Project name: d9d94129df9b0bb

Status: done

Started: 2025-12-30 05:39:26
Chain sequence(s) A: VVLAALLQGVQAQVQPVESGGGSVQAGASLRLSCTVSSSTINRYAMAWFRQAPGKEREFVGGVSHIGGASHYADSVKGRFTLSRDDAKRTLYLQMSNLRPEDTAVYYCAVGFEASNWRYNSWDYWGQGTQVTVSS
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                                          (00:01:34)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/d9d94129df9b0bb/tmp/folded.pdb                (00:01:34)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:29)
Show buried residues
Minimal score value
-3.4418
Maximal score value
3.4035
Average score
-0.6726
Total score value
-90.8011
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 V A 3.0447
2 V A 3.4035
3 L A 3.1161
4 A A 2.1716
5 A A 1.7634
6 L A 2.1308
7 L A 1.8880
8 Q A 0.1636
9 G A 0.2544
10 V A 0.7326
11 Q A -0.9314
12 A A -0.7950
13 Q A -1.3802
14 V A -0.9062
15 Q A -0.6572
16 P A 0.0000
17 V A 1.1760
18 E A 0.0449
19 S A -0.4737
20 G A -1.1270
21 G A -1.1710
22 G A -0.9084
23 S A -0.6922
24 V A -0.7723
25 Q A -1.7285
26 A A -1.8130
27 G A -1.6798
28 A A -1.1557
29 S A -1.2316
30 L A -1.0284
31 R A -1.8240
32 L A 0.0000
33 S A -0.4126
34 C A 0.0000
35 T A -0.3280
36 V A 0.0000
37 S A -0.7409
38 S A 0.0000
39 S A -1.1376
40 T A -1.1240
41 I A 0.0000
42 N A -1.8817
43 R A -1.8140
44 Y A -0.6922
45 A A 0.0000
46 M A 0.0000
47 A A 0.0000
48 W A 0.0000
49 F A 0.0000
50 R A 0.0000
51 Q A -1.9449
52 A A -1.9504
53 P A -1.5509
54 G A -1.9100
55 K A -3.2806
56 E A -3.4418
57 R A -2.3480
58 E A -2.0645
59 F A -0.7367
60 V A 0.0000
61 G A 0.0000
62 G A 0.0000
63 V A 0.0000
64 S A -0.2622
65 H A -0.3206
66 I A 1.1225
67 G A 0.2077
68 G A -0.4133
69 A A -0.1966
70 S A -0.6604
71 H A -1.0345
72 Y A -1.0370
73 A A -1.4074
74 D A -2.4651
75 S A -1.4861
76 V A 0.0000
77 K A -2.6455
78 G A -1.7676
79 R A -1.4456
80 F A 0.0000
81 T A -0.9058
82 L A 0.0000
83 S A -0.6503
84 R A -1.4050
85 D A -1.9355
86 D A -2.2354
87 A A -1.7014
88 K A -2.5169
89 R A -2.2294
90 T A 0.0000
91 L A 0.0000
92 Y A -0.6736
93 L A 0.0000
94 Q A -1.2324
95 M A 0.0000
96 S A -1.4261
97 N A -2.0245
98 L A 0.0000
99 R A -2.4430
100 P A -1.8641
101 E A -2.2967
102 D A 0.0000
103 T A -1.1548
104 A A 0.0000
105 V A -0.6004
106 Y A 0.0000
107 Y A -0.2539
108 C A 0.0000
109 A A 0.0000
110 V A 0.0000
111 G A 0.0000
112 F A -0.0063
113 E A -1.6736
114 A A 0.0000
115 S A -1.2991
116 N A -1.9342
117 W A -1.5314
118 R A -2.2036
119 Y A -1.1961
120 N A -1.8345
121 S A -1.6751
122 W A 0.0000
123 D A -1.4111
124 Y A -0.1912
125 W A 0.0262
126 G A 0.0088
127 Q A -0.8859
128 G A -0.5916
129 T A -0.7962
130 Q A -1.3709
131 V A 0.0000
132 T A -1.0072
133 V A 0.0000
134 S A -1.2231
135 S A -0.8993
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 -0.6559 3.7683 View CSV PDB
4.5 -0.7028 3.7683 View CSV PDB
5.0 -0.7574 3.7683 View CSV PDB
5.5 -0.8104 3.7683 View CSV PDB
6.0 -0.8528 3.7683 View CSV PDB
6.5 -0.8791 3.7683 View CSV PDB
7.0 -0.8897 3.7683 View CSV PDB
7.5 -0.8898 3.7683 View CSV PDB
8.0 -0.8833 3.7683 View CSV PDB
8.5 -0.8707 3.7683 View CSV PDB
9.0 -0.8515 3.7683 View CSV PDB