Project name: R3mu3

Status: done

Started: 2026-02-28 13:38:15
Chain sequence(s) A: SMLESLVGKISLLLTMIRLTGQNIDDLYADLVAGYEAGTLGQIETYRNQLIQLLAQLGILLDELVVLIRELQLYVKENNVSENLLIILEEMLTALDEYKWIFQQANALFTQLLLGLATGRTTQEQLDAIIAQLEALRKLGEQVSTKIDSLMNKIKEELYE
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                                          (00:05:45)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/e9a5c44305ff88c/tmp/folded.pdb                (00:05:45)
[INFO]       Main:     Simulation completed successfully.                                          (00:07:15)
Show buried residues
Minimal score value
-3.4489
Maximal score value
0.938
Average score
-1.0143
Total score value
-162.2822
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 -0.4218
2 M A 0.1870
3 L A -0.6289
4 E A -1.8637
5 S A -1.1987
6 L A 0.0000
7 V A 0.0000
8 G A -0.9627
9 K A -1.2052
10 I A 0.0000
11 S A 0.0803
12 L A 0.9380
13 L A 0.0000
14 L A 0.0000
15 T A 0.4103
16 M A 0.6471
17 I A 0.0000
18 R A -1.0412
19 L A 0.3297
20 T A 0.0000
21 G A 0.0000
22 Q A -2.3679
23 N A -2.2923
24 I A 0.0000
25 D A -2.5609
26 D A -3.1025
27 L A -2.0071
28 Y A 0.0000
29 A A -1.7505
30 D A -2.1047
31 L A 0.0000
32 V A -1.1737
33 A A -1.0412
34 G A -1.0259
35 Y A -1.1143
36 E A -1.8993
37 A A -0.9332
38 G A -0.9301
39 T A -0.6527
40 L A -0.6612
41 G A -1.0911
42 Q A -1.8020
43 I A -1.2397
44 E A -2.6547
45 T A -1.9567
46 Y A -1.4910
47 R A -1.7599
48 N A -2.0425
49 Q A -1.5666
50 L A 0.0000
51 I A 0.2028
52 Q A -1.0394
53 L A -0.5575
54 L A 0.1917
55 A A 0.3422
56 Q A 0.1836
57 L A 0.0000
58 G A -0.1727
59 I A 0.8930
60 L A 0.0000
61 L A 0.0000
62 D A -1.4682
63 E A -0.9228
64 L A 0.0000
65 V A -0.6802
66 V A 0.0992
67 L A 0.0000
68 I A 0.0000
69 R A -1.4980
70 E A -1.0317
71 L A 0.0000
72 Q A -0.8056
73 L A -0.6073
74 Y A -1.0829
75 V A 0.0000
76 K A -3.0684
77 E A -3.0720
78 N A -2.8328
79 N A -2.8951
80 V A -1.8603
81 S A -1.5237
82 E A -2.1972
83 N A -1.2051
84 L A 0.0000
85 L A -0.7111
86 I A 0.2431
87 I A 0.0000
88 L A 0.0000
89 E A -2.0047
90 E A -2.0285
91 M A 0.0000
92 L A -1.5153
93 T A -1.8672
94 A A 0.0000
95 L A 0.0000
96 D A -2.4847
97 E A -1.6923
98 Y A 0.0000
99 K A -1.6984
100 W A -0.7640
101 I A 0.0000
102 F A -0.6832
103 Q A -1.3296
104 Q A -0.9762
105 A A 0.0000
106 N A -0.5606
107 A A -0.6336
108 L A -0.3623
109 F A 0.0000
110 T A -0.1423
111 Q A -0.2784
112 L A 0.0000
113 L A 0.0000
114 L A 0.8160
115 G A 0.0000
116 L A 0.1074
117 A A -0.1445
118 T A -0.4192
119 G A -1.2167
120 R A -1.9948
121 T A -1.7603
122 T A -2.2697
123 Q A -2.9878
124 E A -3.3418
125 Q A -2.7873
126 L A 0.0000
127 D A -2.7350
128 A A -1.8038
129 I A -1.3417
130 I A 0.0000
131 A A -1.1446
132 Q A -1.5535
133 L A 0.0000
134 E A -1.8123
135 A A -1.3265
136 L A 0.0000
137 R A -2.3378
138 K A -2.9089
139 L A -1.6775
140 G A -2.0682
141 E A -3.3758
142 Q A -2.6214
143 V A 0.0000
144 S A -1.9484
145 T A -1.6783
146 K A -1.9654
147 I A 0.0000
148 D A -1.5628
149 S A -1.4205
150 L A 0.0000
151 M A 0.0000
152 N A -2.8099
153 K A -2.7997
154 I A 0.0000
155 K A -2.5976
156 E A -3.4489
157 E A -2.5585
158 L A -1.3977
159 Y A -1.0111
160 E A -2.3285
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 -0.5044 2.8142 View CSV PDB
4.5 -0.6053 2.6557 View CSV PDB
5.0 -0.74 2.4578 View CSV PDB
5.5 -0.8875 2.2441 View CSV PDB
6.0 -1.0238 2.0316 View CSV PDB
6.5 -1.1287 1.8337 View CSV PDB
7.0 -1.1928 1.6583 View CSV PDB
7.5 -1.2225 1.5017 View CSV PDB
8.0 -1.2313 1.4257 View CSV PDB
8.5 -1.2274 1.4257 View CSV PDB
9.0 -1.2117 1.5227 View CSV PDB