Project name: R5mu_4

Status: done

Started: 2026-02-28 22:01:41
Chain sequence(s) A: SMLESLVGKILNLLTQVRLTGQNIDDLYADLVAGYEAGTLGQIETYRNQFMQLLAQLLMLLDELLRLIRELMRYIRENNVSENLLIILEEMLTALDEYKWIFQQANALFTQLLIGLATGTLTQEQLDAIIAQLEALRKLGEQVSTKIDSLMNKIKEELYE
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                                          (00:04:05)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/2b63920e7c6249a/tmp/folded.pdb                (00:04:05)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:22)
Show buried residues
Minimal score value
-4.0909
Maximal score value
0.8341
Average score
-1.0933
Total score value
-174.9326
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 -0.3662
2 M A 0.2895
3 L A -0.3627
4 E A -1.7881
5 S A -1.1189
6 L A -0.8092
7 V A 0.0000
8 G A -1.6548
9 K A -1.9974
10 I A 0.0000
11 L A -1.1410
12 N A -1.8172
13 L A 0.0000
14 L A 0.0000
15 T A -0.8096
16 Q A -0.9560
17 V A 0.0000
18 R A -1.3107
19 L A -0.0047
20 T A 0.0000
21 G A 0.0000
22 Q A -2.1782
23 N A -2.1889
24 I A 0.0000
25 D A -2.3262
26 D A -3.0068
27 L A -1.9426
28 Y A 0.0000
29 A A -1.6409
30 D A -2.0897
31 L A 0.0000
32 V A -0.9013
33 A A -1.0237
34 G A -0.9988
35 Y A -0.9448
36 E A -1.7434
37 A A -0.9203
38 G A -0.9249
39 T A -0.6515
40 L A -0.6932
41 G A -1.0472
42 Q A -1.7001
43 I A -1.0629
44 E A -2.1193
45 T A -1.7716
46 Y A -1.6259
47 R A -1.8064
48 N A -2.3597
49 Q A -1.9858
50 F A 0.0000
51 M A -1.1450
52 Q A -1.7503
53 L A -0.9349
54 L A 0.0000
55 A A -0.2036
56 Q A -0.3947
57 L A 0.0000
58 L A -0.0872
59 M A 0.3372
60 L A 0.0000
61 L A 0.0000
62 D A -2.0151
63 E A -1.3788
64 L A 0.0000
65 L A -1.8754
66 R A -2.4161
67 L A 0.0000
68 I A 0.0000
69 R A -2.8382
70 E A -2.3485
71 L A 0.0000
72 M A -2.5202
73 R A -3.7327
74 Y A -2.3646
75 I A 0.0000
76 R A -4.0909
77 E A -3.7876
78 N A -2.8692
79 N A -2.9792
80 V A -1.1587
81 S A -1.6663
82 E A -2.4157
83 N A -1.8947
84 L A 0.0000
85 L A 0.0000
86 I A -0.4179
87 I A 0.0000
88 L A 0.0000
89 E A -2.4827
90 E A -2.6306
91 M A 0.0000
92 L A 0.0000
93 T A -2.0520
94 A A 0.0000
95 L A 0.0000
96 D A -2.5011
97 E A -1.6937
98 Y A 0.0000
99 K A -1.3390
100 W A -0.5153
101 I A 0.0000
102 F A 0.0000
103 Q A -1.2643
104 Q A -0.9227
105 A A -0.8159
106 N A -0.7197
107 A A -0.5776
108 L A -0.2838
109 F A 0.0000
110 T A -0.0575
111 Q A -0.1917
112 L A 0.0000
113 L A 0.0000
114 I A 0.8341
115 G A 0.0000
116 L A 0.3986
117 A A 0.0919
118 T A 0.1614
119 G A -0.3089
120 T A -0.1748
121 L A -0.7625
122 T A -1.6412
123 Q A -2.6667
124 E A -3.1750
125 Q A -2.4366
126 L A 0.0000
127 D A -2.4383
128 A A -1.5507
129 I A -0.9973
130 I A -0.6638
131 A A -0.7004
132 Q A -0.9218
133 L A 0.0000
134 E A -0.9201
135 A A -0.9040
136 L A 0.0000
137 R A -2.0979
138 K A -2.6773
139 L A -1.6107
140 G A 0.0000
141 E A -3.2401
142 Q A -2.6424
143 V A 0.0000
144 S A -2.1215
145 T A -1.6894
146 K A -2.0542
147 I A 0.0000
148 D A -1.4670
149 S A -1.3683
150 L A 0.0000
151 M A -1.5442
152 N A -2.7121
153 K A -2.8038
154 I A 0.0000
155 K A -2.1312
156 E A -2.8360
157 E A -2.0844
158 L A -0.7428
159 Y A -0.1941
160 E A -1.6421
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 -0.6671 2.1299 View CSV PDB
4.5 -0.7629 1.9811 View CSV PDB
5.0 -0.8898 1.8007 View CSV PDB
5.5 -1.0295 1.7249 View CSV PDB
6.0 -1.1611 1.6927 View CSV PDB
6.5 -1.2657 1.6713 View CSV PDB
7.0 -1.3344 1.6608 View CSV PDB
7.5 -1.3727 1.6568 View CSV PDB
8.0 -1.3924 1.6554 View CSV PDB
8.5 -1.4008 1.6549 View CSV PDB
9.0 -1.3978 1.6548 View CSV PDB