Project name: 77df941e8be97f6

Status: done

Started: 2025-02-26 08:26:26
Chain sequence(s) A: NHSNELPSLCMLNNSFYYMRGGVNTFLIRVSDISVLMKEYDVSIYEPEDLGNCLNKSDSSWAIHWFSNALGHDWLMDPPMLCRNKTKKEGSNIQFNISKADDARVYGKKIRNGMRHLFRGFHDPCEEGKVCYLTINQCGDPSSFDYCGVNHLSKCQFDHVNT
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]                                                (00:00:01)
[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-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                                          (00:02:10)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/77df941e8be97f6/tmp/folded.pdb                (00:02:10)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:00)
Show buried residues
Minimal score value
-3.3437
Maximal score value
2.3001
Average score
-0.8153
Total score value
-132.0745
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 N A -2.0251
2 H A -1.9585
3 S A -1.5593
4 N A -2.1055
5 E A -1.9534
6 L A -0.8505
7 P A 0.0000
8 S A -1.3146
9 L A 0.0000
10 C A 0.0000
11 M A -0.7856
12 L A -0.5987
13 N A -1.2741
14 N A -1.9979
15 S A -1.0985
16 F A -0.2944
17 Y A 0.0000
18 Y A 0.0000
19 M A 0.0000
20 R A -1.0625
21 G A 0.0000
22 G A -0.3059
23 V A 1.0587
24 N A 0.0000
25 T A -0.1667
26 F A 0.0000
27 L A 0.0000
28 I A 0.0000
29 R A -0.5174
30 V A -0.3651
31 S A 0.0420
32 D A 0.0913
33 I A 2.2379
34 S A 1.8337
35 V A 2.3001
36 L A 0.0000
37 M A 0.0622
38 K A -1.8658
39 E A -1.8109
40 Y A -0.0470
41 D A -0.3486
42 V A -0.4811
43 S A -0.4955
44 I A 0.0000
45 Y A 0.3937
46 E A -1.7484
47 P A -1.8366
48 E A -2.6292
49 D A -1.8420
50 L A 0.0000
51 G A -2.1911
52 N A -1.8830
53 C A 0.0000
54 L A 0.0000
55 N A -2.9511
56 K A -3.1385
57 S A -2.3516
58 D A -2.6007
59 S A 0.0000
60 S A -1.5195
61 W A -1.0285
62 A A 0.0000
63 I A 0.0000
64 H A -0.9175
65 W A -0.2776
66 F A 0.0000
67 S A 0.0000
68 N A -1.2941
69 A A -0.6613
70 L A 0.0000
71 G A -1.0407
72 H A 0.0000
73 D A -0.5689
74 W A 0.2943
75 L A 1.6775
76 M A 1.5322
77 D A 0.6039
78 P A -0.0400
79 P A -0.0452
80 M A 0.0000
81 L A 0.0000
82 C A 0.0000
83 R A -0.9894
84 N A -2.0889
85 K A -2.9454
86 T A -2.2564
87 K A -3.0529
88 K A -3.2753
89 E A -2.7608
90 G A -2.0768
91 S A 0.0000
92 N A 0.0000
93 I A 0.0000
94 Q A 0.0000
95 F A 0.0000
96 N A -0.5918
97 I A 0.0000
98 S A 0.0000
99 K A -2.7815
100 A A -2.5707
101 D A -3.2140
102 D A -2.9159
103 A A 0.0000
104 R A -3.0252
105 V A -0.5279
106 Y A 0.0000
107 G A 0.0000
108 K A -2.1504
109 K A -1.5822
110 I A 0.0000
111 R A 0.0000
112 N A -2.2932
113 G A 0.0000
114 M A 0.0000
115 R A -3.2735
116 H A -2.3994
117 L A -1.3117
118 F A 0.0000
119 R A -2.7450
120 G A -2.3975
121 F A 0.0000
122 H A -2.2462
123 D A -2.0133
124 P A -1.6379
125 C A 0.0000
126 E A -3.2139
127 E A -3.3437
128 G A -2.6336
129 K A -2.0853
130 V A 0.2371
131 C A 0.0000
132 Y A 0.3859
133 L A 0.0000
134 T A 0.2705
135 I A 0.0000
136 N A 0.0000
137 Q A 0.0000
138 C A -0.2510
139 G A -0.5488
140 D A -1.1032
141 P A -0.8224
142 S A -0.4585
143 S A 0.0000
144 F A 0.9508
145 D A -0.7643
146 Y A 0.0833
147 C A -0.0773
148 G A -0.1410
149 V A 0.4567
150 N A -1.1002
151 H A -0.8425
152 L A -0.4411
153 S A -0.7150
154 K A -1.7964
155 C A -1.2955
156 Q A -1.7084
157 F A -1.4196
158 D A -2.2850
159 H A -1.4810
160 V A -0.6732
161 N A -1.4354
162 T A -0.9787
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 -0.6818 4.8944 View CSV PDB
4.5 -0.7629 4.6975 View CSV PDB
5.0 -0.8559 4.48 View CSV PDB
5.5 -0.9463 4.2549 View CSV PDB
6.0 -1.02 4.0274 View CSV PDB
6.5 -1.0658 3.7995 View CSV PDB
7.0 -1.083 3.5729 View CSV PDB
7.5 -1.0813 3.3507 View CSV PDB
8.0 -1.0682 3.1415 View CSV PDB
8.5 -1.0437 2.9641 View CSV PDB
9.0 -1.0043 2.8423 View CSV PDB