Project name: del

Status: done

Started: 2025-05-04 17:41:53
Chain sequence(s) A: YMLTNSELLSLINDMPITNDQKKLMSSNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNIDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVAEAAAKEAAAKAQRQNKPPNKKKPNNDFHFEVFNFVPCSICSNNPTCWAICKRIPNKKNKKPGKKNQTTTKPTKKPTTKTTNKKDPKPQTTKPKKERKKEKEVLLAEAAAKEAAAKAPFNNESFNWTGVTQNLGTSSACIRRSNNNSFFSRLNWLTHLNGFKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQASGRITVSTAEAAAKEAAAKAIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHPDPGVKGWAFDDGNDVWMGRTINETSRLGYETFKVIEGWSNPK
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 partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:05:13)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/839a00633e51e8b/tmp/folded.pdb                (00:05:13)
[INFO]       Main:     Simulation completed successfully.                                          (00:07:32)
Show buried residues

Minimal score value
-6.439
Maximal score value
3.1675
Average score
-0.8564
Total score value
-421.3511

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 Y A 1.4551
2 M A 1.5487
3 L A 0.1512
4 T A -0.6229
5 N A -1.5865
6 S A -1.2283
7 E A -1.5530
8 L A 0.0000
9 L A -1.0173
10 S A -1.1777
11 L A -0.7015
12 I A 0.0000
13 N A -2.4291
14 D A -2.1570
15 M A -0.9074
16 P A -0.3916
17 I A -0.7128
18 T A -1.6483
19 N A -2.8709
20 D A -3.2294
21 Q A 0.0000
22 K A -2.3810
23 K A -3.0441
24 L A 0.0000
25 M A 0.0000
26 S A -1.2810
27 S A -0.7516
28 N A 0.0000
29 V A -0.7661
30 Q A -1.7239
31 I A -1.0038
32 V A 0.0000
33 R A -1.4648
34 Q A -1.6796
35 Q A -1.1135
36 S A -0.2877
37 Y A 1.1393
38 S A 1.4504
39 I A 1.8305
40 M A 2.2789
41 S A 1.8137
42 I A 2.5681
43 I A 1.9939
44 K A -0.9895
45 E A -2.3958
46 E A -1.7850
47 V A 1.1170
48 L A 2.1719
49 A A 2.3345
50 Y A 2.3791
51 V A 2.3285
52 V A 1.3948
53 Q A 0.1514
54 L A 0.3934
55 P A 0.2518
56 L A 1.4411
57 Y A 1.1504
58 G A 1.0141
59 V A 1.4638
60 I A -0.0817
61 D A -1.6290
62 T A -0.8535
63 P A -0.8542
64 C A -0.6067
65 W A -0.0200
66 K A -0.5872
67 L A -0.6582
68 H A -0.1352
69 T A 0.0845
70 S A 0.0000
71 P A 0.0000
72 L A 1.3268
73 C A 0.0000
74 T A -0.2514
75 T A -0.9565
76 N A -2.0500
77 T A -1.9846
78 K A -3.1292
79 E A -3.1752
80 G A -2.3458
81 S A -1.8860
82 N A -1.5494
83 I A 0.0574
84 C A 0.0000
85 L A 1.0011
86 T A 0.0000
87 R A -0.1326
88 T A -0.4962
89 D A 0.0000
90 R A -1.5308
91 G A 0.0000
92 W A -0.5970
93 Y A 0.0000
94 C A 0.0000
95 D A -1.2888
96 N A -0.5637
97 A A -0.3372
98 G A -0.8192
99 S A -0.8330
100 V A 0.0000
101 S A 0.0000
102 F A 0.0000
103 F A 0.0000
104 P A -1.0940
105 Q A -2.0763
106 A A -1.8766
107 E A -2.1259
108 T A -1.6544
109 C A 0.0000
110 K A -0.6865
111 V A 0.6148
112 Q A -0.5007
113 S A -0.7964
114 N A -1.4018
115 R A -1.2194
116 V A -0.1231
117 F A 0.0000
118 C A -0.9713
119 D A -1.4894
120 T A -0.4272
121 M A -0.1422
122 N A -0.8929
123 S A -0.0634
124 L A 1.0417
125 T A 0.4264
126 L A 0.0053
127 P A -0.6896
128 S A -0.9950
129 E A -1.6338
130 V A 0.0000
131 N A -0.5627
132 L A -0.2653
133 C A 0.0000
134 N A -0.1822
135 I A 1.3408
