Project name: P04405

Status: done

Started: 2025-06-28 13:02:21
Chain sequence(s) A: MAKLVLSLCFLLFSGCFALREQAQQNECQIQKLNALKPDNRIESEGGFIETWNPNNKPFQCAGVALSRCTLNRNALRRPSYTNGPQEIYIQQGNGIFGMIFPGCPSTYQEPQESQQRGRSQRPQDRHQKVHRFREGDLIAVPTGVAWWMYNNEDTPVVAVSIIDTNSLENQLDQMPRRFYLAGNQEQEFLKYQQQQQGGSQSQKGKQQEEENEGSNILSGFAPEFLKEAFGVNMQIVRNLQGENEEEDSGAIVTVKGGLRVTAPAMRKPQQEEDDDDEEEQPQCVETDKGCQRQSKRSRNGIDETICTMRLRQNIGQNSSPDIYNPQAGSITTATSLDFPALWLLKLSAQYGSLRKNAMFVPHYTLNANSIIYALNGRALVQVVNCNGERVFDGELQEGGVLIVPQNFAVAAKSQSDNFEYVSFKTNDRPSIGNLAGANSLLNALPEEVIQHTFNLKSQQARQVKNNNPFSFLVPPQESQRRAVA
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage A:

MAKLVLSLCFLLFSGCFALREQAQ

QNECQIQKLNALKPDNRIESEGGFIETWNPNNKPFQCAGVALSRCTLNRNALRRPSYTNGPQEIYIQQGNGIFGMIFPGCPSTYQEPQESQQRGRSQRPQDRHQKVHRFREGDLIAVPTGVAWWMYNNEDTPVVAVSIIDTNSLENQLDQMPRRFYLAGNQEQEFLKYQQQQQGGSQSQKGKQQEEENEGSNILSGFAPEFLKEAFGVNMQIVRNLQGENEEEDSGAIVTVKGGLRVTAPAMRKPQQEEDDDDEEEQPQCVETDKGCQRQSKRSRNGIDETICTMRLRQNIGQNSSPDIYNPQAGSITTATSLDFPALWLLKLSAQYGSLRKNAMFVPHYTLNANSIIYALNGRALVQVVNCNGERVFDGELQEGGVLIVPQNFAVAAKSQSDNFEYVSFKTNDRPSIGNLAGANSLLNALPEEVIQHTFNLKSQQARQVKNNNPFSFLVPPQESQRRAVA
(Red indicates removed residues)
Dynamic mode No
Automated mutations No
Downloads Download all the data
Simulation log
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       PDB:      Running AlphaCutter                                                         (00:00:01)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:11)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:11)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:09:26)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/ce587860f162843/tmp/folded.pdb                (00:09:26)
[INFO]       Main:     Simulation completed successfully.                                          (00:16:18)
Show buried residues

Minimal score value
-5.9127
Maximal score value
1.2043
Average score
-1.2682
Total score value
-584.6428

