Project name: d68ac50db4c8120

Status: done

Started: 2026-05-12 16:26:19
Chain sequence(s) A: MAQKEATKENVLKALASALASNPQLSAQQRFLIQANVYEDVEYIDLSTNPSEVKDLESQVKANLKALLQSAQSKAPLAAQKEATKENVLKALASALASNPQLSAQQRFLIQANVYEDVEYIDLSTNPSEVKDLESQVKANLKALLQSAQSKAPLAAQKEATKENVLKDLASALASNPQLSAQQRFLIQANVYEDVEYIDLSTNPSEVKSLESQVKANLKALLQSAQSKAP
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]                                                (00:00:13)
[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:      Running AlphaCutter                                                         (00:00:13)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:52)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:53)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:53)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:10:47)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/d68ac50db4c8120/tmp/folded.pdb                (00:10:47)
[INFO]       Main:     Simulation completed successfully.                                          (00:14:54)
Show buried residues
Minimal score value
-3.6085
Maximal score value
1.7166
Average score
-1.059
Total score value
-243.5666
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 0.1331
2 A A -0.3803
3 Q A -1.3639
4 K A -2.0204
5 E A -2.7389
6 A A -1.9939
7 T A 0.0000
8 K A -2.8964
9 E A -3.5451
10 N A -3.2320
11 V A 0.0000
12 L A -1.5688
13 K A -2.5575
14 A A -1.6807
15 L A 0.0000
16 A A -0.6982
17 S A -0.5606
18 A A -0.5637
19 L A -0.2564
20 A A -0.2649
21 S A -0.4082
22 N A 0.0000
23 P A -0.9028
24 Q A -1.4867
25 L A 0.0000
26 S A -0.5715
27 A A -0.2346
28 Q A -0.4302
29 Q A -0.2487
30 R A 0.2613
31 F A 1.7166
32 L A 1.7160
33 I A 0.0000
34 Q A 0.3861
35 A A 0.4041
36 N A -0.3415
37 V A 0.0000
38 Y A -0.1387
39 E A -1.9570
40 D A -1.6993
41 V A 0.0000
42 E A -1.7638
43 Y A -0.2068
44 I A 0.0000
45 D A -0.8542
46 L A 0.7420
47 S A 0.0000
48 T A -0.3582
49 N A -1.2179
50 P A -1.6577
51 S A -2.0663
52 E A -2.2318
53 V A 0.0000
54 K A -3.5618
55 D A -3.5103
56 L A -2.3788
57 E A -2.8160
58 S A -2.3183
59 Q A -2.6457
60 V A 0.0000
61 K A -1.8449
62 A A -1.5207
63 N A -1.6592
64 L A 0.0000
65 K A -2.2563
66 A A -1.2910
67 L A -0.8132
68 L A -1.3142
69 Q A -1.9899
70 S A -1.4195
71 A A 0.0000
72 Q A -1.6482
73 S A -1.5177
74 K A -2.2088
75 A A -1.5606
76 P A -1.3055
77 L A -1.3847
78 A A -1.4363
79 A A -1.2466
80 Q A -1.4743
81 K A -2.3099
82 E A -2.9896
83 A A -1.9300
84 T A 0.0000
85 K A -2.9875
86 E A -3.1436
87 N A -3.0096
88 V A 0.0000
89 L A -1.3427
90 K A -2.4017
91 A A -1.5709
92 L A 0.0000
93 A A -0.6485
94 S A -0.5632
95 A A -0.6229
96 L A -0.2712
97 A A -0.2703
98 S A -0.4342
99 N A -0.7529
100 P A -0.7750
101 Q A -1.1371
102 L A 0.0000
103 S A -0.5579
104 A A -0.1968
105 Q A -0.4347
106 Q A -0.2500
107 R A 0.2699
108 F A 1.7143
109 L A 1.6628
110 I A 0.0000
111 Q A 0.4164
112 A A 0.3657
113 N A -0.3726
114 V A 0.0000
115 Y A -0.3260
116 E A -2.0537
117 D A -1.8549
118 V A 0.0000
119 E A -2.1263
120 Y A -0.5257
121 I A 0.0000
122 D A -1.7880
123 L A 0.3440
124 S A 0.0000
125 T A -0.7476
126 N A -1.4723
127 P A -1.6651
128 S A -2.0157
129 E A -2.2030
130 V A 0.0000
131 K A -3.4875
132 D A -3.4779
133 L A -2.2860
134 E A -2.7205
135 S A -2.2573
136 Q A -2.5904
137 V A 0.0000
138 K A -1.7184
139 A A -1.4718
140 N A -1.6344
141 L A 0.0000
142 K A -2.2752
143 A A -1.3341
144 L A -0.8955
145 L A 0.0000
146 Q A -2.1019
147 S A -1.5113
148 A A 0.0000
149 Q A -1.7931
150 S A -1.6100
151 K A -2.2803
152 A A -1.3580
153 P A -1.0714
154 L A -1.3629
155 A A -1.3481
156 A A -1.0288
157 Q A -1.4743
158 K A -2.1648
159 E A -2.9163
160 A A -2.0213
161 T A 0.0000
162 K A -3.0039
163 E A -3.6085
164 N A -3.3507
165 V A 0.0000
166 L A -1.7677
167 K A -2.9009
168 D A -2.3259
169 L A 0.0000
170 A A -0.8954
171 S A -0.7948
172 A A -0.7900
173 L A -0.2010
174 A A -0.3081
175 S A -0.4447
176 N A -0.7869
177 P A -0.8226
178 Q A -1.2363
179 L A 0.0000
180 S A -0.5326
181 A A -0.2080
182 Q A -0.4495
183 Q A -0.2757
184 R A 0.2505
185 F A 1.6985
186 L A 1.6924
187 I A 0.0000
188 Q A 0.3765
189 A A 0.4003
190 N A -0.3311
191 V A 0.0000
192 Y A -0.1331
193 E A -1.9579
194 D A -1.6503
195 V A 0.0000
196 E A -1.8492
197 Y A -0.2507
198 I A 0.0000
199 D A -1.1942
200 L A 0.6275
201 S A 0.0000
202 T A -0.6915
203 N A -1.5304
204 P A -1.4539
205 S A -1.5682
206 E A -1.5756
207 V A 0.0000
208 K A -2.6210
209 S A -1.7873
210 L A -1.3354
211 E A -1.9722
212 S A -1.6119
213 Q A -2.0681
214 V A 0.0000
215 K A -1.7490
216 A A -1.3776
217 N A -1.4862
218 L A 0.0000
219 K A -2.2626
220 A A -1.2607
221 L A -0.8254
222 L A -1.4135
223 Q A -2.0795
224 S A -1.5205
225 A A 0.0000
226 Q A -1.9162
227 S A -1.7281
228 K A -2.2885
229 A A -1.4661
230 P A -0.9228
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 -0.6402 4.2021 View CSV PDB
4.5 -0.7263 4.2021 View CSV PDB
5.0 -0.8364 4.2021 View CSV PDB
5.5 -0.9471 4.2021 View CSV PDB
6.0 -1.0295 4.2021 View CSV PDB
6.5 -1.0605 4.2021 View CSV PDB
7.0 -1.0379 4.2021 View CSV PDB
7.5 -0.9788 4.2021 View CSV PDB
8.0 -0.9012 4.2021 View CSV PDB
8.5 -0.8139 4.2021 View CSV PDB
9.0 -0.7189 4.2021 View CSV PDB