136 D A 0.2978
137 I A 0.5110
138 F A 1.3804
139 N A -0.2045
140 P A -1.0103
141 K A -2.0384
142 Y A -1.8527
143 D A -2.1119
144 C A 0.0000
145 K A -1.7078
146 I A 0.0999
147 M A 0.6124
148 T A 0.4284
149 S A -0.4059
150 K A -1.6700
151 T A -1.0588
152 D A -0.8435
153 V A 0.2137
154 S A -0.3921
155 S A 0.0359
156 S A 0.4338
157 V A 1.4079
158 I A 2.3245
159 T A 1.2795
160 S A 0.5965
161 L A 1.2596
162 G A 0.8702
163 A A 1.0844
164 I A 0.7853
165 V A 0.0000
166 S A 0.0000
167 C A 0.0000
168 Y A 0.0000
169 G A -1.8619
170 K A -2.4576
171 T A -1.9021
172 K A -2.2808
173 C A -1.3683
174 T A -0.3975
175 A A 0.0448
176 S A -0.6088
177 N A -2.1440
178 K A -2.8491
179 N A -2.7876
180 R A -2.4341
181 G A -1.1715
182 I A 0.6819
183 I A -0.1989
184 K A -0.8310
185 T A -0.6133
186 F A -1.0604
187 S A -1.2695
188 N A -1.8484
189 G A -0.6682
190 C A -0.2377
191 D A -1.0524
192 Y A 0.4553
193 V A 0.1794
194 A A -0.4186
195 E A -1.5851
196 A A -1.5533
197 A A -1.4752
198 A A -2.3980
199 K A -3.3843
200 E A -3.4119
201 A A -2.2467
202 A A -3.0062
203 A A -2.9385
204 K A -3.8299
205 A A -3.3353
206 Q A -3.8751
207 R A -4.5765
208 Q A -3.9819
209 N A -3.8692
210 K A -3.7942
211 P A -2.2345
212 P A -2.4973
213 N A -2.8529
214 K A -3.5926
215 K A -3.8722
216 K A -3.4592
217 P A -2.6150
218 N A -2.8934
219 N A -2.6262
220 D A -1.9145
221 F A 0.3990
222 H A 0.0183
223 F A 1.5393
224 E A 0.3098
225 V A 2.0853
226 F A 2.6639
227 N A 1.2500
228 F A 2.8633
229 V A 3.0303
230 P A 1.6189
231 C A 1.4015
232 S A 1.0768
233 I A 2.0110
234 C A 0.0000
235 S A -0.4332
236 N A -1.5303
237 N A -1.2981
238 P A -0.5572
239 T A 0.1436
240 C A 0.6164
241 W A 0.3554
242 A A 0.2711
243 I A 1.5884
244 C A 0.8473
245 K A -1.3560
246 R A -1.2617
247 I A 0.3552
248 P A -1.2023
249 N A -2.6626
250 K A -3.2403
251 K A -3.8562
252 N A -3.8905
253 K A -3.5657
254 K A -3.0354
255 P A -2.0415
256 G A -2.0582
257 K A -3.0740
258 K A -3.5605
259 N A -3.1161
260 Q A -2.2294
261 T A -0.9999
262 T A -0.7437
263 T A -0.9857
264 K A -1.8874
265 P A -1.4818
266 T A -1.6642
267 K A -2.6585
268 K A -2.6816
269 P A -1.5732
270 T A -0.9669
271 T A -0.9822
272 K A -1.7974
273 T A -1.1971
274 T A -1.4299
275 N A -2.5618
276 K A -3.5321
277 K A -3.7541
278 D A -3.4447
279 P A -2.5784
280 K A -2.5903
281 P A -1.7351
282 Q A -2.0048
283 T A -1.3498
284 T A -1.5862
285 K A -3.1346
286 P A -3.2256
287 K A -4.5628
288 K A -5.1842
289 E A -5.8627
290 R A -6.4390
291 K A -6.1760
292 K A -5.5836
293 E A -4.8008
294 K A -4.1604
295 E A -3.3473
296 V A -1.0795
297 L A 0.2011
298 L A 0.4587
299 A A -0.4034
300 E A -1.2735
301 A A -0.7528
302 A A -0.7548
303 A A -1.5616
304 K A -2.9318
305 E A -3.1679
306 A A -2.0671
307 A A -1.6210
308 A A -1.8296
309 K A -2.1486
310 A A -1.0280
311 P A -0.4387
312 F A 0.0264
313 N A -1.7472
314 N A -2.4266
315 E A -2.0242
316 S A -1.5847
317 F A -0.7709
318 N A -1.2433
319 W A -0.1569
320 T A 0.0014
321 G A 0.0000
322 V A 0.0000
323 T A -0.2224
324 Q A -0.8195
325 N A -0.8728
326 L A 0.7686
327 G A -0.0603
328 T A 0.2165
329 S A 0.1981
330 S A 0.1725
331 A A 0.4217
