Project name: Dimer cogombre

Status: done

Started: 2026-05-22 09:38:23
Chain sequence(s) A: QAVCVLQGQIVSGTIVFSQEGSEVTVSGEVKGLTKGLHGFHIHEFGDNTNGCTSAGGHFNPEGKTHGGPTDDIRHVGDLGNVEAGDDGVATVNIKDPVISLSGAHSIIGRSLVVHEGVDDLGKGGHEQSLTTGNAGGRAACGVIGI
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                                          (00:01:12)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/7b06e0e91c86269/tmp/folded.pdb                (00:01:12)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:35)
Show buried residues
Minimal score value
-3.2572
Maximal score value
1.9865
Average score
-0.6651
Total score value
-97.1103
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 Q A -0.7377
2 A A 0.0000
3 V A 1.5628
4 C A 0.0000
5 V A 1.7344
6 L A 0.0000
7 Q A -0.8587
8 G A -1.0583
9 Q A -0.6690
10 I A 0.8013
11 V A 0.0000
12 S A -0.6639
13 G A -0.6213
14 T A 0.2471
15 I A 0.0000
16 V A 0.6854
17 F A 0.0000
18 S A -1.3920
19 Q A -2.3935
20 E A -2.8440
21 G A -1.9464
22 S A -1.4999
23 E A -2.3925
24 V A 0.0000
25 T A -1.6950
26 V A 0.0000
27 S A -0.7410
28 G A -0.5933
29 E A -1.2864
30 V A 0.0000
31 K A -1.7703
32 G A -1.0828
33 L A 0.0000
34 T A -2.1699
35 K A -2.9606
36 G A -1.3635
37 L A -0.4377
38 H A 0.0000
39 G A 0.0000
40 F A 0.0000
41 H A 0.0000
42 I A 0.0000
43 H A 0.0000
44 E A -0.1108
45 F A 0.8649
46 G A -0.1261
47 D A -1.2336
48 N A -1.9085
49 T A -1.6776
50 N A -2.0681
51 G A -1.9351
52 C A -1.1503
53 T A -0.9062
54 S A -1.0048
55 A A 0.0000
56 G A -0.2266
57 G A -0.3205
58 H A 0.0000
59 F A 0.0000
60 N A -1.4692
61 P A -1.5790
62 E A -2.4269
63 G A -1.8497
64 K A -1.6017
65 T A -0.1561
66 H A 0.0000
67 G A 0.0000
68 G A 0.0000
69 P A -0.5179
70 T A -0.6175
71 D A -1.1923
72 D A -1.7659
73 I A -0.6488
74 R A 0.0000
75 H A 0.0000
76 V A 0.0000
77 G A 0.0000
78 D A 0.0000
79 L A 0.0000
80 G A 0.0000
81 N A -0.1906
82 V A 0.0000
83 E A -1.8464
84 A A 0.0000
85 G A -2.7057
86 D A -3.2516
87 D A -3.2572
88 G A -2.7717
89 V A -2.2353
90 A A 0.0000
91 T A -1.2138
92 V A 0.0000
93 N A -1.6325
94 I A -1.3519
95 K A -2.1867
96 D A 0.0000
97 P A -1.1727
98 V A -0.0328
99 I A 0.0000
100 S A -0.5982
101 L A -0.1904
102 S A -0.3686
103 G A -0.5296
104 A A -0.5286
105 H A -0.4560
106 S A -0.1962
107 I A 0.0000
108 I A 0.5249
109 G A 0.2533
110 R A -0.0103
111 S A 0.0000
112 L A 0.0000
113 V A 0.0000
114 V A 0.0000
115 H A 0.0000
116 E A -1.8707
117 G A -0.6639
118 V A 0.6913
119 D A 0.0000
120 D A -0.6893
121 L A -0.2414
122 G A -0.9226
123 K A -2.0136
124 G A -2.0546
125 G A -1.9821
126 H A -2.4225
127 E A -2.4357
128 Q A -1.6992
129 S A 0.0000
130 L A 0.2081
131 T A -0.1215
132 T A -0.4785
133 G A 0.0000
134 N A -1.4205
135 A A 0.0000
136 G A -1.2805
137 G A -1.4335
138 R A -1.4217
139 A A -1.2302
140 A A 0.0000
141 C A 0.0000
142 G A -0.0034
143 V A 0.8320
144 I A 0.0000
145 G A 1.2808
146 I A 1.9865
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 -0.2181 3.4362 View CSV PDB
4.5 -0.2703 3.3441 View CSV PDB
5.0 -0.3348 3.2341 View CSV PDB
5.5 -0.4036 3.1158 View CSV PDB
6.0 -0.4665 3.0916 View CSV PDB
6.5 -0.512 3.0916 View CSV PDB
7.0 -0.5345 3.0916 View CSV PDB
7.5 -0.5373 3.0916 View CSV PDB
8.0 -0.5271 3.0916 View CSV PDB
8.5 -0.5073 3.0916 View CSV PDB
9.0 -0.4792 3.0916 View CSV PDB