Project name: 2a84bc429a79d19

Status: done

Started: 2025-03-12 11:09:11
Chain sequence(s) A: QVQLVESGGGSVQAGGSLRLSCTASTFDDYAMHWFRQAPGQEREAVAAIAAITWNSGHIDYADSVEGRFTISRDNAKNTVTLQMNNLKPEDTAIYYCAAVSYLSTASSLDYWGQGTQVTVSS
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                                          (00:00:50)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/2a84bc429a79d19/tmp/folded.pdb                (00:00:50)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:20)
Show buried residues
Minimal score value
-3.235
Maximal score value
2.0499
Average score
-0.6845
Total score value
-83.5068
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 -1.5646
2 V A 0.0000
3 Q A -1.1777
4 L A 0.0000
5 V A 1.0921
6 E A 0.1075
7 S A -0.5644
8 G A -1.2498
9 G A -1.2152
10 G A -0.9540
11 S A -0.7387
12 V A -0.8318
13 Q A -1.7435
14 A A -1.7970
15 G A -1.7462
16 G A -1.3461
17 S A -1.4271
18 L A -1.1884
19 R A -2.1118
20 L A 0.0000
21 S A -0.5410
22 C A 0.0000
23 T A -0.3156
24 A A 0.0000
25 S A -0.8210
26 T A -1.1274
27 F A 0.0000
28 D A -1.7104
29 D A -0.8482
30 Y A -0.0365
31 A A 0.0875
32 M A 0.0000
33 H A 0.0164
34 W A 0.0000
35 F A -0.1984
36 R A 0.0000
37 Q A -1.6601
38 A A -1.6983
39 P A -1.1640
40 G A -1.6658
41 Q A -2.7806
42 E A -3.2350
43 R A -2.4525
44 E A -2.0722
45 A A -0.7346
46 V A 0.0000
47 A A 0.0000
48 A A -0.4087
49 I A 0.0000
50 A A -0.2618
51 A A 0.0000
52 I A 1.0424
53 T A 0.4929
54 W A 0.4810
55 N A -0.4703
56 S A 0.0444
57 G A -0.0786
58 H A -0.8793
59 I A -0.5515
60 D A -1.6758
61 Y A -1.3715
62 A A -1.7160
63 D A -2.6598
64 S A -1.7310
65 V A 0.0000
66 E A -2.9066
67 G A -1.9338
68 R A -1.8484
69 F A 0.0000
70 T A -0.9021
71 I A 0.0000
72 S A -0.3524
73 R A -0.9631
74 D A -1.7820
75 N A -1.5728
76 A A -1.4209
77 K A -2.2072
78 N A -1.8042
79 T A -1.1608
80 V A 0.0000
81 T A -0.8312
82 L A 0.0000
83 Q A -1.1391
84 M A 0.0000
85 N A -1.8214
86 N A -2.2208
87 L A 0.0000
88 K A -2.2350
89 P A -1.7296
90 E A -2.1928
91 D A 0.0000
92 T A -1.0523
93 A A 0.0000
94 I A -0.3224
95 Y A 0.0000
96 Y A -0.1273
97 C A 0.0000
98 A A 0.0000
99 A A 0.0000
100 V A 0.5572
101 S A 0.7407
102 Y A 1.8678
103 L A 2.0499
104 S A 0.9932
105 T A 0.5513
106 A A 0.2914
107 S A -0.2726
108 S A -0.0937
109 L A 0.1148
110 D A -0.3909
111 Y A -0.1170
112 W A 0.2856
113 G A -0.0953
114 Q A -0.8466
115 G A -0.4614
116 T A -0.7290
117 Q A -1.2691
118 V A 0.0000
119 T A -0.9593
120 V A 0.0000
121 S A -1.1924
122 S A -0.8472
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 -0.3482 2.7127 View CSV PDB
4.5 -0.4125 2.6669 View CSV PDB
5.0 -0.4904 2.6124 View CSV PDB
5.5 -0.5709 2.5545 View CSV PDB
6.0 -0.6443 2.4953 View CSV PDB
6.5 -0.7038 2.4358 View CSV PDB
7.0 -0.7467 2.3763 View CSV PDB
7.5 -0.7771 2.3174 View CSV PDB
8.0 -0.8004 2.2601 View CSV PDB
8.5 -0.817 2.2167 View CSV PDB
9.0 -0.824 2.1963 View CSV PDB