Project name: R3mu4

Status: done

Started: 2026-02-28 13:38:38
Chain sequence(s) A: SMLESLVGKISLLLTQVRLTGQNIDDLYADLVAGYEAGTLGQIETYRNQLIQLLAQLLLLLDELVVLIRELQLYVKENNVSENLLIILEEMLTALDEYKWIFQQANALFTQLLIGLATGRTTQEQLDAIIAQLEALRKLGEQVSTKIDSLMNKIKEELYE
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                                          (00:04:40)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/187615dc7ba92ff/tmp/folded.pdb                (00:04:40)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:07)
Show buried residues
Minimal score value
-3.4792
Maximal score value
1.1465
Average score
-0.9879
Total score value
-158.0637
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 -0.5563
2 M A -0.1051
3 L A -0.6395
4 E A -1.8951
5 S A -1.2689
6 L A 0.0000
7 V A 0.0000
8 G A -0.8829
9 K A -0.9320
10 I A 0.0000
11 S A -0.2190
12 L A 0.8113
13 L A 0.0000
14 L A -0.3589
15 T A -0.4082
16 Q A -0.4210
17 V A 0.0000
18 R A -2.2794
19 L A -0.9539
20 T A 0.0000
21 G A -1.9885
22 Q A -2.6182
23 N A -2.4756
24 I A 0.0000
25 D A -2.6609
26 D A -2.8422
27 L A -1.8128
28 Y A 0.0000
29 A A -1.4206
30 D A -1.7658
31 L A 0.0000
32 V A -0.9625
33 A A -0.8581
34 G A 0.0000
35 Y A 0.0000
36 E A -2.0471
37 A A -0.9278
38 G A -0.9721
39 T A -0.5849
40 L A -0.4172
41 G A -0.9783
42 Q A -1.5199
43 I A 0.0000
44 E A -2.6665
45 T A -1.7500
46 Y A -1.6448
47 R A -2.2987
48 N A -2.3450
49 Q A -2.0573
50 L A 0.0000
51 I A -0.4269
52 Q A -1.4428
53 L A -0.6194
54 L A 0.0000
55 A A 0.0009
56 Q A 0.0499
57 L A 0.0000
58 L A 0.1839
59 L A 0.6451
60 L A 0.0375
61 L A 0.0000
62 D A -1.4239
63 E A -0.9360
64 L A 0.0000
65 V A -0.4599
66 V A 0.3515
67 L A 0.0000
68 I A 0.0000
69 R A -0.9441
70 E A -0.7547
71 L A 0.0000
72 Q A 0.0000
73 L A -0.4053
74 Y A -0.8293
75 V A 0.0000
76 K A -3.0258
77 E A -2.9816
78 N A -2.7465
79 N A -2.8283
80 V A -1.5659
81 S A -1.7006
82 E A -2.1425
83 N A -1.1836
84 L A 0.0000
85 L A -0.4688
86 I A 0.4777
87 I A 0.0000
88 L A 0.0000
89 E A -1.6554
90 E A -2.1054
91 M A 0.0000
92 L A 0.0000
93 T A -1.8478
94 A A 0.0000
95 L A 0.0000
96 D A -2.4265
97 E A -1.5837
98 Y A 0.0000
99 K A -1.2292
100 W A -0.5633
101 I A 0.0000
102 F A 0.0000
103 Q A -1.3581
104 Q A -1.0363
105 A A 0.0000
106 N A -0.7868
107 A A -0.7689
108 L A -0.4016
109 F A 0.0000
110 T A 0.0499
111 Q A -0.0459
112 L A 0.0000
113 L A 0.5006
114 I A 1.1465
115 G A 0.0000
116 L A 0.2267
117 A A 0.2529
118 T A -0.2890
119 G A -1.1307
120 R A -2.0404
121 T A -1.7168
122 T A -2.2359
123 Q A -2.9437
124 E A -3.2992
125 Q A -2.8461
126 L A 0.0000
127 D A -2.6428
128 A A -1.6640
129 I A -1.1702
130 I A 0.0000
131 A A -0.8369
132 Q A -1.2144
133 L A 0.0000
134 E A -1.2420
135 A A -1.2058
136 L A 0.0000
137 R A -2.1541
138 K A -2.8160
139 L A -1.5836
140 G A 0.0000
141 E A -3.4792
142 Q A -2.6735
143 V A 0.0000
144 S A -2.5881
145 T A -2.3093
146 K A -2.6114
147 I A 0.0000
148 D A -2.9370
149 S A -2.1244
150 L A 0.0000
151 M A 0.0000
152 N A -3.2560
153 K A -2.8606
154 I A 0.0000
155 K A -2.5319
156 E A -3.1785
157 E A -2.2691
158 L A -1.1845
159 Y A -0.6097
160 E A -1.9235
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 -0.5414 2.2089 View CSV PDB
4.5 -0.6453 2.0227 View CSV PDB
5.0 -0.7795 1.937 View CSV PDB
5.5 -0.924 1.937 View CSV PDB
6.0 -1.0558 1.937 View CSV PDB
6.5 -1.1554 1.937 View CSV PDB
7.0 -1.216 1.937 View CSV PDB
7.5 -1.2449 1.937 View CSV PDB
8.0 -1.2546 1.937 View CSV PDB
8.5 -1.2518 1.937 View CSV PDB
9.0 -1.2369 1.937 View CSV PDB