Project name: R4mu_5

Status: done

Started: 2026-02-28 20:10:11
Chain sequence(s) A: SMLESLVGKISLLLTQVRLTGQNIDDLYADLVAGYEAGTLGQIETYRNQLIQLLRMLLMLLDELLRLIRELMRYVKENNVSENLLIILEEMLTALDEYKWIFQQANALFTQLLIGLATGRTTQEQLDAIIAQLEALRKLGEQVSTKIDSLMNKIKEELYE
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                                          (00:04:51)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/bd172e9bebf18fb/tmp/folded.pdb                (00:04:51)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:09)
Show buried residues
Minimal score value
-3.9287
Maximal score value
1.2763
Average score
-1.0807
Total score value
-172.9047
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 -0.3449
2 M A 0.3401
3 L A -0.3783
4 E A -1.8005
5 S A -1.0569
6 L A -0.6894
7 V A 0.0000
8 G A -0.9001
9 K A -1.0743
10 I A 0.0000
11 S A -0.2340
12 L A 0.6062
13 L A 0.0000
14 L A -0.0675
15 T A -0.0280
16 Q A -0.0512
17 V A 0.0000
18 R A -0.8743
19 L A -0.1670
20 T A 0.0000
21 G A -1.4605
22 Q A -2.0441
23 N A -2.3182
24 I A 0.0000
25 D A -2.4211
26 D A -2.9415
27 L A -1.7710
28 Y A 0.0000
29 A A -1.3856
30 D A -1.8977
31 L A 0.0000
32 V A -0.5736
33 A A -0.9139
34 G A -1.0038
35 Y A -1.1777
36 E A -2.0273
37 A A -0.9137
38 G A -0.9772
39 T A -0.6690
40 L A -0.4847
41 G A -0.8819
42 Q A -1.3687
43 I A 0.0000
44 E A -1.6831
45 T A -1.4074
46 Y A -1.2219
47 R A -1.4202
48 N A -1.8430
49 Q A -1.7415
50 L A 0.0000
51 I A -1.2237
52 Q A -1.8830
53 L A -1.0393
54 L A 0.0000
55 R A -1.3185
56 M A -0.1332
57 L A 0.0000
58 L A -0.3262
59 M A 0.1470
60 L A 0.0000
61 L A 0.0000
62 D A -2.1639
63 E A -1.4111
64 L A 0.0000
65 L A -2.0992
66 R A -2.5392
67 L A 0.0000
68 I A 0.0000
69 R A -3.1960
70 E A -2.5651
71 L A 0.0000
72 M A -2.3047
73 R A -3.7722
74 Y A -2.3715
75 V A 0.0000
76 K A -3.9287
77 E A -3.7633
78 N A -2.8919
79 N A -2.9766
80 V A -1.3287
81 S A -1.4464
82 E A -2.2372
83 N A -1.3740
84 L A 0.0000
85 L A -0.9384
86 I A 0.4070
87 I A 0.0000
88 L A 0.0000
89 E A -1.6297
90 E A -1.9491
91 M A 0.0000
92 L A -1.8285
93 T A -1.7805
94 A A 0.0000
95 L A 0.0000
96 D A -2.5927
97 E A -1.8397
98 Y A 0.0000
99 K A -1.4550
100 W A -0.6504
101 I A 0.0000
102 F A -0.7418
103 Q A -1.2767
104 Q A -0.8407
105 A A 0.0000
106 N A -0.7336
107 A A -0.5465
108 L A -0.2575
109 F A 0.0000
110 T A -0.0885
111 Q A -0.0104
112 L A 0.0000
113 L A 0.4145
114 I A 1.2763
115 G A 0.0000
116 L A 0.0365
117 A A 0.1242
118 T A -0.2226
119 G A -1.0943
120 R A -2.0301
121 T A -1.6838
122 T A -2.2986
123 Q A -3.0084
124 E A -3.3952
125 Q A -2.9586
126 L A 0.0000
127 D A -2.8516
128 A A -1.7883
129 I A -1.2866
130 I A 0.0000
131 A A -0.9933
132 Q A -1.1658
133 L A 0.0000
134 E A -1.5385
135 A A -1.2132
136 L A 0.0000
137 R A -2.3199
138 K A -2.8273
139 L A -1.6751
140 G A 0.0000
141 E A -3.1745
142 Q A -2.6572
143 V A 0.0000
144 S A 0.0000
145 T A -1.9105
146 K A -2.3551
147 I A 0.0000
148 D A -2.1918
149 S A -1.7945
150 L A 0.0000
151 M A 0.0000
152 N A -2.8826
153 K A -2.6647
154 I A 0.0000
155 K A -2.2589
156 E A -2.9079
157 E A -2.2491
158 L A -1.0127
159 Y A -0.3875
160 E A -1.7903
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 -0.7003 2.2931 View CSV PDB
4.5 -0.8 2.262 View CSV PDB
5.0 -0.9327 2.225 View CSV PDB
5.5 -1.078 2.1879 View CSV PDB
6.0 -1.2126 2.1566 View CSV PDB
6.5 -1.3168 2.1362 View CSV PDB
7.0 -1.3816 2.1264 View CSV PDB
7.5 -1.4134 2.1227 View CSV PDB
8.0 -1.4252 2.1214 View CSV PDB
8.5 -1.425 2.121 View CSV PDB
9.0 -1.413 2.1209 View CSV PDB