Project name: P04405

Status: done

Started: 2025-06-28 11:26:13
Chain sequence(s) A: MAKLVLSLCFLLFSGCFALREQAQQNECQIQKLNALKPDNRIESEGGFIETWNPNNKPFQCAGVALSRCTLNRNALRRPSYTNGPQEIYIQQGNGIFGMIFPGCPSTYQEPQESQQRGRSQRPQDRHQKVHRFREGDLIAVPTGVAWWMYNNEDTPVVAVSIIDTNSLENQLDQMPRRFYLAGNQEQEFLKYQQQQQGGSQSQKGKQQEEENEGSNILSGFAPEFLKEAFGVNMQIVRNLQGENEEEDSGAIVTVKGGLRVTAPAMRKPQQEEDDDDEEEQPQCVETDKGCQRQSKRSRNGIDETICTMRLRQNIGQNSSPDIYNPQAGSITTATSLDFPALWLLKLSAQYGSLRKNAMFVPHYTLNANSIIYALNGRALVQVVNCNGERVFDGELQEGGVLIVPQNFAVAAKSQSDNFEYVSFKTNDRPSIGNLAGANSLLNALPEEVIQHTFNLKSQQARQVKNNNPFSFLVPPQESQRRAVA
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                                          (00:06:23)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/7a67d6a92b5de2f/tmp/folded.pdb                (00:06:23)
[INFO]       Main:     Simulation completed successfully.                                          (00:09:35)
Show buried residues

Minimal score value
-6.285
Maximal score value
4.2382
Average score
-1.142
Total score value
-553.8505

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 0.8364
2 A A 0.4049
3 K A 0.0468
4 L A 2.1298
5 V A 2.9360
6 L A 2.9576
7 S A 2.4653
8 L A 3.3096
9 C A 3.2499
10 F A 4.1919
11 L A 4.2382
12 L A 3.6606
13 F A 3.3340
14 S A 1.9208
15 G A 1.3750
16 C A 2.0105
17 F A 2.3475
18 A A 1.0730
19 L A 0.5967
20 R A -1.9503
21 E A -3.0005
22 Q A -2.8682
23 A A -2.7974
24 Q A -3.2286
25 Q A -3.1630
26 N A -3.1850
27 E A -3.3336
28 C A -1.9084
29 Q A -2.5739
30 I A 0.0000
31 Q A -2.8616
32 K A -3.3418
33 L A 0.0000
34 N A -2.1238
35 A A -1.3491
36 L A -1.3225
37 K A -2.4865
38 P A -2.0282
39 D A -2.4268
40 N A -2.2879
41 R A -2.5973
42 I A -1.8642
43 E A -2.8688
44 S A -2.4874
45 E A -2.5892
46 G A 0.0000
47 G A -1.1433
48 F A -1.1636
49 I A 0.0000
50 E A -1.7301
51 T A 0.0000
52 W A 0.0000
53 N A -1.2812
54 P A 0.0000
55 N A -1.4110
56 N A -1.1786
57 K A -1.8439
58 P A -1.2502
59 F A 0.0000
60 Q A -1.7383
61 C A -1.2279
62 A A 0.0000
63 G A 0.0000
64 V A 0.0000
65 A A 0.0000
66 L A 0.0000
67 S A 0.0000
68 R A -0.4973
69 C A 0.0000
70 T A -0.3727
71 L A 0.0000
72 N A -2.3530
73 R A -3.5524
74 N A -2.5967
75 A A 0.0000
76 L A -0.2736
77 R A 0.0000
78 R A 0.0000
79 P A 0.4552
80 S A 0.0000
81 Y A 0.4350
82 T A 0.0000
83 N A -0.8321
84 G A 0.0000
85 P A 0.0000
86 Q A 0.0000
87 E A 0.0000
88 I A 0.0000
89 Y A 0.0000
90 I A 0.0000
91 Q A -1.1609
92 Q A -1.3477
93 G A 0.0000
94 N A -2.0880
95 G A 0.0000
96 I A 0.0000
97 F A 0.0000
98 G A 0.0000
99 M A 0.0000
100 I A 0.7083
101 F A 0.0000
102 P A -0.1093
103 G A -0.3429
104 C A -0.1063
105 P A -0.7088
106 S A -1.5515
107 T A -1.1606
108 Y A -1.9397
109 Q A -3.2755
110 E A -3.2272
111 P A -2.3869
112 Q A -3.3169
113 E A -3.4007
114 S A -2.5781
115 Q A -3.7804
116 Q A -3.5911
117 R A -3.5690
118 G A -2.9741
119 R A -3.7410
120 S A -2.8606
121 Q A -3.4300
122 R A -3.4296
123 P A -2.6853
124 Q A -3.7472
125 D A -3.9108
126 R A -3.8285
127 H A -2.1390
128 Q A -1.0932
129 K A -1.1746
130 V A 0.0000