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
25 Q A -2.3650
26 N A -2.8819
27 E A -2.9655
28 C A -1.7283
29 Q A -2.5878
30 I A 0.0000
31 Q A -2.8659
32 K A -3.3827
33 L A 0.0000
34 N A -2.1333
35 A A -1.3689
36 L A -1.3746
37 K A -2.4718
38 P A -2.0362
39 D A -2.4404
40 N A -2.3363
41 R A -2.6646
42 I A 0.0000
43 E A -3.0977
44 S A 0.0000
45 E A -3.1121
46 G A 0.0000
47 G A -1.2941
48 F A -1.2791
49 I A 0.0000
50 E A -1.7699
51 T A 0.0000
52 W A 0.0000
53 N A -1.3171
54 P A 0.0000
55 N A -1.4376
56 N A -1.1703
57 K A -1.7949
58 P A -1.1784
59 F A 0.0000
60 Q A -1.4041
61 C A -1.0796
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 -0.4906
69 C A 0.0000
70 T A -0.3642
71 L A 0.0000
72 N A -2.2889
73 R A -3.2822
74 N A -2.2994
75 A A 0.0000
76 L A -0.2826
77 R A 0.0000
78 R A 0.0000
79 P A 0.4410
80 S A 0.0000
81 Y A 0.4398
82 T A 0.0000
83 N A -0.6842
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 -1.0861
92 Q A -1.2639
93 G A 0.0000
94 N A -1.7329
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 0.7040
101 F A 0.0000
102 P A -0.1100
103 G A -0.3435
104 C A -0.1063
105 P A -0.7079
106 S A -1.5473
107 T A -1.1567
108 Y A -1.8328
109 Q A -3.1200
110 E A -2.8775
111 P A -2.2356
112 Q A -3.2410
113 E A -3.3314
114 S A -2.5046
115 Q A -3.6286
116 Q A -3.5159
117 R A -3.5199
118 G A -2.9479
119 R A -3.7146
120 S A -2.8436
121 Q A -3.4513
122 R A -3.5014
123 P A -2.7654
124 Q A -3.8837
125 D A -3.8890
126 R A -3.7787
127 H A -2.0871
128 Q A -1.0902
129 K A -1.1790
130 V A 0.0000
131 H A -0.6366
132 R A -0.7162
133 F A 0.0000
134 R A -2.2937
135 E A -2.7883
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 -0.4464
144 G A -0.3122
145 V A 0.0000
146 A A 0.5093
147 W A 0.0000
148 W A 0.3399
149 M A 0.0000
150 Y A 0.0000
151 N A 0.0000
152 N A -2.0697
153 E A -2.5451
154 D A -3.0519
155 T A -1.8296
156 P A -1.6249
157 V A 0.0000
158 V A -0.3748
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 -1.5828
167 S A -0.8509
168 L A 0.3148
169 E A -1.1036
170 N A -1.1297
171 Q A -1.0610
172 L A 0.0585
173 D A -1.1264
174 Q A -1.6897
175 M A -0.8463
176 P A 0.0000
177 R A -0.4509
178 R A 0.0000
179 F A 0.6926
180 Y A 0.0000
181 L A 0.8703
182 A A 0.2618
183 G A 0.0000
184 N A -2.4607
185 Q A 0.0000
186 E A -2.7978
187 Q A -1.4980
188 E A 0.0000
189 F A 0.0000
190 L A -0.8076
191 K A -1.7683
192 Y A 0.0000
193 Q A -2.2948
194 Q A -2.7811
195 Q A -3.1284
196 Q A -3.2496
197 Q A -3.1679
198 G A -2.6099
199 G A -1.8475
200 S A -1.5802
201 Q A -2.3681
202 S A -2.1127
203 Q A -2.9611
204 K A -4.0636
205 G A -3.9939
206 K A -4.7499
207 Q A -4.9415
208 Q A -5.3406
209 E A -5.5484
210 E A -5.4216
211 E A -5.1133
212 N A -4.4425
213 E A -4.4269
214 G A -2.4692
215 S A -1.3587
216 N A 0.0000
217 I A 1.0252
218 L A 0.5023
219 S A -0.2956
220 G A 0.2565
221 F A 1.2043
222 A A 0.4209
223 P A -0.9283
224 E A -1.5439
225 F A 0.6362
226 L A 0.0000
227 K A -1.6745
228 E A -1.7954
229 A A -0.1921
230 F A 0.7526
231 G A -0.3646
232 V A -0.5937
233 N A -1.7583
234 M A -1.8310
235 Q A -2.1970
236 I A -0.7981
237 V A 0.0000
238 R A -3.4276
239 N A -2.8099
240 L A -0.9925
241 Q A 0.0000
242 G A 0.0000
243 E A -3.8631
244 N A -3.7454
245 E A -3.5964
246 E A -4.2368
247 E A -4.2866
248 D A -4.2129
249 S A 0.0000
250 G A 0.0000
251 A A 0.0000
252 I A 0.0000
253 V A -0.8050
254 T A -1.2154
255 V A -1.3070
256 K A -1.8216
257 G A -1.5094
258 G A -1.5328
259 L A -0.9930
260 R A -1.5395
261 V A -0.8818
262 T A -1.3525
263 A A -0.4413
264 P A -0.3696
265 A A -0.2720
266 M A -0.6216
267 R A -2.9917
268 K A -3.3936
269 P A -3.1993
270 Q A -3.8752
271 Q A -4.3864
272 E A -4.5333
273 E A -5.3046
