Project name: C2fix

Status: done

Started: 2026-08-18 04:27:48
Chain sequence(s) A: MSTVPEEFARRVTAAPDAVAVIDGDRVLTYRELDELAGRLSGRLIGRGVRRGDRVAVLLPNSADLIVTLLAIWKAGAAFVPIDAGFPAPRVAFMVADSGASRMVCSAATRDGVPEGIEAIVVTDEEAFEASAAGARPGDLAYVLYTSGSTGIPKGVAVPHRAVHARATDRCWDLDTGSRVLFHSPFAFDIAIFEIWAPLLAGGEVVVAPAGDLDAAVLQRTLAAYGVTSLLLTAGLLGVIADEAPEVFTGVKDVWTGGDVVSPTAVRRVLEACPGTVVKTLYGPTEVTLGASWLPFTDPRRIPPVVPIGRPREGQTLQVLDASLRAVAPGVIGDIYISGAGLADGYLRRAGLTAERLVADPSAPGARMFRTGDLGQWTADGYLVFAGRADDQVKVRGFRIEPAEVEAALTAQPGVHEAVVRAVDGRLVGYVVAEGDAEPAVLRERVGAVLPEYMVPAAVITLDALPLTGNGKVDRAALPAPVFAADGSHHHHHH
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                                          (00:08:53)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/a0257763b199efe/tmp/folded.pdb                (00:08:53)
[INFO]       Main:     Simulation completed successfully.                                          (00:16:03)
Show buried residues

Minimal score value
-3.3085
Maximal score value
2.0656
Average score
-0.6359
Total score value
-314.1515

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 0.4182
2 S A -0.3541
3 T A 0.0000
4 V A 0.0000
5 P A -0.6740
6 E A -1.0220
7 E A -1.1926
8 F A 0.0000
9 A A -1.4834
10 R A -2.2282
11 R A -1.7331
12 V A -1.5947
13 T A -1.1856
14 A A -0.8645
15 A A -1.0322
16 P A -1.7434
17 D A -2.1167
18 A A -1.0389
19 V A -0.1127
20 A A 0.0000
21 V A 0.0000
22 I A -0.4582
23 D A -1.4967
24 G A -1.8294
25 D A -2.6458
26 R A -2.2988
27 V A -0.1904
28 L A 0.0000
29 T A -1.0646
30 Y A 0.0000
31 R A -2.5872
32 E A -2.2978
33 L A 0.0000
34 D A -2.0771
35 E A -2.9235
36 L A -1.5271
37 A A 0.0000
38 G A -1.9627
39 R A -2.6551
40 L A 0.0000
41 S A 0.0000
42 G A 0.0000
43 R A 0.0000
44 L A 0.0000
45 I A -0.7395
46 G A -0.6430
47 R A -0.9549
48 G A -1.0900
49 V A 0.0000
50 R A -2.7989
51 R A -2.6720
52 G A -1.9049
53 D A -1.9496
54 R A -1.3204
55 V A 0.0000
56 A A 0.0000
57 V A 0.0000
58 L A 0.0000
59 L A 0.0000
60 P A -0.6407
61 N A -0.7541
62 S A -0.8027
63 A A 0.0000
64 D A -0.5177
65 L A 0.0000
66 I A 0.0000
67 V A 0.0000
68 T A 0.0000
69 L A 0.0000
70 L A 0.0000
71 A A 0.0000
72 I A 0.0000
73 W A 0.0000
74 K A -0.5504
75 A A 0.0000
76 G A 0.0000
77 A A 0.0000
78 A A 0.0000
79 F A 0.0000
80 V A 0.0000
81 P A 0.0000
82 I A 0.0000
83 D A -0.7170
84 A A -0.4488
85 G A -0.9034
86 F A -0.4526
87 P A -0.2150
88 A A -0.0814
89 P A 0.1313
90 R A 0.0000
91 V A 0.0000
92 A A -0.0779
93 F A 0.6058
94 M A 0.0000
95 V A 0.0000
96 A A 0.1052
97 D A 0.0000
98 S A 0.0000
99 G A -0.7470
100 A A 0.0000
101 S A -0.9460
102 R A -1.1910
103 M A 0.0000
104 V A 0.0000
105 C A 0.0000
106 S A -0.9219
107 A A -0.8919
108 A A -0.8168
109 T A -1.3971
110 R A -2.5388
111 D A -2.8865
112 G A -1.9284
113 V A -1.7265
114 P A -1.6376
115 E A -2.3613
116 G A -1.5899
117 I A -1.2895
118 E A -1.8918
119 A A -1.5116
120 I A 0.0000
121 V A -0.9565
122 V A 0.0000
123 T A -1.2525
124 D A -2.4853
125 E A -2.9259
126 E A -2.0708
127 A A -1.0114
128 F A -0.3660
129 E A -1.6376
130 A A -0.8505
131 S A -0.4746
132 A A -0.7502
