Project name: ATPase 4

Status: done

Started: 2026-02-12 12:42:44
Chain sequence(s) A: MYVGVIPDVTLEQMAELEAAEVGKTAVENAFARRMVEELPERCRVREVTTASGKTVTVVTFYVTSKPTGKTVAITERIYDDSEVTKEERVAIARAVHAELLAEGYVPVYLDVWAEEDRAALEARCARFGGRLYRVETPEELAEILAEM
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.  (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:12)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/60546ba2154de68/tmp/folded.pdb                (00:03:12)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:19)
Show buried residues
Minimal score value
-3.3515
Maximal score value
1.2158
Average score
-1.0459
Total score value
-154.7981
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 M A -1.9407
2 Y A 0.0000
3 V A 0.0000
4 G A 0.0000
5 V A 0.0000
6 I A 0.0000
7 P A -1.0568
8 D A -1.6698
9 V A -0.9874
10 T A -1.1320
11 L A -1.1084
12 E A -2.2300
13 Q A -1.9646
14 M A 0.0000
15 A A -1.9510
16 E A -2.3240
17 L A 0.0000
18 E A 0.0000
19 A A -0.7568
20 A A -0.0293
21 E A 0.0000
22 V A 1.2158
23 G A 0.3123
24 K A 0.0000
25 T A 0.0000
26 A A -0.0516
27 V A 0.2071
28 E A 0.0000
29 N A -0.7162
30 A A -0.6265
31 F A 0.0000
32 A A 0.0000
33 R A -2.4937
34 R A -2.2056
35 M A 0.0000
36 V A -1.8527
37 E A -2.9352
38 E A -2.7525
39 L A -2.1504
40 P A -2.1731
41 E A -2.6674
42 R A -1.8317
43 C A -1.5524
44 R A -1.5828
45 V A -0.3357
46 R A -1.8657
47 E A -2.0271
48 V A -1.0721
49 T A -0.7342
50 T A -0.9427
51 A A -0.5530
52 S A -0.8623
53 G A -1.0286
54 K A -1.5128
55 T A -1.2616
56 V A 0.0000
57 T A -0.7086
58 V A 0.0000
59 V A 0.0000
60 T A 0.0000
61 F A 0.0000
62 Y A -0.4257
63 V A 0.0000
64 T A -1.4975
65 S A 0.0000
66 K A -2.7623
67 P A -1.8730
68 T A -1.6927
69 G A -1.9208
70 K A -2.1513
71 T A -0.9642
72 V A 0.0000
73 A A 0.0000
74 I A 0.0000
75 T A 0.0224
76 E A 0.0000
77 R A 0.0000
78 I A -0.7614
79 Y A 0.0000
80 D A -2.7144
81 D A -2.0709
82 S A -1.6176
83 E A -2.3590
84 V A 0.0000
85 T A -1.6154
86 K A -1.8559
87 E A -2.2859
88 E A -1.6550
89 R A 0.0000
90 V A -1.3731
91 A A -0.8726
92 I A 0.0000
93 A A -0.7343
94 R A -1.4289
95 A A -0.8131
96 V A -0.4801
97 H A -0.5044
98 A A -0.6921
99 E A -1.5396
100 L A 0.0000
101 L A 0.4731
102 A A -0.6391
103 E A -1.7899
104 G A -1.0385
105 Y A -0.2694
106 V A 0.1431
107 P A 0.1883
108 V A 0.0000
109 Y A -0.1576
110 L A 0.0000
111 D A 0.0000
112 V A 0.0000
113 W A -1.0699
114 A A -1.8069
115 E A -3.3515
116 E A -3.2037
117 D A -2.5914
118 R A -2.9401
119 A A -1.6943
120 A A -1.1514
121 L A 0.0000
122 E A -2.3756
123 A A -1.2947
124 R A 0.0000
125 C A 0.0000
126 A A -1.6178
127 R A -2.0693
128 F A -1.5258
129 G A -1.5283
130 G A -1.7908
131 R A -2.0641
132 L A -1.5636
133 Y A -1.5691
134 R A -2.5536
135 V A 0.0000
136 E A -2.6412
137 T A -2.2037
138 P A 0.0000
139 E A -3.1160
140 E A -3.0097
141 L A 0.0000
142 A A 0.0000
143 E A -2.8394
144 I A -1.5060
145 L A 0.0000
146 A A -2.1983
147 E A -2.5269
148 M A -1.3544
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 -0.7146 1.9088 View CSV PDB
4.5 -0.8341 1.7404 View CSV PDB
5.0 -0.994 1.5202 View CSV PDB
5.5 -1.168 1.283 View CSV PDB
6.0 -1.3289 1.1947 View CSV PDB
6.5 -1.4507 1.1766 View CSV PDB
7.0 -1.5189 1.1695 View CSV PDB
7.5 -1.5443 1.1693 View CSV PDB
8.0 -1.5466 1.1753 View CSV PDB
8.5 -1.5373 1.1901 View CSV PDB
9.0 -1.5197 1.2166 View CSV PDB