Project name: A421

Status: done

Started: 2025-04-25 19:25:42
Chain sequence(s) A: QVQLQESGGGLVQAGGSLRLSCAASGTSRHRNLMGWFRQAPGKEREFVAAITSEPVRTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCATDLVAVSKVAKDYWGQGTQVTVSS
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.  (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:13)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/690936a0432ed3b/tmp/folded.pdb                (00:01:13)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:53)
Show buried residues
Minimal score value
-3.3671
Maximal score value
1.6609
Average score
-0.8081
Total score value
-97.7811
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 -1.7276
2 V A 0.0000
3 Q A -1.9817
4 L A 0.0000
5 Q A -1.7924
6 E A 0.0000
7 S A -1.0754
8 G A -1.1566
9 G A -0.7628
10 G A 0.1719
11 L A 1.0780
12 V A 0.1058
13 Q A -1.1793
14 A A -1.3598
15 G A -1.2420
16 G A -0.7900
17 S A -0.9193
18 L A -0.8017
19 R A -1.9703
20 L A 0.0000
21 S A -0.7671
22 C A 0.0000
23 A A -1.1526
24 A A 0.0000
25 S A -1.6629
26 G A -1.6393
27 T A -1.6994
28 S A -2.1602
29 R A -2.6832
30 H A -2.4311
31 R A 0.0000
32 N A -1.8569
33 L A -0.5175
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 -1.7646
40 A A -1.6977
41 P A -1.3315
42 G A -1.9000
43 K A -3.2463
44 E A -3.3671
45 R A -2.2671
46 E A -2.2147
47 F A -0.3628
48 V A 0.0000
49 A A 0.0000
50 A A 0.0000
51 I A 0.0000
52 T A -0.9185
53 S A -1.7237
54 E A -2.1873
55 P A -1.1491
56 V A 0.1860
57 R A -1.1763
58 T A -0.0497
59 Y A 0.2592
60 Y A -0.2781
61 A A -1.0507
62 D A -2.3265
63 S A -1.8367
64 V A 0.0000
65 K A -2.4727
66 G A -1.7236
67 R A -1.3016
68 F A 0.0000
69 T A -0.6998
70 I A 0.0000
71 S A -0.3774
72 R A -1.5728
73 D A -2.5031
74 N A -2.5838
75 A A -1.7437
76 K A -2.5846
77 N A -2.2171
78 T A 0.0000
79 V A 0.0000
80 Y A -0.5405
81 L A 0.0000
82 Q A -1.0936
83 M A 0.0000
84 N A -1.3033
85 S A -1.0745
86 L A 0.0000
87 K A -2.1171
88 P A -1.7710
89 E A -2.2798
90 D A 0.0000
91 T A -0.8039
92 A A 0.0000
93 V A -0.4463
94 Y A 0.0000
95 Y A -0.5349
96 C A 0.0000
97 A A 0.0000
98 T A 0.0000
99 D A -0.8617
100 L A 0.0000
101 V A 1.6609
102 A A 1.1734
103 V A 1.3594
104 S A 0.7129
105 K A 0.2670
106 V A 1.4977
107 A A 0.9125
108 K A 0.0000
109 D A -1.1993
110 Y A -0.8807
111 W A -0.6251
112 G A -1.0387
113 Q A -1.5110
114 G A -1.0348
115 T A -1.0687
116 Q A -0.9852
117 V A 0.0000
118 T A -0.2503
119 V A 0.0000
120 S A -0.7863
121 S A -1.0014
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 -0.7434 1.7897 View CSV PDB
4.5 -0.7901 1.7633 View CSV PDB
5.0 -0.8462 1.7272 View CSV PDB
5.5 -0.9009 1.6775 View CSV PDB
6.0 -0.9421 1.6188 View CSV PDB
6.5 -0.962 1.5594 View CSV PDB
7.0 -0.962 1.534 View CSV PDB
7.5 -0.9495 1.534 View CSV PDB
8.0 -0.9305 1.534 View CSV PDB
8.5 -0.9064 1.534 View CSV PDB
9.0 -0.8776 1.534 View CSV PDB