Project name: mi2699_6T13_monomer_conf3

Status: done

Started: 2026-05-29 17:06:42
Chain sequence(s) A: ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWHRQ
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]                                                (00:00:02)
[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-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                                          (00:03:50)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/23aef2bb8bda5a2/tmp/folded.pdb                (00:03:50)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:37)
Show buried residues

Minimal score value
-3.1866
Maximal score value
2.8079
Average score
-0.5095
Total score value
-253.234

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 A A -1.4792
2 R A -1.5913
3 P A -1.2522
4 C A -0.2608
5 I A 0.5708
6 P A -0.1164
7 K A -0.2588
8 S A -0.1703
9 F A 0.4432
10 G A 0.0050
11 Y A 0.3750
12 S A -0.3960
13 S A 0.0000
14 V A 0.0000
15 V A 0.0000
16 C A 0.0000
17 V A 0.3481
18 C A 0.0000
19 N A -0.9167
20 A A -0.5325
21 T A -0.0285
22 Y A 0.0710
23 C A 0.0000
24 D A -0.8951
25 S A -1.4862
26 F A -2.0729
27 D A -2.5676
28 P A -1.6752
29 P A -0.8453
30 T A 0.2790
31 F A 1.4012
32 P A 0.0000
33 A A 1.0334
34 L A 1.3731
35 G A 0.4025
36 T A 0.4891
37 F A 0.0000
38 S A 0.0000
39 R A 0.0777
40 Y A -0.1442
41 E A -0.6938
42 S A -1.0628
43 T A -1.2237
44 R A -1.3058
45 S A -1.1912
46 G A -1.3789
47 R A -1.9724
48 R A 0.0000
49 M A -1.0778
50 E A -1.6578
51 L A 0.4354
52 S A 0.4321
53 M A 0.9302
54 G A -0.2557
55 P A -0.3858
56 I A 0.0000
57 Q A -1.4079
58 A A -0.9294
59 N A -1.5729
60 H A -1.2863
61 T A -0.6648
62 G A -0.8206
63 T A -0.4189
64 G A -0.5597
65 L A -0.5079
66 L A -0.1855
67 L A 0.0000
68 T A 0.3358
69 L A 0.0000
70 Q A -1.3399
71 P A -1.8542
72 E A -2.9270
73 Q A -2.8328
74 K A -2.7379
75 F A -0.8815
76 Q A -1.0026
77 K A -2.0976
78 V A 0.0000
79 K A -0.9483
80 G A 0.0000
81 F A 0.0000
82 G A 0.0000
83 G A 0.0000
84 A A 0.0000
85 M A 0.0000
86 T A 0.0000
87 D A 0.0000
88 A A 0.0000
89 A A 0.0000
90 A A 0.0000
91 L A 0.8990
92 N A 0.0000
93 I A 0.0000
94 L A 0.5029
95 A A 0.4746
96 L A 0.0000
97 S A -0.6332
98 P A -0.4266
99 P A -0.4457
100 A A 0.0000
101 Q A 0.0000
102 N A -0.5863
103 L A -0.3065
104 L A 0.0000
105 L A 0.0000
106 K A -1.2490
107 S A 0.0000
108 Y A 0.0000
109 F A 0.0000
110 S A 0.0000
111 E A -3.1866
112 E A -2.6769
113 G A 0.0000
114 I A 0.0000
115 G A -1.3527
116 Y A 0.0000
117 N A 0.0000
118 I A 0.0000
119 I A 0.0000
120 R A 0.0000
121 V A 0.0000
122 P A 0.0000
123 M A 0.0000
124 A A 0.0000
125 S A -0.2728
126 C A -0.2452
127 D A -0.6672
128 F A 0.0000
