Project name: A520

Status: done

Started: 2025-04-25 19:25:22
Chain sequence(s) A: QVQLQESGGGLVQAGGSLRLSCAASGTSRHRNLMGWFRQAPGKEREFVAAITSEPVRTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCATDLVAVSKVANDYWGQGTQVTMSS
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]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:00)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:04)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/56b811e1f05ff9a/tmp/folded.pdb                (00:01:04)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:53)
Show buried residues
Minimal score value
-3.3907
Maximal score value
1.6349
Average score
-0.8223
Total score value
-99.4928
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 -1.6960
2 V A 0.0000
3 Q A -1.9217
4 L A 0.0000
5 Q A -1.7300
6 E A 0.0000
7 S A -1.0041
8 G A -1.1243
9 G A -0.7460
10 G A -0.0012
11 L A 1.0582
12 V A -0.0159
13 Q A -1.3125
14 A A -1.6135
15 G A -1.4493
16 G A -0.9180
17 S A -1.0190
18 L A -0.8099
19 R A -1.9703
20 L A 0.0000
21 S A -0.7391
22 C A 0.0000
23 A A -1.1354
24 A A 0.0000
25 S A -1.6564
26 G A -1.6372
27 T A -1.6948
28 S A -2.1552
29 R A -2.6823
30 H A -2.4275
31 R A 0.0000
32 N A -1.8447
33 L A -0.5188
34 M A 0.0000
35 G A 0.0000
36 W A 0.0000
37 F A 0.0000
38 R A 0.0000
39 Q A -1.7868
40 A A -1.7069
41 P A -1.3317
42 G A -1.8992
43 K A -3.2565
44 E A -3.3907
45 R A -2.3127
46 E A -2.3059
47 F A -0.4167
48 V A 0.0000
49 A A 0.0000
50 A A 0.0000
51 I A 0.0000
52 T A -0.8765
53 S A -1.7167
54 E A -2.1831
55 P A -1.1557
56 V A 0.1744
57 R A -1.0857
58 T A 0.1305
59 Y A 0.6531
60 Y A -0.1546
61 A A -1.0170
62 D A -2.2907
63 S A -1.8542
64 V A 0.0000
65 K A -2.4511
66 G A -1.7681
67 R A -1.3850
68 F A 0.0000
69 T A -0.6702
70 I A 0.0000
71 S A -0.3806
72 R A -1.5739
73 D A -2.4973
74 N A -2.5671
75 A A -1.7353
76 K A -2.5808
77 N A -2.2126
78 T A 0.0000
79 V A 0.0000
80 Y A -0.5327
81 L A 0.0000
82 Q A -1.0930
83 M A 0.0000
84 N A -1.4349
85 S A -1.3432
86 L A 0.0000
87 K A -2.8200
88 P A -2.0773
89 E A -2.4960
90 D A 0.0000
91 T A -0.9254
92 A A 0.0000
93 V A -0.4491
94 Y A 0.0000
95 Y A -0.5274
96 C A 0.0000
97 A A 0.0000
98 T A 0.0000
99 D A -0.7317
100 L A 0.0000
101 V A 1.6349
102 A A 1.1775
103 V A 1.2819
104 S A 0.6433
105 K A 0.2109
106 V A 1.4770
107 A A 0.9191
108 N A 0.0000
109 D A -1.0712
110 Y A -0.6198
111 W A -0.4927
112 G A -0.9620
113 Q A -1.4926
114 G A -1.0060
115 T A -1.0462
116 Q A -0.9784
117 V A 0.0000
118 T A -0.3352
119 M A 0.0000
120 S A -0.9079
121 S A -1.1245
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 -0.7915 1.787 View CSV PDB
4.5 -0.8434 1.7414 View CSV PDB
5.0 -0.904 1.6811 View CSV PDB
5.5 -0.9599 1.6137 View CSV PDB
6.0 -0.998 1.5474 View CSV PDB
6.5 -1.0108 1.5216 View CSV PDB
7.0 -1.0018 1.5216 View CSV PDB
7.5 -0.9811 1.5216 View CSV PDB
8.0 -0.9551 1.5216 View CSV PDB
8.5 -0.9247 1.5216 View CSV PDB
9.0 -0.8894 1.5216 View CSV PDB