Project name: R4mu_3

Status: done

Started: 2026-02-28 20:09:35
Chain sequence(s) A: SMLESLVGKILALLTQVRLTGQNIDDLYADLVAGYEAGTLGQIETYRNQLIQLLAQLLMLLDELVVLIRELMRYVKENNVSENLLIILEEMLTALDEYKWIFQQANALFTQLLIGLATGTLTQEQLDAIIAQLEALRKLGEQVSTKIDSLMNKIKEELYE
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                                          (00:04:58)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/b3fa0e35efd016a/tmp/folded.pdb                (00:04:58)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:14)
Show buried residues
Minimal score value
-4.0263
Maximal score value
1.0389
Average score
-1.0321
Total score value
-165.1283
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 -0.3617
2 M A 0.3300
3 L A -0.4516
4 E A -1.7669
5 S A -1.2381
6 L A 0.0000
7 V A 0.0000
8 G A -1.3581
9 K A -2.0791
10 I A 0.0000
11 L A -0.2522
12 A A -0.4253
13 L A -0.5066
14 L A -0.1831
15 T A -0.2513
16 Q A -0.3545
17 V A 0.0000
18 R A -0.8170
19 L A -0.1475
20 T A 0.0000
21 G A 0.0000
22 Q A -2.5348
23 N A -2.5017
24 I A 0.0000
25 D A -2.9536
26 D A -3.2920
27 L A -2.1324
28 Y A 0.0000
29 A A -1.7691
30 D A -2.2345
31 L A 0.0000
32 V A -0.9280
33 A A -1.0260
34 G A -0.9864
35 Y A -0.9534
36 E A -2.1117
37 A A -0.9398
38 G A -0.9455
39 T A -0.6806
40 L A -0.6543
41 G A -1.1248
42 Q A -1.8751
43 I A -1.1728
44 E A -2.4599
45 T A -1.8422
46 Y A -1.3203
47 R A -1.5489
48 N A -1.5913
49 Q A -1.4561
50 L A 0.0000
51 I A 0.2373
52 Q A -1.0545
53 L A -0.4460
54 L A 0.0000
55 A A 0.3170
56 Q A -0.0735
57 L A 0.0000
58 L A 0.1265
59 M A 0.2186
60 L A -0.2740
61 L A 0.0000
62 D A -1.7736
63 E A -1.6647
64 L A 0.0000
65 V A -0.6512
66 V A 0.1813
67 L A -0.8994
68 I A 0.0000
69 R A -1.7656
70 E A -1.9806
71 L A 0.0000
72 M A -2.2388
73 R A -3.7407
74 Y A -2.4147
75 V A 0.0000
76 K A -4.0263
77 E A -3.7200
78 N A -2.8380
79 N A -2.8901
80 V A -1.2174
81 S A -1.3631
82 E A -2.0804
83 N A -1.2118
84 L A 0.0000
85 L A -1.1060
86 I A 0.3414
87 I A 0.0000
88 L A 0.0000
89 E A -1.9117
90 E A -2.1524
91 M A 0.0000
92 L A -1.2776
93 T A -1.8819
94 A A 0.0000
95 L A 0.0000
96 D A -2.4328
97 E A -1.6759
98 Y A 0.0000
99 K A -1.2887
100 W A -0.5292
101 I A 0.0000
102 F A 0.0000
103 Q A -1.2363
104 Q A -0.9302
105 A A 0.0000
106 N A -0.6122
107 A A -0.6537
108 L A -0.2895
109 F A 0.0000
110 T A 0.0447
111 Q A -0.0213
112 L A 0.0000
113 L A 0.0000
114 I A 1.0389
115 G A 0.0000
116 L A 0.5580
117 A A 0.1628
118 T A 0.2529
119 G A -0.2304
120 T A -0.1106
121 L A -0.7387
122 T A -1.6397
123 Q A -2.6861
124 E A -3.2620
125 Q A -2.4630
126 L A 0.0000
127 D A -2.9382
128 A A -1.6681
129 I A -1.1478
130 I A -0.8471
131 A A -0.8828
132 Q A -1.0156
133 L A 0.0000
134 E A -1.3728
135 A A -1.0533
136 L A 0.0000
137 R A -2.2388
138 K A -2.7543
139 L A -1.6473
140 G A -2.1024
141 E A -3.3052
142 Q A -2.6484
143 V A 0.0000
144 S A 0.0000
145 T A -1.7292
146 K A -2.2173
147 I A 0.0000
148 D A -1.8222
149 S A -1.6525
150 L A 0.0000
151 M A 0.0000
152 N A -2.9077
153 K A -2.8948
154 I A 0.0000
155 K A -2.3317
156 E A -3.2029
157 E A -2.2294
158 L A -1.0981
159 Y A -0.5696
160 E A -1.9777
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 -0.4738 2.1988 View CSV PDB
4.5 -0.5844 2.1584 View CSV PDB
5.0 -0.7305 2.1075 View CSV PDB
5.5 -0.8892 2.0547 View CSV PDB
6.0 -1.036 2.008 View CSV PDB
6.5 -1.1502 1.9753 View CSV PDB
7.0 -1.2225 1.9584 View CSV PDB
7.5 -1.2597 1.9517 View CSV PDB
8.0 -1.2753 1.9494 View CSV PDB
8.5 -1.2773 1.9486 View CSV PDB
9.0 -1.2666 1.9484 View CSV PDB