129 S A 0.0000
130 I A 0.3407
131 R A -1.2715
132 T A -0.7213
133 Y A 0.0000
134 T A -0.3436
135 Y A 0.0000
136 A A 0.0000
137 D A -2.5718
138 T A -1.8363
139 P A -1.7085
140 D A -2.2704
141 D A -2.1375
142 F A -1.2207
143 Q A -1.8966
144 L A 0.0000
145 H A -2.1754
146 N A -2.3755
147 F A -1.4427
148 S A -0.9778
149 L A -0.5357
150 P A -1.1040
151 E A -2.3483
152 E A 0.0000
153 D A 0.0000
154 T A -1.4723
155 K A -2.2048
156 L A -0.7645
157 K A 0.0000
158 I A 0.0000
159 P A -0.5224
160 L A 0.0000
161 I A 0.0000
162 H A -0.9170
163 R A -0.9103
164 A A 0.0000
165 L A -0.4059
166 Q A -1.2124
167 L A -0.9941
168 A A -1.3147
169 Q A -2.2817
170 R A -1.9546
171 P A -0.9044
172 V A -0.2747
173 S A 0.0000
174 L A 0.0000
175 L A 0.0000
176 A A 0.0000
177 S A 0.0000
178 P A 0.0000
179 W A -0.0060
180 T A 0.0003
181 S A 0.0000
182 P A 0.0000
183 T A -0.2044
184 W A -0.5663
185 L A 0.0000
186 K A 0.0000
187 T A -1.1118
188 N A -1.6726
189 G A -0.8945
190 A A -0.6167
191 V A -0.0793
192 N A -0.7422
193 G A -0.8624
194 K A -1.4951
195 G A 0.0000
196 S A -0.9004
197 L A 0.0000
198 K A -1.1468
199 G A -1.4067
200 Q A -1.8512
201 P A -1.8494
202 G A -1.8560
203 D A -1.6189
204 I A -0.2206
205 Y A -0.4530
206 H A 0.0000
207 Q A -0.8714
208 T A 0.0000
209 W A 0.0000
210 A A 0.0000
211 R A -0.8637
212 Y A 0.0000
213 F A 0.0000
214 V A 0.0000
215 K A -0.9928
216 F A 0.0000
217 L A 0.0000
218 D A -1.4240
219 A A -1.1396
220 Y A 0.0000
221 A A -2.1758
222 E A -2.7943
223 H A -2.3187
224 K A -2.8554
225 L A 0.0000
226 Q A -1.8794
227 F A 0.0000
228 W A -0.4454
229 A A 0.0000
230 V A 0.0000
231 T A 0.0000
232 A A -0.0529
233 E A 0.0000
234 N A -0.3039
235 E A -0.4214
236 P A 0.0000
237 S A -0.0250
238 A A 0.0303
239 G A 0.0000
240 L A 0.0857
241 L A 0.5378
242 S A -0.1443
243 G A -0.3430
244 Y A 0.0070
245 P A -0.2047
246 F A 0.0658
247 Q A -0.2961
248 C A 0.0000
249 L A 0.0000
250 G A 0.0000
251 F A 0.0000
252 T A -0.5072
253 P A 0.0000
254 E A -1.6185
255 H A -1.2239
256 Q A 0.0000
257 R A -1.6818
258 D A -2.0691
259 F A 0.0000
260 I A 0.0000
261 A A -2.0666
262 R A -2.6032
263 D A 0.0000
264 L A 0.0000
265 G A 0.0000
266 P A -0.9335
267 T A -1.0433
268 L A 0.0000
269 A A -1.2357
270 N A -1.5530
271 S A -1.2962
272 T A -0.9786
273 H A -1.4894
274 H A -2.0127
275 N A -1.8643
276 V A -1.2649
277 R A -1.1907
278 L A 0.0000
279 L A 0.0000
280 M A 0.0000
281 L A 0.0000
282 D A 0.0000
283 D A 0.0000
284 Q A 0.3179
285 R A 0.0000
286 L A 1.3941
287 L A 0.3305
288 L A 0.0000
289 P A -0.7822
290 H A -1.0922
291 W A 0.0000
292 A A 0.0000
293 K A -1.0601
294 V A -0.9508
295 V A 0.0000
296 L A 0.0000
297 T A -0.7569
298 D A -1.6188
299 P A -1.6642
