Project name: R3mu2

Status: done

Started: 2026-02-28 13:37:58
Chain sequence(s) A: SMLESLVGKISLLLTMIRLTGQNIDDLYADLVAGYEAGTLGQIETYRNQLIQLLAQLGILLDELVVLIRELQLYVKENNVSENLLIILEEMLTALDEYKWIFQQANALFTQLLMGLATGRTTQEQLDAIIAQLEALRKLGEQVSTKIDSLMNKIKEELYE
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                                          (00:04:34)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/2dbce28ccaaa607/tmp/folded.pdb                (00:04:34)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:48)
Show buried residues
Minimal score value
-3.4518
Maximal score value
0.9314
Average score
-1.0073
Total score value
-161.1746
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 -0.3259
2 M A 0.3956
3 L A -0.5202
4 E A -1.6789
5 S A -1.1031
6 L A -0.7700
7 V A 0.0000
8 G A -0.9351
9 K A -1.2309
10 I A 0.0000
11 S A 0.0165
12 L A 0.9314
13 L A 0.0000
14 L A 0.0000
15 T A 0.3766
16 M A 0.7026
17 I A 0.0000
18 R A -1.0324
19 L A 0.0391
20 T A 0.0000
21 G A 0.0000
22 Q A -2.4668
23 N A -2.4855
24 I A 0.0000
25 D A -2.5664
26 D A -3.2104
27 L A -2.0853
28 Y A 0.0000
29 A A -1.6413
30 D A -2.1265
31 L A 0.0000
32 V A -1.0298
33 A A -1.0498
34 G A -1.1646
35 Y A -1.0172
36 E A -1.9483
37 A A -0.9545
38 G A -0.9812
39 T A -0.7461
40 L A -0.8167
41 G A -1.1753
42 Q A -1.9032
43 I A -1.4913
44 E A -2.6974
45 T A -2.0234
46 Y A -1.6158
47 R A -1.8838
48 N A -2.2050
49 Q A -1.7890
50 L A 0.0000
51 I A -0.3140
52 Q A -1.3301
53 L A -0.7563
54 L A -0.0668
55 A A 0.1567
56 Q A 0.1085
57 L A 0.0000
58 G A -0.3227
59 I A 0.8233
60 L A 0.0000
61 L A 0.0000
62 D A -1.4124
63 E A -0.8576
64 L A 0.0000
65 V A -0.4727
66 V A 0.3853
67 L A 0.0000
68 I A 0.0000
69 R A -0.9047
70 E A -0.8404
71 L A 0.0000
72 Q A 0.0000
73 L A -0.4171
74 Y A -0.8154
75 V A 0.0000
76 K A -2.9049
77 E A -2.8625
78 N A -2.4543
79 N A -2.6019
80 V A -1.2566
81 S A -1.3795
82 E A -2.1412
83 N A -1.2109
84 L A 0.0000
85 L A -0.4464
86 I A 0.4622
87 I A 0.0000
88 L A 0.0000
89 E A -1.6003
90 E A -2.2094
91 M A 0.0000
92 L A 0.0000
93 T A -1.9338
94 A A 0.0000
95 L A 0.0000
96 D A -2.5511
97 E A -1.6976
98 Y A 0.0000
99 K A -1.6404
100 W A -0.5750
101 I A 0.0000
102 F A -0.6665
103 Q A -1.2585
104 Q A -0.8850
105 A A 0.0000
106 N A -0.5677
107 A A -0.6366
108 L A -0.4328
109 F A 0.0000
110 T A -0.2686
111 Q A -0.6655
112 L A 0.0000
113 L A 0.0000
114 M A -0.2446
115 G A 0.0000
116 L A -0.2272
117 A A -0.5379
118 T A -0.6353
119 G A -1.3313
120 R A -2.2137
121 T A -1.9105
122 T A -2.3149
123 Q A -3.0778
124 E A -3.4518
125 Q A -3.0937
126 L A 0.0000
127 D A -2.9983
128 A A -1.7963
129 I A -1.2518
130 I A -0.8491
131 A A -0.8972
132 Q A -1.1022
133 L A 0.0000
134 E A -1.2390
135 A A -1.0360
136 L A 0.0000
137 R A -2.2082
138 K A -2.6709
139 L A -1.5599
140 G A -1.9625
141 E A -3.0938
142 Q A -2.5601
143 V A 0.0000
144 S A -2.0064
145 T A -1.7096
146 K A -2.2858
147 I A 0.0000
148 D A -1.9171
149 S A -1.6113
150 L A 0.0000
151 M A 0.0000
152 N A -2.8062
153 K A -2.8798
154 I A 0.0000
155 K A -2.4449
156 E A -3.1693
157 E A -2.4404
158 L A -1.1362
159 Y A -0.9683
160 E A -1.9048
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 -0.4882 2.6712 View CSV PDB
4.5 -0.5896 2.4995 View CSV PDB
5.0 -0.7225 2.2945 View CSV PDB
5.5 -0.8664 2.0796 View CSV PDB
6.0 -0.9984 1.8716 View CSV PDB
6.5 -1.0994 1.6825 View CSV PDB
7.0 -1.1617 1.5142 View CSV PDB
7.5 -1.1915 1.36 View CSV PDB
8.0 -1.2013 1.2159 View CSV PDB
8.5 -1.1982 1.3212 View CSV PDB
9.0 -1.1826 1.4452 View CSV PDB