Project name: E1fix

Status: done

Started: 2026-08-18 04:28:41
Chain sequence(s) A: MAMTIPEMFARRVTAAPDAVAVVDGDRVLTYRELDELAGRLSGRLIGRGVRRGDRVAVLLPLSADLVVTLLAIWKAGAAFVPIDAGFPAPRVAFIVADSGASRMVCSAATRDGVPEGIEAIVVTDEEAFEASAAGARPGDLAAVIYTSGSTGIPKGVAIPHRAVAAMAEALVRLLDITPDDQVLHYSPISFDAFLSEVWGSLVAGATLVIPEADQASFLGSVSRHLAAHGCDLAMLSPSVYARLDEAARSRIRKVEFCGEALGEGEYDKAARYSRVFNAYGPTEATVCATLAELTSYTPSIGRPVEGRTVQVLDASLRAVAPGVIGDLYISGAGLADGYLRRAGLTAERLVADPSAPGARMFRTGDLAQFTADGQLIFAGRADDQVKVRGFRIEPAEVEAALTAQPGVHEAVVRAVDGRLVGYVVAEGDAEPAVLRERVGAVLPEYMVPAAVITLDALPLTGNGKVDRAALPAPVFAADGSHHHHHH
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.  (00:00:03)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:03)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:08:54)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/37e6b3385b584bb/tmp/folded.pdb                (00:08:54)
[INFO]       Main:     Simulation completed successfully.                                          (00:15:52)
Show buried residues

Minimal score value
-3.4829
Maximal score value
1.9826
Average score
-0.6544
Total score value
-318.6837

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 0.9060
2 A A 0.3847
3 M A 0.2268
4 T A 0.0000
5 I A 0.0000
6 P A -0.9238
7 E A -1.1557
8 M A 0.0000
9 F A 0.0000
10 A A -1.6557
11 R A -2.3504
12 R A -1.9170
13 V A 0.0000
14 T A -1.4134
15 A A -0.9409
16 A A -1.2396
17 P A -2.1230
18 D A -2.2623
19 A A -1.2964
20 V A -0.0715
21 A A 0.0000
22 V A 0.0000
23 V A -0.0956
24 D A 0.0000
25 G A -1.8785
26 D A -2.5776
27 R A -1.9465
28 V A 0.2411
29 L A -0.1976
30 T A -1.1375
31 Y A 0.0000
32 R A -3.4241
33 E A -2.7135
34 L A 0.0000
35 D A -2.5083
36 E A -3.2629
37 L A -1.8674
38 A A 0.0000
39 G A -1.9153
40 R A -2.7013
41 L A 0.0000
42 S A 0.0000
43 G A 0.0000
44 R A 0.0000
45 L A 0.0000
46 I A -0.9179
47 G A -0.7911
48 R A -0.9768
49 G A -0.9993
50 V A 0.0000
51 R A -3.1217
52 R A -3.3270
53 G A -2.1787
54 D A -2.1381
55 R A -1.4112
56 V A 0.0000
57 A A 0.0000
58 V A 0.0000
59 L A 0.0000
60 L A 0.0000
61 P A -0.4581
62 L A -0.2370
63 S A -0.5990
64 A A 0.0000
65 D A -0.6343
66 L A 0.0000
67 V A 0.0000
68 V A 0.0000
69 T A 0.0000
70 L A 0.0000
71 L A 0.0000
72 A A 0.0000
73 I A 0.0000
74 W A 0.0000
75 K A -0.8613
76 A A 0.0000
77 G A 0.0000
78 A A 0.0000
79 A A 0.0000
80 F A 0.0000
81 V A 0.0000
82 P A 0.0000
83 I A 0.0000
84 D A -0.4070
85 A A -0.5363
86 G A -0.8206
87 F A -0.3817
88 P A -0.1589
89 A A -0.0700
90 P A 0.1596
91 R A 0.0000
92 V A 0.0000
93 A A -0.0671
94 F A 0.4585
95 I A 0.0000
96 V A 0.0000
97 A A 0.0226
98 D A -0.4325
99 S A 0.0000
100 G A -0.7209
101 A A 0.0000
102 S A -0.6795
103 R A -0.8134
104 M A 0.0000
105 V A 0.0000
106 C A 0.0000
107 S A -1.0261
108 A A -0.9814
109 A A -0.8570
110 T A -1.5023
111 R A -2.6615
112 D A -2.9235
113 G A -1.8650
114 V A -1.5783
115 P A -1.4955
116 E A -2.2020
117 G A -1.3524
118 I A -0.8108
119 E A -0.9358
120 A A -1.0766
121 I A 0.0000
122 V A -1.0018
123 V A 0.0000
124 T A -1.3734
125 D A -2.6342
126 E A -2.9434
127 E A -1.9846
