Project name: Wild-Type Human PrP

Status: done

Started: 2026-03-26 18:58:33
Chain sequence(s) A: LGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQR
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 partially or entirely disordered. Average 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                                          (00:01:37)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/c2f126f10fac83f/tmp/folded.pdb                (00:01:37)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:10)
Show buried residues
Minimal score value
-3.5618
Maximal score value
1.2387
Average score
-1.0671
Total score value
-110.9796
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
125 L A 1.2387
126 G A 0.2273
127 G A -0.2050
128 Y A 0.6189
129 M A 0.9569
130 L A 1.0043
131 G A 0.0000
132 S A -0.3079
133 A A -0.3582
134 M A -0.4617
135 S A -0.5995
136 R A -1.1088
137 P A -0.8212
138 I A -0.6460
139 I A -1.1792
140 H A -1.5037
141 F A -0.9923
142 G A -1.0562
143 S A -1.2571
144 D A -2.3240
145 Y A -0.7252
146 E A -1.7175
147 D A -2.3586
148 R A -3.2156
149 Y A -1.7626
150 Y A 0.0000
151 R A -3.5618
152 E A -3.4566
153 N A -2.3217
154 M A -2.1471
155 H A -2.0543
156 R A -1.5144
157 Y A 0.0000
158 P A 0.0000
159 N A -1.1401
160 Q A -0.5143
161 V A 0.0000
162 Y A 0.7129
163 Y A 0.1925
164 R A -0.5003
165 P A -1.0444
166 M A -1.1623
167 D A -2.4669
168 E A -2.1938
169 Y A -0.6208
170 S A -1.2885
171 N A -1.6330
172 Q A -2.4922
173 N A -2.9406
174 N A -3.0575
175 F A 0.0000
176 V A 0.0000
177 H A -2.7982
178 D A -2.3691
179 C A 0.0000
180 V A 0.0000
181 N A -1.7489
182 I A -0.7345
183 T A 0.0000
184 I A 0.0000
185 K A -0.9210
186 Q A -0.0708
187 H A -0.3958
188 T A -0.3442
189 V A 0.6480
190 T A -0.0686
191 T A -0.9669
192 T A -1.2551
193 T A -0.9679
194 K A -2.2292
195 G A -1.9093
196 E A -2.0874
197 N A -1.8349
198 F A -1.0929
199 T A -1.2425
200 E A -2.0414
201 T A -1.3216
202 D A 0.0000
203 V A -1.5325
204 K A -2.1258
205 M A 0.0000
206 M A 0.0000
207 E A -2.2012
208 R A -2.3367
209 V A 0.0000
210 V A 0.0000
211 E A -1.9532
212 Q A -1.1355
213 M A 0.0000
214 C A 0.0000
215 I A -0.6222
216 T A -0.9520
217 Q A 0.0000
218 Y A -1.8887
219 E A -2.9089
220 R A -3.1367
221 E A -2.1314
222 S A -1.5475
223 Q A -2.1832
224 A A -1.3365
225 Y A -0.3135
226 Y A 0.1459
227 Q A -1.4812
228 R A -1.8272
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 partially or entirely disordered. Average score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -1.227 1.7813 View CSV PDB
4.5 -1.3073 1.783 View CSV PDB
5.0 -1.405 1.788 View CSV PDB
5.5 -1.5016 1.8005 View CSV PDB
6.0 -1.5822 1.8252 View CSV PDB
6.5 -1.6393 1.8613 View CSV PDB
7.0 -1.6717 1.9037 View CSV PDB
7.5 -1.6845 1.9486 View CSV PDB
8.0 -1.6847 1.9944 View CSV PDB
8.5 -1.6751 2.04 View CSV PDB
9.0 -1.6559 2.0849 View CSV PDB