Project name: R5mu_1

Status: done

Started: 2026-02-28 22:01:08
Chain sequence(s) A: SMLESLVGKILNLLTQVRLTGQNIDDLYADLVAGYEAGTLGQIETYRNQFMQLLAQLLMLLDELLRLIRELMRYVKENNVSENLLIILEEMLTALDEYKWIFQQANALFTQLLIGIMTGTLTQEQLDAIIAQLEALRKLGEQVSTKIDSLMNKIKEELYE
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                                          (00:04:14)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/cb60c57c8ca539f/tmp/folded.pdb                (00:04:14)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:24)
Show buried residues
Minimal score value
-3.9879
Maximal score value
1.0803
Average score
-1.1018
Total score value
-176.2884
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 -0.4703
2 M A 0.1274
3 L A -0.6089
4 E A -1.7409
5 S A -1.2220
6 L A 0.0000
7 V A 0.0000
8 G A -1.5052
9 K A -2.0239
10 I A 0.0000
11 L A -1.0149
12 N A -1.8286
13 L A 0.0000
14 L A 0.0000
15 T A -1.0939
16 Q A -1.3202
17 V A 0.0000
18 R A -1.6770
19 L A -0.5102
20 T A 0.0000
21 G A 0.0000
22 Q A -2.5921
23 N A -2.3471
24 I A 0.0000
25 D A -2.5885
26 D A -3.1167
27 L A -2.0632
28 Y A 0.0000
29 A A -1.5784
30 D A -2.0793
31 L A 0.0000
32 V A -0.6355
33 A A -0.9969
34 G A -0.9978
35 Y A -0.9109
36 E A -1.7317
37 A A -0.9122
38 G A -0.9211
39 T A -0.6546
40 L A -0.7237
41 G A -1.1673
42 Q A -1.9439
43 I A 0.0000
44 E A -2.5044
45 T A -1.9952
46 Y A -1.9622
47 R A -2.4365
48 N A -2.2398
49 Q A -1.9395
50 F A 0.0000
51 M A -1.1780
52 Q A -1.7094
53 L A -0.9791
54 L A 0.0000
55 A A -0.2346
56 Q A -0.4528
57 L A 0.0000
58 L A -0.1030
59 M A 0.2652
60 L A 0.0000
61 L A 0.0000
62 D A -2.2496
63 E A -1.8853
64 L A 0.0000
65 L A -2.1374
66 R A -3.0924
67 L A 0.0000
68 I A 0.0000
69 R A -3.4150
70 E A -2.7215
71 L A 0.0000
72 M A 0.0000
73 R A -3.7367
74 Y A -2.3927
75 V A 0.0000
76 K A -3.9879
77 E A -3.7489
78 N A -2.9073
79 N A -2.9094
80 V A -1.2582
81 S A -1.3877
82 E A -2.0996
83 N A -1.2268
84 L A 0.0000
85 L A -1.0307
86 I A 0.2582
87 I A 0.0000
88 L A 0.0000
89 E A -2.1234
90 E A -2.4136
91 M A 0.0000
92 L A -2.0899
93 T A -1.9531
94 A A 0.0000
95 L A 0.0000
96 D A -2.4324
97 E A -1.5200
98 Y A 0.0000
99 K A -1.2643
100 W A -0.3454
101 I A 0.0000
102 F A 0.0000
103 Q A -0.7607
104 Q A -0.6829
105 A A -0.7090
106 N A -0.6486
107 A A -0.4778
108 L A -0.2196
109 F A 0.0000
110 T A -0.2143
111 Q A 0.0022
112 L A 0.0000
113 L A 0.0000
114 I A 1.0803
115 G A 0.0000
116 I A 0.8015
117 M A 0.7477
118 T A 0.5391
119 G A -0.0502
120 T A -0.0183
121 L A -0.6056
122 T A -1.5537
123 Q A -2.5255
124 E A -3.1025
125 Q A -2.3088
126 L A 0.0000
127 D A -2.3832
128 A A -1.5747
129 I A -1.0221
130 I A -0.7027
131 A A -0.8065
132 Q A -1.2328
133 L A 0.0000
134 E A -1.2958
135 A A -1.0870
136 L A 0.0000
137 R A -2.3713
138 K A -2.9146
139 L A -1.6800
140 G A 0.0000
141 E A -3.4897
142 Q A -2.7744
143 V A 0.0000
144 S A -2.0117
145 T A -1.6512
146 K A -2.2478
147 I A 0.0000
148 D A -1.5894
149 S A -1.4368
150 L A 0.0000
151 M A 0.0000
152 N A -2.7661
153 K A -2.7451
154 I A 0.0000
155 K A -2.3386
156 E A -3.1929
157 E A -2.2009
158 L A -1.0932
159 Y A -0.5964
160 E A -1.9870
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 -0.7012 2.216 View CSV PDB
4.5 -0.7972 2.0797 View CSV PDB
5.0 -0.9251 1.9088 View CSV PDB
5.5 -1.0651 1.8313 View CSV PDB
6.0 -1.1947 1.7929 View CSV PDB
6.5 -1.2944 1.7652 View CSV PDB
7.0 -1.3559 1.7504 View CSV PDB
7.5 -1.3855 1.7444 View CSV PDB
8.0 -1.3957 1.7423 View CSV PDB
8.5 -1.3942 1.7417 View CSV PDB
9.0 -1.3817 1.7414 View CSV PDB