128 A A -0.8113
129 F A -0.5925
130 E A -1.6310
131 A A -0.8900
132 S A -0.4853
133 A A -0.7986
134 A A -0.9639
135 G A -1.2999
136 A A -1.6182
137 R A -2.1972
138 P A -1.1145
139 G A -1.4876
140 D A -1.6493
141 L A -1.0427
142 A A 0.0000
143 A A 0.0000
144 V A 0.0000
145 I A 0.0000
146 Y A 0.2859
147 T A 0.0000
148 S A 0.0000
149 G A 0.0000
150 S A -0.3167
151 T A 0.1809
152 G A 0.3620
153 I A 1.1469
154 P A 0.0000
155 K A 0.0000
156 G A 0.0000
157 V A 0.0000
158 A A 0.0000
159 I A 0.0000
160 P A 0.0000
161 H A 0.0000
162 R A -0.8440
163 A A 0.0000
164 V A 0.0000
165 A A 0.0000
166 A A -0.8695
167 M A 0.0000
168 A A 0.0000
169 E A -1.5122
170 A A 0.0000
171 L A 0.0000
172 V A -0.9153
173 R A -1.4789
174 L A -0.7798
175 L A 0.0000
176 D A -1.3451
177 I A 0.0000
178 T A -1.2013
179 P A -1.1747
180 D A -1.9236
181 D A 0.0000
182 Q A -0.9320
183 V A 0.0000
184 L A 0.0000
185 H A 0.0000
186 Y A 0.0000
187 S A 0.0000
188 P A -0.0752
189 I A 0.0000
190 S A -0.0172
191 F A 0.1641
192 D A 0.0000
193 A A 0.0000
194 F A 0.0000
195 L A 0.0000
196 S A 0.0000
197 E A 0.0000
198 V A 0.0000
199 W A 0.0000
200 G A 0.0000
201 S A 0.0000
202 L A 0.0000
203 V A 0.0000
204 A A 0.0000
205 G A 0.0000
206 A A 0.0000
207 T A 0.0000
208 L A 0.0000
209 V A 0.0000
210 I A 0.0000
211 P A 0.0000
212 E A -2.7453
213 A A -1.8125
214 D A -2.3175
215 Q A -1.9751
216 A A -0.9200
217 S A -0.7260
218 F A -0.8405
219 L A -0.5422
220 G A -1.5030
221 S A 0.0000
222 V A 0.0000
223 S A -1.9887
224 R A -2.4706
225 H A -1.7133
226 L A 0.0000
227 A A -1.7803
228 A A -1.0378
229 H A -1.3482
230 G A 0.0000
231 C A 0.0000
232 D A 0.0000
233 L A 0.0000
234 A A 0.0000
235 M A 0.0000
236 L A 0.0000
237 S A 0.0000
238 P A 0.0000
239 S A -1.0975
240 V A 0.0000
241 Y A 0.0000
242 A A -1.5963
243 R A -2.4949
244 L A 0.0000
245 D A -3.4829
246 E A -3.1795
247 A A -2.0265
248 A A 0.0000
249 R A -2.3489
250 S A -1.9311
251 R A -1.9156
252 I A 0.0000
253 R A -2.2590
254 K A 0.0000
255 V A 0.0000
256 E A 0.0000
257 F A 0.0000
258 C A 0.0000
259 G A -0.4897
260 E A -0.6418
261 A A -0.3068
262 L A 0.0000
263 G A -1.3707
264 E A -2.5712
265 G A -1.9687
266 E A -1.7801
267 Y A 0.0000
268 D A -3.1144
269 K A -2.7046
270 A A 0.0000
271 A A -1.7399
272 R A -2.3082
273 Y A -1.6197
274 S A -1.6001
275 R A -1.6284
276 V A 0.0000
277 F A 0.0000
278 N A 0.0000
279 A A 0.0000
280 Y A 0.0000
281 G A -0.0891
282 P A -0.0964
283 T A 0.0000
284 E A 0.0000
285 A A 0.0000
286 T A 0.0000
287 V A 0.0000
288 C A 0.0000
289 A A 0.0000
290 T A 0.0000
291 L A 0.0000
292 A A 0.0000
293 E A -1.2069
294 L A 0.0000
295 T A -0.4495
296 S A -0.6344
297 Y A -0.6587
298 T A -0.2716
299 P A -0.2360
300 S A 0.0000
301 I A 0.0000
302 G A 0.0000
303 R A -1.8683
304 P A -1.3452
305 V A 0.0000
306 E A -2.3309
307 G A -1.4385
308 R A 0.0000
309 T A -0.7250
310 V A 0.0000
311 Q A -0.5738
312 V A 0.0000
313 L A 0.0000
314 D A -0.6162
315 A A -0.4048
316 S A -0.5071
317 L A -0.3159
318 R A -1.5994
319 A A -0.6456
320 V A 0.1793
321 A A 0.2622
322 P A -0.0581
323 G A 0.3797
