Project name: SmNPC2

Status: done

Started: 2026-02-04 05:30:13
Chain sequence(s) A: FRDCGSKFGKLYSLTVTPCDRTPCALYKGQNATITIEFTTQETVKDGHISVHGVIAHVPIPFALDNSNLCEFVSPTCPLIPSIGKYTHTYSLYVKAMYPSISLTIRWELQDSSNEDIVCVEFPV
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]                                                (00:00:11)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:11)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:11)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:11)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:11)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:12)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:01)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/ddb76bc9065ab93/tmp/folded.pdb                (00:02:01)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:36)
Show buried residues
Minimal score value
-2.7598
Maximal score value
1.9581
Average score
-0.4327
Total score value
-53.653
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 F A 0.3600
2 R A -1.4528
3 D A -1.1373
4 C A -0.6517
5 G A -1.0402
6 S A -1.4192
7 K A -2.3512
8 F A -1.6450
9 G A 0.0000
10 K A -1.5793
11 L A -0.4563
12 Y A 0.5031
13 S A 0.5099
14 L A 0.2879
15 T A -0.1181
16 V A 0.0000
17 T A -0.5049
18 P A -0.6132
19 C A -1.2313
20 D A -2.6579
21 R A -2.7467
22 T A -0.9861
23 P A -0.7869
24 C A -0.4363
25 A A -0.0207
26 L A 0.3582
27 Y A 0.3877
28 K A -0.8597
29 G A -1.0648
30 Q A -1.5660
31 N A -1.3234
32 A A 0.0000
33 T A -0.2251
34 I A 0.0000
35 T A -0.1043
36 I A 0.0000
37 E A -0.4427
38 F A 0.0000
39 T A 0.0000
40 T A 0.0000
41 Q A -1.1874
42 E A -1.8198
43 T A -1.0054
44 V A 0.0000
45 K A -2.1322
46 D A -2.0694
47 G A 0.0000
48 H A -1.2131
49 I A 0.0000
50 S A -0.4990
51 V A 0.0000
52 H A 0.3872
53 G A 0.6863
54 V A 0.0000
55 I A 1.3999
56 A A 0.4151
57 H A 0.2253
58 V A 1.7658
59 P A 1.2271
60 I A 1.6861
61 P A 0.6746
62 F A 0.4087
63 A A -0.1384
64 L A -0.7232
65 D A -2.2063
66 N A -2.2497
67 S A -1.5330
68 N A -1.5677
69 L A 0.0000
70 C A -1.0745
71 E A -1.8320
72 F A -0.6984
73 V A 0.0000
74 S A -0.5282
75 P A -0.4460
76 T A -0.8896
77 C A 0.0000
78 P A -0.7363
79 L A 0.0000
80 I A 0.8673
81 P A 0.0568
82 S A 0.1632
83 I A 1.7392
84 G A 0.0238
85 K A -1.3475
86 Y A -0.5746
87 T A -0.3652
88 H A 0.0000
89 T A -0.2427
90 Y A 0.0000
91 S A -0.1125
92 L A -0.1738
93 Y A 0.1987
94 V A 0.0000
95 K A -0.6846
96 A A -0.1302
97 M A 0.6020
98 Y A 0.5216
99 P A 0.5875
100 S A 0.7324
101 I A 1.9581
102 S A 0.9067
103 L A 0.0000
104 T A 0.0750
105 I A 0.0000
106 R A -0.7909
107 W A 0.0000
108 E A -1.0514
109 L A 0.0000
110 Q A -1.9947
111 D A -2.3059
112 S A -1.9678
113 S A -1.7165
114 N A -2.4917
115 E A -2.7598
116 D A -2.3415
117 I A 0.0000
118 V A 0.0000
119 C A 0.0000
120 V A 0.0000
121 E A -1.0071
122 F A 0.0000
123 P A -0.1042
124 V A 0.7651
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 -0.1291 3.5839 View CSV PDB
4.5 -0.1848 3.5883 View CSV PDB
5.0 -0.2502 3.6003 View CSV PDB
5.5 -0.3124 3.6264 View CSV PDB
6.0 -0.3587 3.6652 View CSV PDB
6.5 -0.3817 3.702 View CSV PDB
7.0 -0.3829 3.7245 View CSV PDB
7.5 -0.3688 3.7342 View CSV PDB
8.0 -0.345 3.7376 View CSV PDB
8.5 -0.3129 3.7388 View CSV PDB
9.0 -0.2721 3.7391 View CSV PDB