Project name: Q9SMJ4

Status: done

Started: 2025-06-28 13:10:25
Chain sequence(s) A: MAKLLALSLSFCFLLFGTCFALRDQPQQNECQLEHLNALKPDNRIKSEGGLIETWNPSNKQFACAGVALSRATLQPNSLLQTFLHQRSPEIFIQQGNGYFGMVFPGCVETFEEPRESEQGEGSKFSDSHQKVNRFREGDIIAVPTGVVFWMFNDQDTPVIAVSLIDTSSFQNQLDQMPRRFYLAGNHEQEFLRYQQEGSEEEENEGGNIFSGFKRDFLEDALNVNRRIVNKLQGRNEDEEKGAIVKVKGGLSITTPPEKEPRQKRGSRQEEDEDEDEKRQPHRHSRQDEDEDEKRQPHHHSRGGSKSQRDNGFEETICTARLHQNIGSSSSPDIYNPQAGRIKTVTSFDLQALRFLKLSAEFGSLHKNAMFVPHYNLNANSILYALKGRARLLYALNCKGNSVFDGELEAGRALIVPQNFAIAAKSLSDRFSYVAFKTNDRALINVCQKKLLQLLSIWKEMRPGSSSSTAPFHFLFHPAVTQTTKQQLDLVPNQYE
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage A: MAKLLALSLSFCFLLFGTCFALRDQPQQNECQLEHLNALKPDNRIKSEGGLIETWNPSNKQFACAGVALSRATLQPNSLLQTFLHQRSPEIFIQQGNGYFGMVFPGCVETFEEPRESEQGEGSKFSDSHQKVNRFREGDIIAVPTGVVFWMFNDQDTPVIAVSLIDTSSFQNQLDQMPRRFYLAGNHEQEFLRYQQEGSEEEENEGGNIFSGFKRDFLEDALNVNRRIVNKLQGRNEDEEKGAIVKVKGGLSITTPPEKEPRQKRGSRQEEDEDEDEKR

QPHRHSRQDEDEDEKRQPHHHSRGGSKSQRDNG

FEETICTARLHQNIGSSSSPDIYNPQAGRIKTVTSFDLQALRFLKLSAEFGSLHKNAMFVPHYNLNANSILYALKGRARLLYALNCKGNSVFDGELEAGRALIVPQNFAIAAKSLSDRFSYVAFKTNDRALINVCQKKLLQLLSIWKEMRPGSSSSTAPFHFLFHPAVTQTTKQQLDLVPNQYE
(Red indicates removed residues)
Dynamic mode No
Automated mutations No
Downloads Download all the data
Simulation log
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       PDB:      Running AlphaCutter                                                         (00:00:02)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:21)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:21)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:15:21)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/fc2a65f3c3479cb/tmp/folded.pdb                (00:15:21)
[INFO]       Main:     Simulation completed successfully.                                          (00:22:10)
Show buried residues

Minimal score value
-5.5004
Maximal score value
4.6051
Average score
-0.9101
Total score value
-421.3621