324 V A 1.4275
325 I A 1.5255
326 G A 0.0000
327 D A -0.1624
328 L A 0.0000
329 Y A 0.0000
330 I A 0.0000
331 S A 0.0000
332 G A -0.7728
333 A A -0.6582
334 G A 0.0000
335 L A 0.0000
336 A A 0.0000
337 D A -1.8859
338 G A 0.0000
339 Y A 0.0000
340 L A -1.0267
341 R A -1.9440
342 R A -1.2757
343 A A -0.9125
344 G A -1.0993
345 L A -0.8872
346 T A -1.1155
347 A A -0.9443
348 E A -1.8958
349 R A -1.1925
350 L A 0.0000
351 V A -0.4663
352 A A -0.5306
353 D A 0.0000
354 P A -0.6298
355 S A -0.5243
356 A A -0.5264
357 P A -0.6542
358 G A -0.7992
359 A A -0.7165
360 R A -1.1368
361 M A 0.0000
362 F A 0.0000
363 R A -0.8682
364 T A 0.0000
365 G A 0.0000
366 D A 0.0000
367 L A 0.4017
368 A A 0.0000
369 Q A 0.7209
370 F A -0.0056
371 T A -0.6054
372 A A -1.0155
373 D A -2.0376
374 G A -1.3713
375 Q A -1.1858
376 L A 0.0000
377 I A 0.3802
378 F A 0.7114
379 A A 0.4614
380 G A 0.0413
381 R A -0.8294
382 A A -0.8583
383 D A -1.7372
384 D A -2.1923
385 Q A 0.0000
386 V A -0.8662
387 K A -1.0125
388 V A -1.1661
389 R A -1.3582
390 G A 0.0000
391 F A 0.0000
392 R A -0.5035
393 I A 0.0000
394 E A 0.0000
395 P A 0.0000
396 A A -0.2821
397 E A 0.0000
398 V A 0.0000
399 E A -0.5544
400 A A -0.1902
401 A A 0.0627
402 L A 0.0000
403 T A -0.8876
404 A A -0.5333
405 Q A 0.0000
406 P A -0.7614
407 G A -1.7326
408 V A 0.0000
409 H A -2.1691
410 E A -2.0904
411 A A -0.9538
412 V A 0.0000
413 V A 0.0000
414 R A -0.7360
415 A A -0.9827
416 V A -0.9612
417 D A -2.0767
418 G A -1.8417
419 R A -1.6591
420 L A 0.0000
421 V A 0.0000
422 G A 0.0000
423 Y A 0.0000
424 V A 0.0000
425 V A -1.6283
426 A A -2.4364
427 E A -2.9316
428 G A -2.6061
429 D A -2.8678
430 A A -1.8087
431 E A -1.6010
432 P A -0.9349
433 A A -0.6757
434 V A -0.2715
435 L A 0.0000
436 R A -1.9975
437 E A -2.2233
438 R A -1.7545
439 V A 0.0000
440 G A -1.4001
441 A A -0.8153
442 V A 0.0718
443 L A 0.0000
444 P A 0.0000
445 E A -1.7347
446 Y A -0.9248
447 M A 0.0000
448 V A -0.9932
449 P A 0.0000
450 A A -0.4322
451 A A 0.2010
452 V A 0.0000
453 I A 0.4622
454 T A -0.8035
455 L A -0.6084
456 D A -1.8145
457 A A -0.6172
458 L A -0.1563
459 P A 0.2291
460 L A 0.5769
461 T A -0.6112
462 G A -1.1354
463 N A -1.8449
464 G A -1.3212
465 K A -1.7033
466 V A -0.2385
467 D A -0.4577
468 R A -0.6492
469 A A -0.0751
470 A A 0.1094
471 L A 0.0000
472 P A 0.1714
473 A A 0.5598
474 P A 0.7693
475 V A 1.9826
476 F A 0.8680
477 A A 0.1577
478 A A -0.6001
479 D A -2.1286
480 G A -1.9240
481 S A -1.9206
482 H A -2.5043
483 H A -2.5985
484 H A -2.8092
485 H A -2.7560
486 H A -2.4451
487 H A -1.9359
Download PDB file
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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 -0.3946 3.2573 View CSV PDB
4.5 -0.4588 3.2057 View CSV PDB
5.0 -0.5374 3.1484 View CSV PDB
5.5 -0.6191 3.089 View CSV PDB
6.0 -0.6941 3.029 View CSV PDB
6.5 -0.7559 2.9688 View CSV PDB
7.0 -0.8047 2.9089 View CSV PDB
7.5 -0.845 2.8501 View CSV PDB
8.0 -0.88 2.7945 View CSV PDB
8.5 -0.9085 2.7469 View CSV PDB
9.0 -0.9274 2.714 View CSV PDB