Project name: ATPase 1

Status: done

Started: 2026-02-12 12:27:22
Chain sequence(s) A: DEIDRMVAYLKEKGYIKTEEEAEIVREAMEFERRCNLLATGIDVVEPPFLYRDVGKTETARRRAERALAAGDEEAARRWAWLFLGGAVERAAAALALGRLTEEEKAKLKEALKLTEETPVEEILALGREIYEGSVTRFREEAGEELRALGEELEATAVTPENRARLDRYYALVRAEAAAERAAAA
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]                                                (00:00:13)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:13)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:13)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:13)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:13)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:13)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:07:14)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/293eb584fd0f41b/tmp/folded.pdb                (00:07:14)
[INFO]       Main:     Simulation completed successfully.                                          (00:09:32)
Show buried residues
Minimal score value
-3.9077
Maximal score value
0.7777
Average score
-1.3179
Total score value
-243.8091
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 D A -2.7893
2 E A -2.2607
3 I A -2.4001
4 D A -3.1582
5 R A -2.5660
6 M A 0.0000
7 V A 0.0000
8 A A -2.0331
9 Y A 0.0000
10 L A 0.0000
11 K A -3.2130
12 E A -3.1074
13 K A -2.4434
14 G A -2.0120
15 Y A -1.4112
16 I A 0.0000
17 K A -3.0751
18 T A -2.9013
19 E A -3.7968
20 E A -3.8332
21 E A -3.2726
22 A A 0.0000
23 E A -3.9077
24 I A -2.8789
25 V A 0.0000
26 R A -3.5161
27 E A -3.3334
28 A A 0.0000
29 M A 0.0000
30 E A -2.1522
31 F A 0.0000
32 E A 0.0000
33 R A -1.2503
34 R A -1.2900
35 C A 0.0000
36 N A 0.0000
37 L A -0.0796
38 L A -0.3491
39 A A 0.0000
40 T A -0.2720
41 G A -0.3246
42 I A -0.6779
43 D A -1.1270
44 V A 0.0000
45 V A 0.0000
46 E A 0.0000
47 P A 0.0000
48 P A 0.0000
49 F A 0.0000
50 L A 0.0000
51 Y A 0.0000
52 R A -0.9685
53 D A -0.1247
54 V A 0.7777
55 G A 0.3080
56 K A 0.0000
57 T A 0.0000
58 E A -1.0687
59 T A -1.2884
60 A A 0.0000
61 R A -2.3976
62 R A -3.0413
63 R A -2.5870
64 A A 0.0000
65 E A -2.9271
66 R A -2.5835
67 A A 0.0000
68 L A -2.2256
69 A A -1.1065
70 A A -1.1772
71 G A -1.9922
72 D A -3.0446
73 E A -3.5300
74 E A -3.3685
75 A A -2.4634
76 A A 0.0000
77 R A -2.4308
78 R A -1.3881
79 W A 0.0000
80 A A 0.0000
81 W A 0.0000
82 L A 0.0000
83 F A 0.0000
84 L A 0.0000
85 G A 0.0000
86 G A 0.0000
87 A A 0.0000
88 V A 0.0000
89 E A 0.0000
90 R A 0.0000
91 A A 0.0000
92 A A 0.0000
93 A A 0.0000
94 A A 0.0000
95 L A 0.0000
96 A A 0.0000
97 L A -0.7342
98 G A -1.4406
99 R A -2.1325
100 L A -1.7217
101 T A -2.1958
102 E A -3.1671
103 E A -3.0890
104 E A 0.0000
105 K A -2.4540
106 A A -2.3145
107 K A -2.3720
108 L A 0.0000
109 K A -2.5573
110 E A -2.9046
111 A A 0.0000
112 L A -1.9985
113 K A -2.3208
114 L A -1.9907
115 T A -1.9094
116 E A -2.7346
117 E A -2.6946
118 T A 0.0000
119 P A -2.0852
120 V A 0.0000
121 E A -2.8755
122 E A -2.8554
123 I A 0.0000
124 L A 0.0000
125 A A -1.8943
126 L A -1.8157
127 G A 0.0000
128 R A -3.0463
129 E A -2.5827
130 I A 0.0000
131 Y A 0.0000
132 E A -3.0095
133 G A -1.9022
134 S A -1.9130
135 V A 0.0000
136 T A -2.3726
137 R A -3.4257
138 F A 0.0000
139 R A -2.7099
140 E A -3.7399
141 E A -3.8724
142 A A -3.2968
143 G A -3.2966
144 E A -3.8988
145 E A -3.7279
146 L A 0.0000
147 R A -3.2619
148 A A -2.4832
149 L A -1.8604
150 G A 0.0000
151 E A -2.2571
152 E A -1.7414
153 L A 0.0000
154 E A -1.0036
155 A A -0.7649
156 T A -0.6702
157 A A 0.0000
158 V A 0.0000
159 T A -1.4252
160 P A -1.4486
161 E A -2.2745
162 N A 0.0000
163 R A -1.9402
164 A A -1.9877
165 R A -2.3123
166 L A 0.0000
167 D A -2.2001
168 R A -2.4063
169 Y A 0.0000
170 Y A 0.0000
171 A A -1.2377
172 L A -0.7475
173 V A 0.0000
174 R A -1.5160
175 A A -0.9152
176 E A -1.0991
177 A A -1.2294
178 A A -1.1140
179 A A -0.9415
180 E A -1.4833
181 R A -1.9368
182 A A -0.8589
183 A A -0.5151
184 A A -0.6838
185 A A -0.3807
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 -1.128 0.8846 View CSV PDB
4.5 -1.2612 0.7126 View CSV PDB
5.0 -1.4377 0.4938 View CSV PDB
5.5 -1.6295 0.4663 View CSV PDB
6.0 -1.8059 0.447 View CSV PDB
6.5 -1.9377 0.44 View CSV PDB
7.0 -2.0117 0.436 View CSV PDB
7.5 -2.0403 0.4341 View CSV PDB
8.0 -2.0441 0.4334 View CSV PDB
8.5 -2.035 0.4332 View CSV PDB
9.0 -2.0166 0.4331 View CSV PDB