Project name: c3-pruned

Status: done

Started: 2026-04-16 15:15:08
Chain sequence(s) D: YTAESLRLAPYPADLRVPTAFPQDHQPRGRILLSHDELMHTDYLLHIRQQFDWLEEPLLRKLVVEKIFAVYNAPNLHTLLAIIDETLSYMKYHHLHGLPVNPHDPYLETVGGMRQLLFNKLNNLDLGCILDHQDGWGDHCSTLKRLVKKPGQMSAWLRDDVCDLQKRPPETFSQPMHRAMAYVCSFSRVAVSLRRRALQVTGTPQFFDQFDTNNAMGTYRCGAVSDLILGALQCHECQNE
input PDB
Selected Chain(s) D
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage D: YTAESLRLAPYPADLRVPTAFPQDHQPRGRILLSHDELMHTDYLLHIRQQFDWLEEPLLRKLVVEKIFAVYNAPNLHTLLAIIDETLSYMKYHHLHGLPVNPHDPYLETVGGMRQLLFNKLNNLDLGCILDHQDGWGDHCSTLKRLVKKPGQMSAWLRDDVCDLQKRPPETFSQPMHRA

MAYVCSFSRVAVSLRRRALQ

VTGTPQFFDQFDTNNAMGTYRCGAVSDLILGALQCHECQNE
(Red indicates removed residues)
Dynamic mode No
Automated mutations No
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:11)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:11)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with D chain(s) selected             (00:00:11)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:11)
[INFO]       PDB:      Running AlphaCutter                                                         (00:00:11)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:46)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:46)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:26)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/7192a8444da083d/tmp/folded.pdb                (00:03:26)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:59)
Show buried residues
Minimal score value
-3.7732
Maximal score value
2.2788
Average score
-0.896
Total score value
-197.13
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
61 Y D 0.7661
62 T D -0.3632
63 A D -1.3235
64 E D -2.3540
65 S D -1.2218
66 L D -1.1980
67 R D -2.5401
68 L D 0.0000
69 A D -0.9919
70 P D -0.6464
71 Y D -0.0732
72 P D -0.4757
73 A D -0.6967
74 D D -1.8527
75 L D 0.0000
76 R D 0.0039
77 V D 1.2618
78 P D 0.0000
79 T D 0.3036
80 A D 0.0000
81 F D 0.6071
82 P D -0.9482
83 Q D -2.4260
84 D D -2.9230
85 H D -2.8450
86 Q D -2.5959
87 P D -2.0708
88 R D -2.3733
89 G D -1.3488
90 R D -0.1152
91 I D 1.8432
92 L D 2.2788
93 L D 0.9104
94 S D -0.5601
95 H D -1.6533
96 D D -2.5223
97 E D -1.2040
98 L D -0.7361
99 M D 0.0000
100 H D -1.8217
101 T D 0.0000
102 D D 0.0000
103 Y D 0.0000
104 L D 0.0000
105 L D 0.0000
106 H D -0.6327
107 I D 0.0000
108 R D -0.7842
109 Q D -0.9129
110 Q D -0.4038
111 F D 0.0000
112 D D -1.3035
113 W D -0.0739
114 L D -1.0481
115 E D -2.6097
116 E D -3.3142
117 P D -2.2858
118 L D -1.5241
119 L D 0.0000
120 R D -3.2173
121 K D -2.3084
122 L D -1.1717
123 V D 0.0000
124 V D -0.0637
125 E D -0.9649
126 K D -0.4480
127 I D 0.8359
128 F D 1.7567
129 A D 0.6091
130 V D 0.0000
131 Y D 0.9954
132 N D -0.3327