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 1.2900
2 A A 0.8005
3 K A 0.1124
4 L A 2.2528
5 L A 2.5390
6 A A 1.9939
7 L A 3.0321
8 S A 2.8822
9 L A 3.4852
10 S A 3.6056
11 F A 4.4753
12 C A 3.9249
13 F A 4.6051
14 L A 4.2969
15 L A 3.8985
16 F A 4.2021
17 G A 2.7540
18 T A 2.1646
19 C A 2.6706
20 F A 2.7867
21 A A 1.0930
22 L A 1.3236
23 R A -0.4829
24 D A -2.3702
25 Q A -2.5260
26 P A -2.2457
27 Q A -2.7091
28 Q A -2.7552
29 N A -2.6044
30 E A -2.3244
31 C A -1.9891
32 Q A -2.5257
33 L A 0.0000
34 E A -2.4366
35 H A -2.3023
36 L A 0.0000
37 N A -2.1714
38 A A -1.7872
39 L A -1.6571
40 K A -2.5609
41 P A 0.0000
42 D A -2.0589
43 N A -2.1007
44 R A -2.5456
45 I A 0.0000
46 K A -3.0997
47 S A -2.8622
48 E A -3.2248
49 G A 0.0000
50 G A -1.1436
51 L A -1.1474
52 I A 0.0000
53 E A 0.0000
54 T A 0.0000
55 W A 0.0000
56 N A -1.4203
57 P A -0.8198
58 S A -1.0701
59 N A -1.3406
60 K A -2.0174
61 Q A 0.0000
62 F A 0.0000
63 A A -1.1119
64 C A 0.0000
65 A A 0.0000
66 G A -1.0020
67 V A 0.0000
68 A A 0.0000
69 L A 0.0000
70 S A 0.0000
71 R A -0.3278
72 A A 0.0000
73 T A -0.2649
74 L A 0.0000
75 Q A -1.5655
76 P A -1.8625
77 N A -2.0506
78 S A 0.0000
79 L A -0.3877
80 L A 0.0000
81 Q A -0.0044
82 T A 0.3520
83 F A 0.0000
84 L A 0.7299
85 H A 0.0000
86 Q A -0.0915
87 R A 0.0000
88 S A 0.0000
89 P A 0.0000
90 E A 0.0000
91 I A 0.0000
92 F A 0.0000
93 I A 0.0000
94 Q A -1.1358
95 Q A -1.3867
96 G A 0.0000
97 N A -2.1415
98 G A 0.0000
99 Y A -0.5184
100 F A 0.0000
101 G A 0.0000
102 M A 0.0000
103 V A 0.7678
104 F A 0.0000
105 P A 0.1353
106 G A -0.1163
107 C A 0.4140
108 V A 0.7406
109 E A -1.5972
110 T A -1.1681
111 F A -1.5710
112 E A -2.7949
113 E A -2.9587
114 P A -2.8342
115 R A -4.0306
116 E A -3.7662
117 S A -3.5548
118 E A -3.4945
119 Q A -3.1415
120 G A -2.4877
121 E A -3.1783
122 G A -2.2402
123 S A -2.2822
124 K A -3.0253
125 F A -2.1390
126 S A -2.3897
127 D A -2.7305
128 S A -1.8752
129 H A -1.5449
130 Q A -1.0735
131 K A -1.5853
132 V A 0.0000
133 N A -0.9422
134 R A -1.4088
135 F A 0.0000
136 R A -3.1295
137 E A -2.9849
138 G A 0.0000
139 D A 0.0000
140 I A 0.0000
141 I A 0.0000
142 A A 0.0000
143 V A 0.0000
144 P A 0.0000
145 T A -0.2577
146 G A -0.1958
147 V A 0.0000
148 V A 0.6871
149 F A 0.0000
150 W A 0.3306
151 M A 0.0000
152 F A 0.0000
153 N A 0.0000
154 D A -1.7644
155 Q A -2.1404
156 D A -2.5124
157 T A -1.4638
158 P A -1.0957
159 V A 0.0000
160 I A -0.2464
161 A A 0.0000
162 V A 0.0000
163 S A 0.0000
164 L A 0.0000
165 I A 0.0000
166 D A 0.0000
167 T A 0.0000
168 S A 0.0000
169 S A 0.0000
170 F A 0.4688
171 Q A -0.0924
172 N A -0.9688
173 Q A -1.0639
174 L A -0.3918
175 D A -1.6194
176 Q A -1.8701
177 M A -0.6776
178 P A 0.0000
179 R A 0.0000
180 R A 0.0000
181 F A 0.8455
182 Y A 0.0000
183 L A 0.7112
184 A A 0.0722
185 G A -1.9107
186 N A -2.9223
187 H A 0.0000
188 E A -3.4775
189 Q A -1.8688
190 E A 0.0000
191 F A 0.0000
192 L A -1.9930
193 R A -2.6377
194 Y A -1.4953
195 Q A -2.1181
196 Q A -2.8158
197 E A -3.4605
198 G A -2.7875
199 S A -2.8755
200 E A -3.6112
201 E A -3.9255
202 E A -4.8904
203 E A -4.4417
204 N A -4.3559
205 E A -4.1574
206 G A -3.1571
207 G A -1.6429
208 N A 0.0000
209 I A 1.0426
210 F A 0.3505
211 S A -0.4832
212 G A -0.3560
213 F A 0.2402
214 K A -1.3279
215 R A -1.6785
216 D A -1.5974
217 F A 0.0501
218 L A 0.0000
219 E A -1.9156
220 D A -1.9965
221 A A -0.5547
222 L A -0.0500
223 N A -1.4796
224 V A -1.1146
225 N A -1.9810
226 R A -2.4044
227 R A -2.2976
228 I A -0.5777
229 V A 0.0000
230 N A -2.3418
231 K A -2.4823
232 L A -0.7307
233 Q A 0.0000
234 G A 0.0000
235 R A -3.2249
236 N A -3.4663
237 E A -4.1587
238 D A -4.7037
239 E A -5.1741
240 E A -4.7237
241 K A -3.9843
242 G A 0.0000
243 A A 0.0000
244 I A 0.0000
245 V A -1.4051
246 K A -1.9720
247 V A -1.2691
248 K A -2.0978