131 H A -0.6488
132 R A -0.7856
133 F A 0.0000
134 R A -2.5403
135 E A -3.0078
136 G A 0.0000
137 D A 0.0000
138 L A 0.0000
139 I A 0.0000
140 A A 0.0000
141 V A 0.0000
142 P A 0.0000
143 T A -0.5455
144 G A -0.3647
145 V A 0.0000
146 A A 0.5165
147 W A 0.0000
148 W A 0.3461
149 M A 0.0000
150 Y A 0.0000
151 N A 0.0000
152 N A -2.5929
153 E A -3.2580
154 D A -3.3973
155 T A -2.0399
156 P A -1.7740
157 V A 0.0000
158 V A -0.4028
159 A A 0.0000
160 V A 0.0000
161 S A 0.0000
162 I A 0.0000
163 I A 0.0000
164 D A 0.0000
165 T A 0.0000
166 N A -1.7261
167 S A 0.0000
168 L A 0.0985
169 E A -1.5272
170 N A -1.4147
171 Q A -1.3268
172 L A -0.3395
173 D A -1.4164
174 Q A -1.8297
175 M A -0.9181
176 P A 0.0000
177 R A -0.5479
178 R A 0.0000
179 F A 0.6976
180 Y A 0.0000
181 L A 0.9193
182 A A 0.3469
183 G A 0.0000
184 N A -2.3710
185 Q A 0.0000
186 E A -2.2890
187 Q A -1.1823
188 E A 0.0000
189 F A 0.0000
190 L A -0.5408
191 K A -1.4724
192 Y A 0.0000
193 Q A -1.9102
194 Q A -2.4731
195 Q A -2.9357
196 Q A -3.0693
197 Q A -3.0441
198 G A -2.5338
199 G A -1.8399
200 S A -1.5764
201 Q A -2.3681
202 S A -2.1127
203 Q A -2.9508
204 K A -4.0450
205 G A -3.9760
206 K A -4.7139
207 Q A -4.8332
208 Q A -5.2619
209 E A -5.4492
210 E A -5.3171
211 E A -4.9770
212 N A -4.0706
213 E A -4.1960
214 G A -2.2261
215 S A -1.2442
216 N A 0.0000
217 I A 1.0538
218 L A 0.6226
219 S A -0.1696
220 G A 0.2743
221 F A 1.1889
222 A A 0.3654
223 P A -0.9488
224 E A -1.6548
225 F A 0.4245
226 L A 0.0000
227 K A -1.7358
228 E A -1.8577
229 A A -0.2305
230 F A 0.7511
231 G A -0.3862
232 V A -0.6299
233 N A -1.7774
234 M A -1.7950
235 Q A -2.0910
236 I A -0.7280
237 V A 0.0000
238 R A -2.9737
239 N A -2.2906
240 L A -0.6620
241 Q A 0.0000
242 G A 0.0000
243 E A -3.6492
244 N A -3.6020
245 E A -3.5550
246 E A -4.2106
247 E A -4.2427
248 D A -4.0584
249 S A 0.0000
250 G A 0.0000
251 A A 0.0000
252 I A 0.0000
253 V A -0.6482
254 T A -1.1097
255 V A -1.3185
256 K A -1.8479
257 G A -1.5313
258 G A -1.6892
259 L A -1.0879
260 R A -1.6287
261 V A -1.0671
262 T A -1.5284
263 A A -0.5024
264 P A -0.3219
265 A A -0.2056
266 M A -0.5456
267 R A -3.0244
268 K A -3.4463
269 P A -3.2265
270 Q A -4.1525
271 Q A -5.0217
272 E A -5.0174
273 E A -5.6958
274 D A -6.0070
275 D A -6.0723
276 D A -5.5136
277 D A -6.1958
278 E A -6.2850
279 E A -5.5009
280 E A -5.1283
281 Q A -3.9451
282 P A -2.8060
283 Q A -1.9664
284 C A -0.5418
285 V A 0.1891
286 E A -1.9193
287 T A -1.9625
288 D A -3.1468
289 K A -3.0663
290 G A -2.1167
291 C A -1.3461
292 Q A -2.5219
293 R A -3.1335
294 Q A -3.1615
295 S A -2.9803
296 K A -4.1402
297 R A -3.5859
298 S A -3.2606
299 R A -3.8145
300 N A -3.2443
301 G A -1.6154
302 I A -0.2101
303 D A -2.2727
304 E A -2.6461
305 T A -0.5674
306 I A 0.4228
307 C A 0.0403
308 T A -0.7875
309 M A 0.0000
310 R A -0.8764
311 L A 0.0000
312 R A -0.8052
313 Q A -1.0618
314 N A -1.5817
315 I A 0.0000
316 G A 0.0000
317 Q A -2.1632
318 N A -2.2120
319 S A -1.6444
320 S A -0.9850
321 P A -0.9668