274 D A -5.4220
275 D A -5.0150
276 D A -5.0648
277 D A -5.8724
278 E A -5.9127
279 E A -5.2774
280 E A -5.0287
281 Q A -3.9439
282 P A -2.8404
283 Q A -2.0448
284 C A -0.6803
285 V A -0.2016
286 E A -2.1011
287 T A -2.0522
288 D A -3.1376
289 K A -3.0537
290 G A -2.1459
291 C A -1.4154
292 Q A -2.5946
293 R A -3.1906
294 Q A -3.2171
295 S A -2.9803
296 K A -4.1502
297 R A -3.6098
298 S A -3.2744
299 R A -3.8401
300 N A -3.2963
301 G A -1.6405
302 I A -0.2263
303 D A -2.2862
304 E A -2.6592
305 T A -0.5681
306 I A 0.4313
307 C A 0.0362
308 T A -0.7919
309 M A 0.0000
310 R A -0.9059
311 L A 0.0000
312 R A -0.7969
313 Q A -1.0759
314 N A -1.5372
315 I A 0.0000
316 G A 0.0000
317 Q A -2.1498
318 N A -2.1956
319 S A -1.6443
320 S A -0.9872
321 P A -0.9693
322 D A -1.3865
323 I A 0.1395
324 Y A 0.8386
325 N A 0.1882
326 P A -0.5288
327 Q A -1.3557
328 A A 0.0000
329 G A 0.0000
330 S A -0.2214
331 I A 0.0000
332 T A 0.0000
333 T A -0.7457
334 A A 0.0000
335 T A -0.4681
336 S A 0.0000
337 L A 0.0752
338 D A -0.9569
339 F A 0.0000
340 P A -0.3495
341 A A 0.0000
342 L A 0.0000
343 W A 0.7552
344 L A 0.6075
345 L A 0.0000
346 K A -0.3766
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 -0.7801
354 L A 0.0000
355 R A -3.3564
356 K A -4.0441
357 N A -2.9048
358 A A 0.0000
359 M A -0.6315
360 F A 0.0000
361 V A 0.0000
362 P A 0.1592
363 H A 0.0000
364 Y A 0.0819
365 T A 0.0000
366 L A 0.1270
367 N A -0.8513
368 A A 0.0000
369 N A -0.6837
370 S A 0.0000
371 I A 0.0000
372 I A 0.1922
373 Y A 0.0000
374 A A 0.0000
375 L A 0.0000
376 N A -1.9610
377 G A -2.6480
378 R A -3.4507
379 A A 0.0000
380 L A -1.2720
381 V A 0.0000
382 Q A -1.7995
383 V A 0.0000
384 V A -1.7876
385 N A -1.7124
386 C A -0.5872
387 N A -1.9004
388 G A -1.7289
389 E A -3.1091
390 R A -3.6364
391 V A 0.0000
392 F A 0.0000
393 D A -2.9347
394 G A -1.6660
395 E A -2.0766
396 L A 0.0000
397 Q A -3.0263
398 E A -2.7397
399 G A -1.6662
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 -0.5386
406 Q A -1.2727
407 N A -1.0983
408 F A -0.4420
409 A A -0.3203
410 V A 0.0000
411 A A -0.3257
412 A A -0.7427
413 K A -1.7179
414 S A 0.0000
415 Q A -2.7439
416 S A -3.0177
417 D A -3.5792
418 N A -2.9689
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 -0.9163
427 N A -0.9930
428 D A 0.0000
429 R A -1.5194
430 P A -0.8766
431 S A -0.1343
432 I A 0.4290
433 G A 0.4311
434 N A 0.0000
435 L A 0.7314
436 A A 0.0823
437 G A 0.0000
438 A A -0.9304
439 N A -0.9860
440 S A 0.0000
441 L A 1.1053
442 L A 0.8570
443 N A -0.4623
444 A A 0.2994
445 L A 0.6610
446 P A -0.5445
447 E A -1.7366
448 E A -2.2491
449 V A -0.3493
450 I A 0.0000
451 Q A -1.9574
452 H A -1.5392
453 T A -0.2278
454 F A 0.2709
455 N A -1.3777
456 L A -1.6703
457 K A -3.1397
458 S A -2.8917
459 Q A -3.0182
460 Q A -3.0717
461 A A 0.0000
462 R A -3.9834
463 Q A -3.3741
464 V A -1.3182
465 K A -2.0307
466 N A -2.8271
467 N A -2.6069
468 N A -1.4561
469 P A -0.9730
470 F A -0.1628
471 S A -0.0538
472 F A 0.5590
473 L A 0.0000
474 V A -0.3360
475 P A 0.0000
476 P A -2.3066
477 Q A -2.8548
478 E A -3.5153
479 S A -2.5808
480 Q A -2.4347
481 R A -3.1233
482 R A -2.7529
483 A A -0.8494
484 V A 0.6154
485 A A -0.1571
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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 -0.9281 4.5542 View CSV PDB
4.5 -1.0151 4.3017 View CSV PDB
5.0 -1.1239 3.9704 View CSV PDB
5.5 -1.2356 3.6214 View CSV PDB
6.0 -1.3317 3.5313 View CSV PDB
6.5 -1.3985 3.4876 View CSV PDB
7.0 -1.4324 3.4637 View CSV PDB
7.5 -1.4419 3.4538 View CSV PDB
8.0 -1.4374 3.4503 View CSV PDB
8.5 -1.4235 3.4492 View CSV PDB
9.0 -1.4006 3.4488 View CSV PDB