249 G A -1.4191
250 G A -1.1252
251 L A -0.1769
252 S A 0.2151
253 I A 0.0576
254 T A -0.8150
255 T A -0.9737
256 P A -1.3717
257 P A -2.0209
258 E A -3.4768
259 K A -3.9475
260 E A -4.0424
261 P A -3.8025
262 R A -4.4397
263 Q A -3.8084
264 K A -4.5227
265 R A -3.9553
266 G A -2.9054
267 S A -2.8377
268 R A -4.1323
269 Q A -4.9455
270 E A -4.8198
271 E A -4.4980
272 D A -4.7253
273 E A -5.3907
274 D A -5.1397
275 E A -5.4187
276 D A -5.5004
277 E A -5.1547
278 K A -4.7267
279 R A -3.9399
313 F A -1.2997
314 E A -2.2997
315 E A -2.4130
316 T A -1.0931
317 I A -0.4752
318 C A 0.0421
319 T A -0.2338
320 A A -0.6007
321 R A -0.9362
322 L A 0.0000
323 H A -0.8504
324 Q A -0.9070
325 N A -1.1573
326 I A 0.0000
327 G A 0.0000
328 S A -0.9260
329 S A -0.6880
330 S A -0.6371
331 S A -0.5393
332 P A -0.3131
333 D A -0.6148
334 I A -0.1570
335 Y A 0.5745
336 N A 0.0000
337 P A -0.7653
338 Q A -1.5428
339 A A 0.0000
340 G A -0.8411
341 R A -0.3790
342 I A 0.0000
343 K A -0.4329
344 T A -0.4669
345 V A 0.0000
346 T A -0.4189
347 S A -0.4770
348 F A 0.7855
349 D A -0.6848
350 L A 0.0000
351 Q A -0.9154
352 A A 0.0000
353 L A 0.0000
354 R A -1.6319
355 F A -0.9220
356 L A 0.0000
357 K A -0.7880
358 L A 0.0000
359 S A 0.0000
360 A A 0.0000
361 E A 0.0000
362 F A 0.0000
363 G A 0.0000
364 S A 0.0000
365 L A 0.0000
366 H A -3.0728
367 K A -3.4098
368 N A -2.0578
369 A A 0.0000
370 M A -0.4402
371 F A 0.0000
372 V A 0.0000
373 P A -0.1705
374 H A 0.0000
375 Y A 0.0000
376 N A 0.0000
377 L A 0.2575
378 N A -0.3724
379 A A 0.0000
380 N A -0.7511
381 S A 0.0000
382 I A 0.0000
383 L A 0.0000
384 Y A 0.0000
385 A A 0.0000
386 L A 0.0000
387 K A -1.9860
388 G A -2.2877
389 R A -3.2444
390 A A 0.0000
391 R A -2.7805
392 L A 0.0000
393 L A -0.4497
394 Y A 0.0000
395 A A 0.0000
396 L A -0.2021
397 N A -0.9668
398 C A -0.9937
399 K A -1.9327
400 G A -1.1063
401 N A -1.4587
402 S A -0.5243
403 V A 0.8624
404 F A -0.2723
405 D A -1.9057
406 G A -2.5812
407 E A -3.5572
408 L A 0.0000
409 E A -3.2110
410 A A -1.8333
411 G A -1.4737
412 R A -2.2554
413 A A 0.0000
414 L A 0.0000
415 I A 0.0000
416 V A 0.0000
417 P A 0.0000
418 Q A -1.3191
419 N A -1.4045
420 F A 0.0000
421 A A 0.0000
422 I A 0.0000
423 A A 0.0000
424 A A 0.0000
425 K A -1.4286
426 S A 0.0000
427 L A -1.9507
428 S A -2.6910
429 D A -3.5198
430 R A -3.3554
431 F A 0.0000
432 S A 0.0000
433 Y A 0.0000
434 V A 0.0000
435 A A 0.0000
436 F A 0.0000
437 K A 0.0000
438 T A 0.0000
439 N A -0.7517
440 D A 0.0000
441 R A -0.8339
442 A A -0.0426
443 L A 1.1573
444 I A 0.9499
445 N A -0.1495
446 V A 0.0000
447 C A -0.8098
448 Q A -0.9023
449 K A -1.5052
450 K A -1.5995
451 L A -0.1702
452 L A 0.1656
453 Q A -0.7260
454 L A 0.5387
455 L A 0.5086
456 S A -0.0855
457 I A 0.5760
458 W A 0.1668
459 K A -2.1442
460 E A -2.2666
461 M A -1.1897
462 R A -2.5956
463 P A -2.0210
464 G A -1.4225
465 S A -1.1101
466 S A -0.6257
467 S A -0.5547
468 S A -0.4396
469 T A 0.0092
470 A A 0.3758
471 P A 1.0045
472 F A 2.3610
473 H A 1.1606
474 F A 2.6133
475 L A 2.5317
476 F A 1.5086
477 H A -0.0096
478 P A -0.2673
479 A A -0.3843
480 V A 0.1102
481 T A -0.5756
482 Q A -1.2899
483 T A -1.0493
484 T A -1.4202
485 K A -2.3076
486 Q A -1.5907
487 Q A -0.8544
488 L A -0.4888
489 D A -0.4276
490 L A 0.0000
491 V A 0.0359
492 P A -0.9343
493 N A -1.4355
494 Q A -1.1293
495 Y A -0.3252
496 E A -1.5657
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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 -0.5834 8.7694 View CSV PDB
4.5 -0.671 8.7694 View CSV PDB
5.0 -0.7798 8.7694 View CSV PDB
5.5 -0.8874 8.7694 View CSV PDB
6.0 -0.972 8.7694 View CSV PDB
6.5 -1.0197 8.7694 View CSV PDB
7.0 -1.031 8.7694 View CSV PDB
7.5 -1.0177 8.7694 View CSV PDB
8.0 -0.9913 8.7694 View CSV PDB
8.5 -0.9566 8.7694 View CSV PDB
9.0 -0.9138 8.7694 View CSV PDB