322 D A -1.3834
323 I A 0.1340
324 Y A 0.8551
325 N A 0.2360
326 P A -0.4250
327 Q A -1.0281
328 A A 0.0000
329 G A 0.0000
330 S A -0.1791
331 I A 0.0000
332 T A 0.0000
333 T A -0.7375
334 A A 0.0000
335 T A -0.4301
336 S A 0.0000
337 L A 0.2236
338 D A -0.8147
339 F A 0.0000
340 P A -0.3078
341 A A 0.0000
342 L A 0.0000
343 W A 0.6761
344 L A 0.4478
345 L A 0.0000
346 K A -0.5045
347 L A 0.0000
348 S A 0.0000
349 A A 0.0000
350 Q A 0.0000
351 Y A 0.0000
352 G A 0.0000
353 S A 0.0000
354 L A 0.0000
355 R A -3.0140
356 K A -3.6244
357 N A -2.3653
358 A A 0.0000
359 M A -0.4637
360 F A 0.0000
361 V A 0.0000
362 P A 0.1794
363 H A 0.0000
364 Y A 0.0893
365 T A 0.0000
366 L A 0.1382
367 N A -0.8502
368 A A 0.0000
369 N A -0.6802
370 S A 0.0000
371 I A 0.0000
372 I A 0.1917
373 Y A 0.0000
374 A A 0.0000
375 L A 0.0000
376 N A -2.0233
377 G A 0.0000
378 R A -3.2721
379 A A 0.0000
380 L A -1.1422
381 V A 0.0000
382 Q A -1.5718
383 V A 0.0000
384 V A -1.7279
385 N A -1.7467
386 C A -0.6303
387 N A -1.9716
388 G A -1.8776
389 E A -3.1800
390 R A -3.5483
391 V A 0.0000
392 F A 0.0000
393 D A -2.6171
394 G A -1.6094
395 E A -2.1908
396 L A 0.0000
397 Q A -2.9782
398 E A -3.0467
399 G A -1.8151
400 G A 0.0000
401 V A 0.0000
402 L A 0.0000
403 I A 0.0000
404 V A 0.0000
405 P A -0.5294
406 Q A -1.2660
407 N A -1.0889
408 F A -0.4467
409 A A -0.3077
410 V A 0.0000
411 A A -0.2241
412 A A -0.6357
413 K A -1.4574
414 S A 0.0000
415 Q A -2.4137
416 S A -2.7188
417 D A -3.3723
418 N A -2.7418
419 F A 0.0000
420 E A 0.0000
421 Y A 0.0000
422 V A 0.0000
423 S A 0.0000
424 F A 0.0000
425 K A 0.0000
426 T A -0.9408
427 N A -1.0407
428 D A 0.0000
429 R A -1.5508
430 P A -0.8995
431 S A -0.1375
432 I A 0.4310
433 G A 0.4381
434 N A 0.0000
435 L A 0.7364
436 A A 0.0802
437 G A 0.0000
438 A A -0.9407
439 N A -0.9892
440 S A 0.0000
441 L A 1.1169
442 L A 0.8581
443 N A -0.4582
444 A A 0.2969
445 L A 0.6476
446 P A -0.5466
447 E A -1.7330
448 E A -2.2446
449 V A -0.3532
450 I A 0.0000
451 Q A -1.9429
452 H A -1.5287
453 T A -0.2099
454 F A 0.3090
455 N A -1.3608
456 L A -1.6585
457 K A -3.1361
458 S A -2.8886
459 Q A -3.0138
460 Q A -3.0745
461 A A 0.0000
462 R A -3.9458
463 Q A -3.3644
464 V A -1.3109
465 K A -2.0184
466 N A -2.8214
467 N A -2.6064
468 N A -1.4668
469 P A -0.9912
470 F A -0.2079
471 S A -0.0734
472 F A 0.5435
473 L A 0.0000
474 V A -0.2366
475 P A 0.0000
476 P A 0.0000
477 Q A -2.5590
478 E A -2.9763
479 S A -2.2803
480 Q A -2.2399
481 R A -2.9710
482 R A -2.6536
483 A A -0.7941
484 V A 0.6157
485 A A -0.1569
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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 -0.7663 7.5262 View CSV PDB
4.5 -0.8501 7.5262 View CSV PDB
5.0 -0.9576 7.5262 View CSV PDB
5.5 -1.0698 7.5262 View CSV PDB
6.0 -1.1679 7.5262 View CSV PDB
6.5 -1.2383 7.5262 View CSV PDB
7.0 -1.2765 7.5262 View CSV PDB
7.5 -1.2891 7.5262 View CSV PDB
8.0 -1.2864 7.5262 View CSV PDB
8.5 -1.2736 7.5262 View CSV PDB
9.0 -1.2518 7.5262 View CSV PDB