Project name: BMP-2

Status: done

Started: 2026-05-09 05:43:23
Chain sequence(s) A: RLKSSCKRHPLYVDFSDVGWNDWIVAPPGYHAFYCHGECPFPLADHLNSTNHAIVQTLVNSVNSKIPKACCVPTELSAISMLYLDENEKVVLKNYQDMVVEGCGCR
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage Used: no changes made
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:      Running AlphaCutter                                                         (00:00:01)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:36)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:36)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:36)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:36)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/17bbf680054536b/tmp/folded.pdb                (00:01:36)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:10)
Show buried residues
Minimal score value
-3.4888
Maximal score value
1.9311
Average score
-0.6965
Total score value
-73.8268
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
9 R A -1.4976
10 L A -0.5634
11 K A -2.1038
12 S A -1.5834
13 S A -1.5550
14 C A 0.0000
15 K A -2.4843
16 R A -1.6913
17 H A -0.8671
18 P A 0.0702
19 L A 0.9212
20 Y A 0.9053
21 V A 0.0518
22 D A -1.2310
23 F A 0.0000
24 S A -1.8689
25 D A -1.9288
26 V A -0.4729
27 G A -1.2344
28 W A -0.8377
29 N A -1.9079
30 D A -1.8268
31 W A -0.6568
32 I A 0.0000
33 V A 1.3606
34 A A 0.6684
35 P A -0.0187
36 P A -0.3837
37 G A 0.0000
38 Y A 0.0404
39 H A -0.1401
40 A A 0.0000
41 F A 0.3248
42 Y A 0.0428
43 C A -0.4643
44 H A -1.3110
45 G A -1.9784
46 E A -2.1215
47 C A 0.0000
48 P A 0.1030
49 F A 1.4800
50 P A 0.5506
51 L A 0.2201
52 A A -0.9802
53 D A -2.4188
54 H A -2.0374
55 L A -1.7164
56 N A -2.0130
57 S A -1.3099
58 T A -1.2795
59 N A -1.5648
60 H A -1.1941
61 A A 0.0000
62 I A 0.4552
63 V A 1.2167
64 Q A 0.3396
65 T A 0.0000
66 L A 1.9311
67 V A 1.4475
68 N A 0.0000
69 S A 0.7910
70 V A 1.4600
71 N A -0.2332
72 S A -1.0046
73 K A -1.7006
74 I A -0.7063
75 P A -1.0187
76 K A -1.0809
77 A A 0.0000
78 C A -0.2363
79 C A -0.6228
80 V A 0.0827
81 P A -0.8597
82 T A -1.1922
83 E A -2.1978
84 L A -1.4514
85 S A -1.1119
86 A A -1.0675
87 I A -0.7628
88 S A -0.4976
89 M A 0.0000
90 L A 1.5057
91 Y A 0.0000
92 L A -0.6489
93 D A -2.2676
94 E A -3.2835
95 N A -3.4888
96 E A -3.3726
97 K A -2.3578
98 V A 0.6547
99 V A 1.0044
100 L A 1.4621
101 K A -0.5992
102 N A -1.6424
103 Y A -1.3289
104 Q A -2.1053
105 D A -2.4522
106 M A -1.0626
107 V A -0.7479
108 V A 0.0000
109 E A -2.0367
110 G A -1.7132
111 C A -1.4115
112 G A 0.0000
113 C A 0.0000
114 R A -1.4104
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 -0.3475 4.2971 View CSV PDB
4.5 -0.4271 4.2728 View CSV PDB
5.0 -0.5273 4.2356 View CSV PDB
5.5 -0.6279 4.194 View CSV PDB
6.0 -0.7084 4.1605 View CSV PDB
6.5 -0.758 4.1471 View CSV PDB
7.0 -0.7776 4.1594 View CSV PDB
7.5 -0.7753 4.192 View CSV PDB
8.0 -0.7584 4.2354 View CSV PDB
8.5 -0.7298 4.2829 View CSV PDB
9.0 -0.6876 4.3315 View CSV PDB