Project name: R3mu1

Status: done

Started: 2026-02-28 13:37:32
Chain sequence(s) A: SMLESLVGKISLLLTMIRLTGQNIDDLYADLVAGYEAGTLGQIETYRNQLIQLLAQLGILLDELVVLIRELQLYVKENNVSENLLIILEEMLTALDEYKWIFQQANALFTQLLIGLATGRTTQEQLDAIIAQLEALRKLGEQVSTKIDSLMNKIKEELYE
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]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[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                                          (00:03:51)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/4a09d1c57808a44/tmp/folded.pdb                (00:03:51)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:09)
Show buried residues
Minimal score value
-3.5865
Maximal score value
1.4286
Average score
-0.9739
Total score value
-155.8203
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 -0.4725
2 M A 0.0749
3 L A -0.7220
4 E A -1.8741
5 S A -1.3099
6 L A 0.0000
7 V A 0.0000
8 G A -1.1510
9 K A -1.5720
10 I A 0.0000
11 S A -0.1320
12 L A 0.9007
13 L A 0.0000
14 L A 0.0000
15 T A 0.4358
16 M A 0.7290
17 I A 0.0000
18 R A -0.8717
19 L A 0.1860
20 T A 0.0000
21 G A 0.0000
22 Q A -2.1195
23 N A -2.2270
24 I A 0.0000
25 D A -2.4330
26 D A -2.8282
27 L A -1.8428
28 Y A 0.0000
29 A A -1.6264
30 D A -2.0842
31 L A 0.0000
32 V A -0.7774
33 A A -0.9685
34 G A -1.0551
35 Y A -0.9494
36 E A -1.8838
37 A A -0.8791
38 G A -0.7559
39 T A -0.5731
40 L A 0.0857
41 G A -0.9446
42 Q A -1.3837
43 I A 0.0000
44 E A -1.5097
45 T A -1.4085
46 Y A -1.2204
47 R A -1.4641
48 N A -1.8586
49 Q A -1.6263
50 L A 0.0000
51 I A -0.5966
52 Q A -1.4703
53 L A -0.7686
54 L A -0.3537
55 A A 0.0261
56 Q A -0.2129
57 L A 0.0000
58 G A -0.2688
59 I A 0.7902
60 L A -0.0354
61 L A 0.0000
62 D A -1.6287
63 E A -1.3639
64 L A 0.0000
65 V A -0.7425
66 V A -0.0322
67 L A 0.0000
68 I A 0.0000
69 R A -1.4577
70 E A -0.7943
71 L A 0.0000
72 Q A -0.8814
73 L A -0.5171
74 Y A -0.9457
75 V A 0.0000
76 K A -2.8283
77 E A -2.8959
78 N A -2.5133
79 N A -2.7006
80 V A -1.8278
81 S A -1.6251
82 E A -2.1920
83 N A -1.6366
84 L A 0.0000
85 L A -0.5314
86 I A 0.2100
87 I A -0.6653
88 L A 0.0000
89 E A -1.8878
90 E A -1.6962
91 M A 0.0000
92 L A -1.1686
93 T A -1.6267
94 A A 0.0000
95 L A 0.0000
96 D A -2.5729
97 E A -1.8164
98 Y A 0.0000
99 K A -1.9622
100 W A -1.1314
101 I A 0.0000
102 F A -0.8554
103 Q A -1.4946
104 Q A -1.1440
105 A A 0.0000
106 N A -0.6156
107 A A -0.6265
108 L A -0.2213
109 F A 0.0000
110 T A -0.0754
111 Q A 0.0484
112 L A 0.0000
113 L A 0.6760
114 I A 1.4286
115 G A 0.0000
116 L A 0.3484
117 A A 0.3823
118 T A -0.1911
119 G A -1.0572
120 R A -2.0144
121 T A -1.6745
122 T A -2.3073
123 Q A -3.0325
124 E A -3.4061
125 Q A -2.9722
126 L A 0.0000
127 D A -2.8677
128 A A -1.8365
129 I A -1.2825
130 I A -0.9718
131 A A -1.1159
132 Q A -1.2922
133 L A 0.0000
134 E A -1.9135
135 A A -1.3904
136 L A 0.0000
137 R A -2.1960
138 K A -2.7570
139 L A -1.5660
140 G A 0.0000
141 E A -2.8338
142 Q A -2.4058
143 V A 0.0000
144 S A -1.7845
145 T A -1.5831
146 K A -1.9646
147 I A 0.0000
148 D A -1.5398
149 S A -1.4361
150 L A 0.0000
151 M A 0.0000
152 N A -2.8880
153 K A -2.8153
154 I A 0.0000
155 K A -2.7140
156 E A -3.5865
157 E A -2.6798
158 L A -1.5279
159 Y A -1.2593
160 E A -2.3735
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 -0.4649 2.8316 View CSV PDB
4.5 -0.5617 2.6491 View CSV PDB
5.0 -0.6943 2.4309 View CSV PDB
5.5 -0.8406 2.4014 View CSV PDB
6.0 -0.9756 2.3723 View CSV PDB
6.5 -1.0789 2.3481 View CSV PDB
7.0 -1.1402 2.3327 View CSV PDB
7.5 -1.166 2.3255 View CSV PDB
8.0 -1.1709 2.3228 View CSV PDB
8.5 -1.1643 2.3218 View CSV PDB
9.0 -1.1473 2.3216 View CSV PDB