133 A D 0.0000
134 P D -1.0765
135 N D -1.5073
136 L D -0.8899
137 H D -1.1092
138 T D -0.8281
139 L D 0.0000
140 L D 0.0000
141 A D -0.3139
142 I D -0.0796
143 I D 0.0000
144 D D 0.0000
145 E D -0.6041
146 T D 0.0000
147 L D 0.0820
148 S D 0.0000
149 Y D 0.0000
150 M D 0.3376
151 K D 0.0000
152 Y D 0.0000
153 H D 0.0000
154 H D -0.3069
155 L D 0.4139
156 H D 0.0745
157 G D -0.0831
158 L D 0.0000
159 P D -0.1062
160 V D 0.0000
161 N D -0.8497
162 P D -1.1064
163 H D -1.9928
164 D D 0.0000
165 P D 0.0000
166 Y D 0.0000
167 L D -0.6976
168 E D -1.7755
169 T D 0.0000
170 V D -0.3931
171 G D -1.1264
172 G D -0.9574
173 M D 0.0000
174 R D -2.4075
175 Q D -2.4146
176 L D -1.2818
177 L D -1.0854
178 F D 0.0000
179 N D -2.1083
180 K D -1.5522
181 L D 0.0000
182 N D -1.9207
183 N D -2.0222
184 L D -1.2164
185 D D -2.4325
186 L D 0.0000
187 G D 0.0000
188 C D 0.0000
189 I D -0.9581
190 L D 0.0000
191 D D -1.8326
192 H D -2.2613
193 Q D -2.5004
194 D D -2.8397
195 G D -1.4468
196 W D -0.7001
197 G D -1.4010
198 D D -2.0654
199 H D -1.6090
200 C D 0.0000
201 S D -1.1776
202 T D -1.0963
203 L D 0.0000
204 K D -1.6979
205 R D -1.4680
206 L D -1.4356
207 V D -1.4924
208 K D -2.2701
209 K D -2.6252
210 P D -2.0680
211 G D -1.8448
212 Q D -2.1474
213 M D 0.0000
214 S D -0.5221
215 A D -0.5145
216 W D 0.1034
217 L D -0.9627
218 R D -2.7304
219 D D -3.2060
220 D D -3.2402
221 V D 0.0000
222 C D -3.0447
223 D D -3.7732
224 L D -2.5075
225 Q D -2.5292
226 K D -3.0593
227 R D -2.6531
228 P D -1.7693
229 P D -1.4481
230 E D -1.3675
231 T D -0.8608
232 F D 0.0000
233 S D -0.6029
234 Q D -0.5976
235 P D -0.6181
236 M D 0.0000
237 H D 0.0000
238 R D -0.9319
239 A D -0.7957
260 V D 1.5324
261 T D 0.4683
262 G D -0.2150
263 T D -0.0482
264 P D -0.3322
265 Q D -0.4701
266 F D -0.4732
267 F D 0.0000
268 D D -1.8997
269 Q D -1.1594
270 F D 0.5147
271 D D -0.7355
272 T D -1.0284
273 N D -1.5725
274 N D -1.9389
275 A D -1.3841
276 M D -0.5628
277 G D -0.9441
278 T D -0.9631
279 Y D -1.0421
280 R D -2.1303
281 C D -1.4536
282 G D -1.0113
283 A D -1.2246
284 V D 0.0000
285 S D -0.8788
286 D D -1.8030
287 L D -0.7239
288 I D 0.0000
289 L D -0.4527
290 G D -0.6663
291 A D 0.0000
292 L D -0.2966
293 Q D -0.9892
294 C D -0.2715
295 H D -0.9763
296 E D -2.2464
297 C D -2.1430
298 Q D -2.5659
299 N D -3.3051
300 E D -2.7227
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 -0.4263 4.5226 View CSV PDB
4.5 -0.5156 4.4502 View CSV PDB
5.0 -0.617 4.3451 View CSV PDB
5.5 -0.714 4.2289 View CSV PDB
6.0 -0.7949 4.1255 View CSV PDB
6.5 -0.856 4.0547 View CSV PDB
7.0 -0.9026 4.0276 View CSV PDB
7.5 -0.9417 4.0369 View CSV PDB
8.0 -0.9752 4.0652 View CSV PDB
8.5 -0.9988 4.1006 View CSV PDB
9.0 -1.0063 4.1371 View CSV PDB