
23 N A -2.2012
24 I A 0.0000
25 D A -2.3149
26 D A -2.9063
27 L A -1.7852
28 Y A 0.0000
29 A A -1.5391
30 D A -1.8972
31 L A 0.0000
32 V A -1.0229
33 A A -0.9296
34 G A -0.8954
35 Y A -0.9852
36 E A -2.0186
37 A A -0.9329
38 G A -0.9199
39 T A -0.4916
40 L A -0.5652
41 G A -0.8954
42 Q A -1.7383
43 I A -1.3113
44 E A -2.5940
45 T A -1.9292
46 Y A -1.3920
47 R A -1.6406
48 N A -1.8986
49 Q A -1.4828
50 L A 0.0000
51 I A 0.4244
52 Q A -0.9407
53 L A -0.3046
54 L A 0.0269
55 A A 0.3215
56 Q A -0.1768
57 L A 0.0000
58 L A 0.0501
59 M A 0.2869
60 L A -0.1540
61 L A 0.0000
62 D A -1.5821
63 E A -0.9868
64 L A 0.0000
65 V A -0.3610
66 V A 0.4167
67 L A 0.0000
68 I A 0.0000
69 R A -0.8986
70 E A -0.7657
71 L A 0.0000
72 Q A 0.0000
73 L A -0.3469
74 Y A -0.7701
75 V A 0.0000
76 K A -2.8909
77 E A -2.8047
78 N A -2.3632
79 N A -2.5841
80 V A -1.3555
81 S A -1.5275
82 E A -2.3401
83 N A -1.4880
84 L A 0.0000
85 L A -0.6577
86 I A 0.1942
87 I A 0.0000
88 L A 0.0000
89 E A -1.5290
90 E A -2.0800
91 M A 0.0000
92 L A 0.0000
93 T A -1.8392
94 A A 0.0000
95 L A 0.0000
96 D A -2.4931
97 E A -1.6536
98 Y A 0.0000
99 K A -1.3539
100 W A -0.4030
101 I A 0.0000
102 F A 0.0000
103 Q A -0.8650
104 Q A -0.7042
105 A A 0.0000
106 N A -0.2094
107 A A -0.4342
108 L A -0.2760
109 F A 0.0000
110 T A -0.0262
111 Q A -0.4091
112 L A 0.0000
113 L A 0.0000
114 I A -0.1120
115 G A 0.0000
116 L A -0.0606
117 A A -0.4182
118 T A -0.5826
119 G A -1.3011
120 R A -2.0546
121 T A -1.8523
122 T A -2.1958
123 Q A -2.8873
124 E A -3.2394
125 Q A -2.7005
126 L A 0.0000
127 D A -2.4161
128 A A -1.4926
129 I A -1.1512
130 I A 0.0000
131 A A -0.8882
132 Q A -1.1453
133 L A 0.0000
134 E A -1.6781
135 A A -1.3021
136 L A 0.0000
137 R A -2.3846
138 K A -2.8923
139 L A -1.7550
140 G A -2.1780
141 E A -3.3305
142 Q A -2.7371
143 V A 0.0000
144 S A -2.1248
145 T A -1.7917
146 K A -2.3744
147 I A 0.0000
148 D A -1.8818
149 S A -1.6218
150 L A 0.0000
151 M A 0.0000
152 N A -2.8995
153 K A -2.8221
154 I A 0.0000
155 K A -2.8333
156 E A -3.4558
157 E A -2.5957
158 L A -1.3675
159 Y A -1.1625
160 E A -2.3052
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 -0.4843 2.0432 View CSV PDB
4.5 -0.5866 1.8792 View CSV PDB
5.0 -0.7208 1.6982 View CSV PDB
5.5 -0.8653 1.5246 View CSV PDB
6.0 -0.9966 1.5127 View CSV PDB
6.5 -1.0942 1.5127 View CSV PDB
7.0 -1.1506 1.5127 View CSV PDB
7.5 -1.1747 1.5127 View CSV PDB
8.0 -1.1802 1.5127 View CSV PDB
8.5 -1.1749 1.5126 View CSV PDB
9.0 -1.1591 1.5126 View CSV PDB