332 C A 0.6839
333 I A 0.4193
334 R A -2.5585
335 R A -3.2130
336 S A -2.4843
337 N A -3.1438
338 N A -3.4814
339 N A -2.8528
340 S A -1.6538
341 F A 0.4196
342 F A 0.5501
343 S A -1.2955
344 R A -1.9495
345 L A -0.1431
346 N A -1.3910
347 W A -0.0499
348 L A 0.4212
349 T A -0.0020
350 H A 0.2984
351 L A 0.0616
352 N A -0.8813
353 G A -0.5162
354 F A 0.4155
355 K A -0.6478
356 Y A 0.2395
357 P A 0.1206
358 A A 0.2215
359 L A 0.6903
360 N A -0.3299
361 V A 0.6110
362 T A 0.1973
363 M A -0.0353
364 P A -1.1516
365 N A -2.9052
366 N A -3.0966
367 E A -3.3907
368 Q A -2.2343
369 F A -0.7907
370 D A -1.9301
371 K A -1.1419
372 L A 1.7299
373 Y A 2.4739
374 I A 3.1675
375 W A 2.5507
376 G A 0.9895
377 V A 1.3217
378 H A -0.6793
379 H A -1.3834
380 P A 0.0000
381 G A -1.7353
382 T A -1.9094
383 D A -2.7534
384 K A -2.4633
385 D A -1.8815
386 Q A -1.3878
387 I A 0.1279
388 F A 0.6883
389 L A 0.2482
390 Y A 0.0346
391 A A -0.0561
392 Q A -1.3242
393 A A -1.2624
394 S A -0.8979
395 G A -1.2419
396 R A -1.2938
397 I A 0.7249
398 T A 0.4640
399 V A 1.6746
400 S A 0.0272
401 T A -0.5748
402 A A -1.1223
403 E A -2.4059
404 A A -1.7044
405 A A -1.3810
406 A A -1.7353
407 K A -2.8752
408 E A -2.3824
409 A A -1.6016
410 A A -1.3097
411 A A -1.3241
412 K A -1.4110
413 A A 0.1468
414 I A 1.9325
415 V A 2.1724
416 S A 1.1578
417 S A 1.0416
418 Y A 1.7181
419 V A 1.4605
420 C A 0.7714
421 S A 0.0000
422 G A -0.5858
423 L A -0.2056
424 V A -0.8778
425 G A -0.4982
426 D A -1.9249
427 T A 0.0000
428 P A -2.3506
429 R A 0.0000
430 K A -2.1141
431 N A -1.9674
432 D A -1.9349
433 S A -1.2762
434 S A -1.1294
435 S A -1.2659
436 S A -1.3935
437 S A -1.6963
438 H A -1.3563
439 C A -0.4385
440 L A 0.1452
441 D A -1.7068
442 P A -1.7283
443 N A -2.7989
444 N A -2.9478
445 E A -2.6491
446 E A -3.1751
447 G A -2.8519
448 G A -2.3215
449 H A -2.3223
450 P A -1.9561
451 D A -2.5981
452 P A -2.0288
453 G A -2.1429
454 V A -1.2621
455 K A -1.9781
456 G A -0.7625
457 W A 0.4848
458 A A 1.2749
459 F A 1.7253
460 D A -0.2456
461 D A -1.2128
462 G A -1.6051
463 N A -2.1571
464 D A -1.0351
465 V A 0.0000
466 W A 1.0450
467 M A 0.0000
468 G A 0.0000
469 R A 0.0000
470 T A 0.0000
471 I A 1.8191
472 N A 0.2998
473 E A -1.2603
474 T A -1.1284
475 S A -0.3045
476 R A -0.1127
477 L A 1.3728
478 G A 1.1678
479 Y A 1.6650
480 E A 0.6295
481 T A 0.4537
482 F A 0.3859
483 K A 0.2057
484 V A 0.5171
485 I A 0.9060
486 E A -1.4395
487 G A 0.0000
488 W A -0.8645
489 S A -1.5750
490 N A -1.9138
491 P A -1.2785
492 K A -1.9688
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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 partially or entirely disordered. Average score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -0.4903 6.0937 View CSV PDB
4.5 -0.559 6.0937 View CSV PDB
5.0 -0.6407 6.0937 View CSV PDB
5.5 -0.7133 6.0937 View CSV PDB
6.0 -0.7515 6.0937 View CSV PDB
6.5 -0.7415 6.0937 View CSV PDB
7.0 -0.6887 6.0937 View CSV PDB
7.5 -0.6086 6.0937 View CSV PDB
8.0 -0.5139 6.0937 View CSV PDB
8.5 -0.4092 6.0937 View CSV PDB
9.0 -0.2947 6.0937 View CSV PDB