Project name: R5mu_2

Status: done

Started: 2026-02-28 22:01:18
Chain sequence(s) A: SMLESLVGKILNLLTQVRLTGQNIDDLYADLVAGYEAGTLGQIETYRNQFMQLLAQLLMLLDELLRLIRELMRFIKENNVSENLLIILEEMLTALDEYKWIFQQANALFTQLLIGLATGTLTQEQLDAIIAQLEALRKLGEQVSTKIDSLMNKIKEELYE
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                                          (00:04:24)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/6dd4298d910d2a4/tmp/folded.pdb                (00:04:24)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:40)
Show buried residues
Minimal score value
-4.0184
Maximal score value
0.4186
Average score
-1.1596
Total score value
-185.5307
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 -0.3793
2 M A 0.2494
3 L A -0.1718
4 E A -1.7693
5 S A -1.0692
6 L A 0.0000
7 V A 0.0000
8 G A -1.4740
9 K A -2.0809
10 I A 0.0000
11 L A -0.9599
12 N A -1.7110
13 L A -1.0845
14 L A 0.0000
15 T A -0.8507
16 Q A -0.8102
17 V A 0.0000
18 R A -1.1290
19 L A -0.1410
20 T A 0.0000
21 G A 0.0000
22 Q A -1.9159
23 N A -2.2413
24 I A 0.0000
25 D A -2.4167
26 D A -3.0492
27 L A -2.0063
28 Y A 0.0000
29 A A -1.5789
30 D A -2.1007
31 L A 0.0000
32 V A -0.7186
33 A A -1.0097
34 G A -0.9850
35 Y A -1.0792
36 E A -1.9212
37 A A -0.9222
38 G A -0.9280
39 T A -0.6581
40 L A -0.6461
41 G A -1.0875
42 Q A -1.9118
43 I A -1.4608
44 E A -2.7638
45 T A -2.0577
46 Y A -1.7874
47 R A -2.3011
48 N A -2.5869
49 Q A -2.0928
50 F A 0.0000
51 M A -1.1410
52 Q A -1.7587
53 L A -0.9905
54 L A 0.0000
55 A A -0.1924
56 Q A -0.3568
57 L A 0.0000
58 L A 0.1074
59 M A 0.4186
60 L A 0.0000
61 L A 0.0000
62 D A -1.7505
63 E A -2.0299
64 L A 0.0000
65 L A -2.1226
66 R A -3.1814
67 L A -2.4121
68 I A 0.0000
69 R A -3.6203
70 E A -3.0558
71 L A 0.0000
72 M A 0.0000
73 R A -3.8359
74 F A -2.4337
75 I A 0.0000
76 K A -4.0184
77 E A -3.7210
78 N A -2.8660
79 N A -2.8797
80 V A -1.0321
81 S A -1.2814
82 E A -2.0512
83 N A -1.2165
84 L A 0.0000
85 L A -1.0784
86 I A 0.2597
87 I A 0.0000
88 L A 0.0000
89 E A -2.2036
90 E A -2.4953
91 M A 0.0000
92 L A 0.0000
93 T A -2.0737
94 A A 0.0000
95 L A 0.0000
96 D A -2.4596
97 E A -1.7216
98 Y A 0.0000
99 K A -1.3764
100 W A -0.5119
101 I A 0.0000
102 F A 0.0000
103 Q A -1.2365
104 Q A -0.9027
105 A A -0.8046
106 N A -0.6061
107 A A -0.5147
108 L A -0.2840
109 F A 0.0000
110 T A -0.1665
111 Q A -0.2736
112 L A 0.0000
113 L A 0.0000
114 I A 0.3020
115 G A 0.0000
116 L A 0.2812
117 A A -0.1936
118 T A 0.0389
119 G A -0.3823
120 T A -0.2383
121 L A -0.8614
122 T A -1.6967
123 Q A -2.8021
124 E A -3.3342
125 Q A -2.5812
126 L A 0.0000
127 D A -3.0500
128 A A -1.7942
129 I A -1.0443
130 I A -0.8295
131 A A -0.8890
132 Q A -1.0848
133 L A 0.0000
134 E A -1.1138
135 A A -1.0133
136 L A 0.0000
137 R A -2.2348
138 K A -2.7516
139 L A -1.6722
140 G A -2.1334
141 E A -3.2233
142 Q A -2.7202
143 V A 0.0000
144 S A -1.9911
145 T A -1.6658
146 K A -2.0808
147 I A 0.0000
148 D A -1.4016
149 S A -1.3871
150 L A 0.0000
151 M A -1.5887
152 N A -2.7005
153 K A -2.8442
154 I A 0.0000
155 K A -2.4108
156 E A -3.2648
157 E A -2.3823
158 L A -0.9545
159 Y A -0.3740
160 E A -1.9827
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 -0.7208 2.1506 View CSV PDB
4.5 -0.8185 2.0106 View CSV PDB
5.0 -0.9498 1.8364 View CSV PDB
5.5 -1.0948 1.6574 View CSV PDB
6.0 -1.2298 1.4987 View CSV PDB
6.5 -1.3335 1.3747 View CSV PDB
7.0 -1.3961 1.2872 View CSV PDB
7.5 -1.4241 1.2262 View CSV PDB
8.0 -1.4309 1.1809 View CSV PDB
8.5 -1.4251 1.1497 View CSV PDB
9.0 -1.4078 1.1405 View CSV PDB