Project name: R4mu_4

Status: done

Started: 2026-02-28 20:09:48
Chain sequence(s) A: SMLESLVGKILALLTQVRLTGQNIDDLYADLVAGYEAGTLGQIETYRNQLIQLLRMLLMLLDELVVLIRELMRYVKENNVSENLLIILEEMLTALDEYKWIFQQANALFTQLLIGLATGRTTQEQLDAIIAQLEALRKLGEQVSTKIDSLMNKIKEELYE
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                                          (00:04:41)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/cb34d00eac0c783/tmp/folded.pdb                (00:04:41)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:59)
Show buried residues
Minimal score value
-3.9945
Maximal score value
1.4439
Average score
-1.0243
Total score value
-163.8921
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 -0.2961
2 M A 0.3076
3 L A -0.4189
4 E A -1.5155
5 S A -1.0299
6 L A 0.0000
7 V A 0.0000
8 G A -1.1457
9 K A -1.6842
10 I A 0.0000
11 L A -0.0734
12 A A -0.3471
13 L A -0.5540
14 L A 0.0000
15 T A -0.5216
16 Q A -0.5886
17 V A 0.0000
18 R A -1.9184
19 L A -0.4914
20 T A 0.0000
21 G A -1.9441
22 Q A -2.4213
23 N A -2.2887
24 I A -1.8283
25 D A -2.4665
26 D A -2.8457
27 L A -1.5882
28 Y A 0.0000
29 A A -1.1036
30 D A -1.5729
31 L A 0.0000
32 V A -0.4228
33 A A -0.7293
34 G A -0.8033
35 Y A -0.7328
36 E A -1.7724
37 A A -0.7341
38 G A -0.6713
39 T A -0.3204
40 L A 0.4465
41 G A -0.4537
42 Q A -1.0431
43 I A 0.0000
44 E A -1.2291
45 T A -1.0904
46 Y A -1.1542
47 R A -1.3022
48 N A -1.5305
49 Q A -1.4681
50 L A 0.0000
51 I A -1.1830
52 Q A -1.8709
53 L A -0.9870
54 L A 0.0000
55 R A -1.7572
56 M A -0.3413
57 L A 0.0000
58 L A -0.6017
59 M A -0.1787
60 L A 0.0000
61 L A 0.0000
62 D A -1.6003
63 E A -0.9901
64 L A 0.0000
65 V A -0.4761
66 V A 0.4067
67 L A 0.0000
68 I A 0.0000
69 R A -2.1288
70 E A -1.8078
71 L A 0.0000
72 M A 0.0000
73 R A -3.7690
74 Y A -2.4080
75 V A 0.0000
76 K A -3.9945
77 E A -3.7576
78 N A -2.9074
79 N A -2.8994
80 V A -1.2279
81 S A -1.3893
82 E A -2.1222
83 N A -1.2842
84 L A 0.0000
85 L A -1.0995
86 I A 0.0863
87 I A 0.0000
88 L A 0.0000
89 E A -2.0939
90 E A -2.2460
91 M A 0.0000
92 L A -1.3671
93 T A -1.9092
94 A A 0.0000
95 L A 0.0000
96 D A -2.4539
97 E A -1.7062
98 Y A 0.0000
99 K A -1.4270
100 W A -0.5079
101 I A 0.0000
102 F A 0.0000
103 Q A -1.4818
104 Q A -0.9131
105 A A 0.0000
106 N A -0.9367
107 A A -0.6425
108 L A -0.3034
109 F A 0.0000
110 T A 0.1259
111 Q A -0.1157
112 L A 0.0000
113 L A 0.6485
114 I A 1.4439
115 G A 0.0000
116 L A 0.2545
117 A A 0.2387
118 T A -0.2416
119 G A -1.1125
120 R A -2.0611
121 T A -1.6758
122 T A -2.2109
123 Q A -2.8387
124 E A -3.1494
125 Q A -2.8333
126 L A -1.7691
127 D A -2.0948
128 A A -1.4686
129 I A 0.0000
130 I A -0.5530
131 A A -0.7355
132 Q A -0.9993
133 L A 0.0000
134 E A -1.3943
135 A A -1.1572
136 L A 0.0000
137 R A -2.5393
138 K A -2.9173
139 L A -1.7290
140 G A 0.0000
141 E A -3.2656
142 Q A -2.6921
143 V A 0.0000
144 S A -2.1463
145 T A -1.6620
146 K A -2.1524
147 I A 0.0000
148 D A -1.7927
149 S A -1.5293
150 L A 0.0000
151 M A 0.0000
152 N A -2.7097
153 K A -2.6326
154 I A 0.0000
155 K A -2.2277
156 E A -2.8882
157 E A -2.0801
158 L A -1.0064
159 Y A -0.5616
160 E A -2.0352
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 -0.6822 2.4104 View CSV PDB
4.5 -0.7773 2.4104 View CSV PDB
5.0 -0.9007 2.4104 View CSV PDB
5.5 -1.0327 2.4104 View CSV PDB
6.0 -1.1518 2.4104 View CSV PDB
6.5 -1.2404 2.4104 View CSV PDB
7.0 -1.2921 2.4104 View CSV PDB
7.5 -1.3144 2.4104 View CSV PDB
8.0 -1.3186 2.4104 View CSV PDB
8.5 -1.3114 2.4104 View CSV PDB
9.0 -1.2932 2.4104 View CSV PDB