Project name: R6mu_3

Status: done

Started: 2026-02-28 23:18:51
Chain sequence(s) A: SMLESLVGKILNLLTQVRLTGQNIDDLYRMLVAGYEAGTLTDIETYRNQFMQLLRMLLMLLDELLRLIRELMRFIKENNVSENLLIILEEMLTALDEYKWIFQQANALFTQLLIGLATGTLTQEQLDAIIAQLEALRKLGEQVSTKIDSLMNKIKEELYE
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                                          (00:05:25)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/d831d3b82db7fd1/tmp/folded.pdb                (00:05:25)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:33)
Show buried residues
Minimal score value
-3.8978
Maximal score value
0.4635
Average score
-1.0488
Total score value
-167.8089
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 -0.2854
2 M A 0.4411
3 L A -0.0897
4 E A -1.6707
5 S A -1.0902
6 L A -0.9689
7 V A 0.0000
8 G A -1.6915
9 K A -2.1406
10 I A 0.0000
11 L A -1.1948
12 N A -1.8495
13 L A 0.0000
14 L A 0.0000
15 T A -0.4433
16 Q A -0.4546
17 V A 0.0000
18 R A -0.2154
19 L A 0.4635
20 T A -0.3322
21 G A 0.0000
22 Q A -1.9313
23 N A -2.3032
24 I A 0.0000
25 D A -2.4363
26 D A -2.9888
27 L A 0.0000
28 Y A 0.0000
29 R A -1.8275
30 M A -0.3605
31 L A 0.0000
32 V A 0.0000
33 A A -0.6500
34 G A -0.5171
35 Y A -0.7647
36 E A -1.9422
37 A A -0.9655
38 G A -0.9098
39 T A -0.5972
40 L A -0.2889
41 T A -0.8196
42 D A -1.8433
43 I A -1.3361
44 E A -2.6114
45 T A -1.9624
46 Y A -1.4454
47 R A -2.0857
48 N A -2.4531
49 Q A -2.0055
50 F A 0.0000
51 M A -1.5191
52 Q A -1.9289
53 L A -1.0837
54 L A 0.0000
55 R A -1.4520
56 M A -0.1389
57 L A 0.0000
58 L A -0.2487
59 M A 0.3016
60 L A -0.2486
61 L A 0.0000
62 D A -2.0333
63 E A -1.3838
64 L A 0.0000
65 L A -2.1143
66 R A -2.7013
67 L A 0.0000
68 I A 0.0000
69 R A -3.3573
70 E A -2.6940
71 L A 0.0000
72 M A 0.0000
73 R A -3.7820
74 F A -2.3172
75 I A 0.0000
76 K A -3.8978
77 E A -3.7112
78 N A -2.8611
79 N A -2.9072
80 V A -1.1502
81 S A -1.3726
82 E A -2.1879
83 N A -1.4654
84 L A 0.0000
85 L A -1.0766
86 I A 0.2257
87 I A 0.0000
88 L A 0.0000
89 E A -1.9735
90 E A -2.0389
91 M A 0.0000
92 L A -1.8133
93 T A -1.8152
94 A A 0.0000
95 L A 0.0000
96 D A -2.3211
97 E A -1.6694
98 Y A 0.0000
99 K A -1.4948
100 W A -0.6592
101 I A 0.0000
102 F A 0.0000
103 Q A -1.3583
104 Q A -1.0677
105 A A -0.8428
106 N A -0.9236
107 A A -0.5753
108 L A -0.3398
109 F A 0.0000
110 T A -0.1724
111 Q A -0.2412
112 L A 0.0000
113 L A 0.0000
114 I A 0.4293
115 G A 0.0000
116 L A 0.1144
117 A A -0.1694
118 T A 0.0658
119 G A -0.3449
120 T A -0.2080
121 L A -0.7534
122 T A -1.5450
123 Q A -2.4892
124 E A -3.0583
125 Q A -2.2828
126 L A 0.0000
127 D A -2.4880
128 A A -1.5235
129 I A -0.8871
130 I A -0.6958
131 A A -0.7024
132 Q A -0.9951
133 L A 0.0000
134 E A -1.0190
135 A A -0.8693
136 L A 0.0000
137 R A -1.8737
138 K A -2.4040
139 L A -1.3964
140 G A -1.8315
141 E A -2.7019
142 Q A -2.3549
143 V A 0.0000
144 S A -1.6307
145 T A -1.4783
146 K A -1.9226
147 I A 0.0000
148 D A -1.4100
149 S A -1.3742
150 L A 0.0000
151 M A -1.5511
152 N A -2.6669
153 K A -2.5820
154 I A 0.0000
155 K A -1.9820
156 E A -2.6143
157 E A -1.8065
158 L A -0.4169
159 Y A 0.0420
160 E A -1.4513
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 -0.669 2.0792 View CSV PDB
4.5 -0.7647 1.8668 View CSV PDB
5.0 -0.8917 1.5562 View CSV PDB
5.5 -1.0308 1.2401 View CSV PDB
6.0 -1.1597 1.0947 View CSV PDB
6.5 -1.258 1.0605 View CSV PDB
7.0 -1.3169 1.042 View CSV PDB
7.5 -1.3437 1.0344 View CSV PDB
8.0 -1.3514 1.0317 View CSV PDB
8.5 -1.3475 1.0308 View CSV PDB
9.0 -1.3328 1.0305 View CSV PDB