133 A A -0.6856
134 G A -1.0442
135 A A 0.0000
136 R A -1.7603
137 P A -1.2934
138 G A -1.5494
139 D A -1.5807
140 L A -0.9919
141 A A 0.0000
142 Y A 0.0000
143 V A 0.0000
144 L A 0.0000
145 Y A 0.3732
146 T A 0.2796
147 S A 0.0000
148 G A 0.0000
149 S A -0.2613
150 T A 0.2847
151 G A 0.5191
152 I A 1.4979
153 P A 0.0000
154 K A 0.0000
155 G A 0.0000
156 V A 0.0000
157 A A 0.0000
158 V A 0.0000
159 P A 0.0000
160 H A 0.0000
161 R A -1.5290
162 A A 0.0000
163 V A 0.0000
164 H A -0.5305
165 A A -0.9285
166 R A 0.0000
167 A A 0.0000
168 T A -0.7540
169 D A 0.0000
170 R A -2.6185
171 C A -1.5954
172 W A 0.0000
173 D A -2.8075
174 L A -2.0247
175 D A -2.3395
176 T A -1.2462
177 G A -1.2198
178 S A 0.0000
179 R A -1.1726
180 V A 0.0000
181 L A 0.0000
182 F A 0.0000
183 H A -0.4982
184 S A 0.0000
185 P A -0.1903
186 F A 0.0000
187 A A 0.1029
188 F A 0.5073
189 D A 0.0000
190 I A 0.2711
191 A A 0.0000
192 I A 0.0000
193 F A 0.0000
194 E A 0.0000
195 I A 0.0000
196 W A 0.0000
197 A A 0.0000
198 P A 0.0000
199 L A 0.0000
200 L A 0.0000
201 A A -1.2697
202 G A 0.0000
203 G A 0.0000
204 E A -0.4363
205 V A 0.0000
206 V A 0.0000
207 V A 0.0000
208 A A -0.4654
209 P A -0.6860
210 A A -0.7960
211 G A -1.4744
212 D A -2.3334
213 L A -1.4558
214 D A -1.8459
215 A A -1.5856
216 A A -0.9971
217 V A -1.0901
218 L A 0.0000
219 Q A -1.6138
220 R A -1.8447
221 T A 0.0000
222 L A 0.0000
223 A A -0.7279
224 A A -0.4353
225 Y A -0.1815
226 G A -0.5085
227 V A 0.0000
228 T A -1.0312
229 S A 0.0000
230 L A 0.0000
231 L A 0.0000
232 L A 0.0000
233 T A -0.5118
234 A A 0.0000
235 G A -0.5192
236 L A -0.1094
237 L A 0.0000
238 G A -0.3237
239 V A 0.1069
240 I A 0.0000
241 A A 0.0000
242 D A -2.3465
243 E A -2.6994
244 A A -2.0061
245 P A -2.1824
246 E A -2.4605
247 V A 0.0000
248 F A 0.0000
249 T A -1.2448
250 G A -1.3002
251 V A 0.0000
252 K A -2.1446
253 D A 0.0000
254 V A 0.0000
255 W A 0.0000
256 T A 0.0000
257 G A 0.0000
258 G A -0.9379
259 D A -0.9082
260 V A 1.4145
261 V A 0.0000
262 S A 0.3075
263 P A -0.0524
264 T A -0.7473
265 A A 0.0000
266 V A 0.0000
267 R A -2.4883
268 R A -2.5118
269 V A 0.0000
270 L A 0.0000
271 E A -3.0268
272 A A -1.9557
273 C A 0.0000
274 P A -1.4139
275 G A -1.2509
276 T A 0.0000
277 V A -0.4422
278 V A 0.0000
279 K A 0.0000
280 T A 0.0000
281 L A 0.0000
282 Y A 0.0884
283 G A -0.0871
284 P A -0.1329
285 T A 0.0583
286 E A 0.0000
287 V A 0.0000
288 T A 0.0000
289 L A 0.0000
290 G A 0.0000
291 A A 0.0000
292 S A 0.0000
293 W A 0.0147
294 L A 0.0504
295 P A -0.0072
296 F A 0.0000
297 T A -1.2029
298 D A -2.1944
299 P A -2.7781
300 R A -3.3085
301 R A -3.0725
302 I A 0.0000
303 P A -0.3998
304 P A 0.3722
305 V A 2.0656
306 V A 1.4554
307 P A 0.0000
308 I A 0.7247
309 G A 0.0000
310 R A -1.0802
311 P A -1.0374
312 R A 0.0000
313 E A -2.4978
314 G A -1.4342
315 Q A 0.0000
316 T A -0.6688
317 L A 0.0000
318 Q A -0.5440
319 V A 0.0000
320 L A 0.0000
321 D A -0.8220
322 A A -0.6404
323 S A -0.7189
324 L A -0.7404
325 R A -1.8297
326 A A -0.8048
327 V A 0.0571
328 A A 0.2473
329 P A -0.0081
330 G A 0.4481
331 V A 1.6758
332 I A 1.9674
333 G A 0.0000
334 D A -0.4284
335 I A 0.0000
336 Y A -0.3009
337 I A 0.0000
338 S A 0.0000
339 G A -0.6681
340 A A -0.7012
341 G A 0.0000
342 L A -0.5558
343 A A 0.0000
344 D A -1.8410
345 G A 0.0000
346 Y A 0.0000
347 L A -0.9808
348 R A -1.9103
349 R A -1.2636
350 A A -0.9088
351 G A -1.0581
352 L A -0.7727
353 T A -1.0817
354 A A -0.9146
355 E A -1.9327
356 R A -1.2743
357 L A 0.0000
358 V A -0.5092
359 A A -0.4283
360 D A 0.0000
361 P A -0.6131
362 S A -0.5036
363 A A -0.4931
364 P A -0.6246
365 G A -0.7456
366 A A -0.5861
367 R A -0.9016
368 M A 0.0000
369 F A 0.0000
370 R A -1.1584
371 T A 0.0000
372 G A -0.8442
373 D A 0.0000
374 L A 0.3584
375 G A 0.0000
376 Q A 0.8045
377 W A 0.0540
378 T A -0.5636
379 A A -0.9852
380 D A -1.8082
381 G A -1.1495
382 Y A -0.4735
383 L A 0.0000
384 V A 0.9255
385 F A 1.4707
386 A A 0.7137
387 G A 0.2317
388 R A -0.8390
389 A A -0.8889
390 D A -1.6290
391 D A -2.0790
392 Q A 0.0000
393 V A -0.8932
394 K A -1.1766
395 V A 0.0000
396 R A -2.4188
397 G A 0.0000
398 F A -0.6592
399 R A -0.6243
400 I A 0.0000
401 E A 0.0000
402 P A 0.0000
403 A A -0.2729
404 E A 0.0000
405 V A 0.0000
406 E A -0.6280
407 A A -0.1875
408 A A 0.0715
409 L A 0.0000
410 T A -0.9237
411 A A -0.5481
412 Q A 0.0000
413 P A -0.8598
414 G A -1.7797
415 V A 0.0000
416 H A -2.1858
417 E A -2.1664
418 A A -1.0202
419 V A 0.0000
420 V A 0.0000
421 R A -0.8722
422 A A -1.0783
423 V A -1.0990
424 D A -2.1853
425 G A -2.3579
426 R A -1.9238
427 L A 0.0000
428 V A 0.0000
429 G A 0.0000
430 Y A 0.0000
431 V A 0.0000
432 V A -1.4568
433 A A -2.3763
434 E A -2.9106
435 G A -2.4281
436 D A -2.7457
437 A A -1.8587
438 E A -1.6349
439 P A -0.9849
440 A A -0.5993
441 V A -0.4618
442 L A 0.0000
443 R A -1.9262
444 E A -2.3684
445 R A -1.7707
446 V A 0.0000
447 G A -1.4069
448 A A -0.8380
449 V A 0.0029
450 L A 0.0000
451 P A 0.0000
452 E A -1.9119
453 Y A -1.0168
454 M A 0.0000
455 V A -0.9991
456 P A 0.0000
457 A A -0.4290
458 A A 0.2136
459 V A 0.0000
460 I A 0.4489
461 T A -0.6501
462 L A -0.6278
463 D A -1.7779
464 A A -0.7252
465 L A -0.2884
466 P A 0.0640
467 L A 0.3985
468 T A -0.7485
469 G A -1.1603
470 N A -1.8828
471 G A -1.3595
472 K A -1.8917
473 V A -0.6230
474 D A -0.8168
475 R A -1.0322
476 A A -0.3497
477 A A -0.0840
478 L A 0.0000
479 P A 0.1018
480 A A 0.5557
481 P A 0.7635
482 V A 1.9893
483 F A 0.8728
484 A A 0.1495
485 A A -0.6203
486 D A -2.1317
487 G A -1.8951
488 S A -1.8837
489 H A -2.4740
490 H A -2.5636
491 H A -2.7732
492 H A -2.7241
493 H A -2.4227
494 H A -1.9103
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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 -0.2952 3.529 View CSV PDB
4.5 -0.3597 3.4805 View CSV PDB
5.0 -0.4391 3.4256 View CSV PDB
5.5 -0.5232 3.3676 View CSV PDB
6.0 -0.6018 3.3088 View CSV PDB
6.5 -0.6687 3.2504 View CSV PDB
7.0 -0.7235 3.1942 View CSV PDB
7.5 -0.7692 3.1433 View CSV PDB
8.0 -0.8079 3.115 View CSV PDB
8.5 -0.8387 3.115 View CSV PDB
9.0 -0.859 3.115 View CSV PDB