300 E A -2.5555
301 A A 0.0000
302 A A -1.6863
303 K A -2.2207
304 Y A -1.1909
305 V A 0.0000
306 H A -1.2088
307 G A 0.0000
308 I A 0.0000
309 A A 0.0000
310 V A 0.0000
311 H A 0.0000
312 W A 0.7025
313 Y A 1.1195
314 L A 1.8288
315 D A 1.5752
316 F A 2.8079
317 L A 2.6738
318 A A 1.2212
319 P A 0.0784
320 A A -0.7790
321 K A -2.0289
322 A A -1.1148
323 T A 0.0000
324 L A 0.0000
325 G A -1.7600
326 E A -2.0812
327 T A 0.0000
328 H A -1.8615
329 R A -2.1274
330 L A -0.9077
331 F A -0.9287
332 P A -1.1303
333 N A -1.3789
334 T A -0.8815
335 M A -0.5807
336 L A 0.0000
337 F A 0.0000
338 A A 0.0000
339 S A 0.0000
340 E A 0.0000
341 A A 0.0000
342 C A 0.0000
343 V A 0.0000
344 G A -0.6475
345 S A -0.5714
346 K A -0.5545
347 F A 1.1921
348 W A 0.9439
349 E A -0.8004
350 Q A -1.5091
351 S A -1.3088
352 V A 0.0000
353 R A -0.9734
354 L A 0.0000
355 G A 0.0000
356 S A 0.0000
357 W A 0.0000
358 D A -1.8891
359 R A 0.0000
360 G A 0.0000
361 M A -1.1538
362 Q A -1.2168
363 Y A 0.0000
364 S A 0.0000
365 H A -0.8778
366 S A 0.0000
367 I A 0.0000
368 I A 0.0000
369 T A -0.2640
370 N A 0.0000
371 L A 0.0000
372 L A 0.1979
373 Y A -0.1515
374 H A -0.0930
375 V A 0.0000
376 V A 0.0000
377 G A 0.0000
378 W A 0.0000
379 T A 0.0000
380 D A 0.0000
381 W A 0.0000
382 N A 0.0000
383 L A 0.0000
384 A A 0.0000
385 L A 0.0000
386 N A -0.7929
387 P A -1.1453
388 E A -2.4035
389 G A 0.0000
390 G A 0.0000
391 P A -0.4288
392 N A 0.0000
393 W A -0.0602
394 V A -0.2846
395 R A -2.0697
396 N A -1.5554
397 F A -1.2750
398 V A 0.0000
399 D A 0.0000
400 S A 0.0000
401 P A 0.0000
402 I A 0.0000
403 I A 0.0000
404 V A 0.0000
405 D A -0.5804
406 I A 0.6226
407 T A -0.5035
408 K A -2.0667
409 D A -2.0637
410 T A 0.0000
411 F A 0.0000
412 Y A 0.0000
413 K A 0.0000
414 Q A 0.0000
415 P A 0.0000
416 M A 0.0000
417 F A 0.0000
418 Y A 0.0000
419 H A 0.0000
420 L A 0.0000
421 G A 0.0000
422 H A 0.0000
423 F A 0.0000
424 S A -0.4040
425 K A -1.0191
426 F A 0.0000
427 I A 0.0000
428 P A -1.0443
429 E A -1.1129
430 G A -1.3089
431 S A 0.0000
432 Q A -1.2913
433 R A 0.0000
434 V A 0.0000
435 G A 0.0000
436 L A 0.7223
437 V A 1.5791
438 A A 0.1517
439 S A -0.5302
440 Q A -1.5479
441 K A -2.6933
442 N A -2.2924
443 D A -2.7451
444 L A -1.7331
445 D A -1.3218
446 A A -0.2466
447 V A 0.0000
448 A A 0.0000
449 L A 0.0000
450 M A -0.6501
451 H A 0.0000
452 P A -1.4541
453 D A -2.1790
454 G A -1.3999
455 S A 0.0000
456 A A 0.0000
457 V A 0.0000
458 V A 0.0000
459 V A 0.0000
460 V A 0.0000
461 L A 0.0000
462 N A 0.0000
463 R A -2.3642
464 S A -1.9485
465 S A -1.7013
466 K A -2.8438
467 D A -2.5645
468 V A -1.0485
469 P A -0.6977
470 L A 0.0000
471 T A 0.0000
472 I A 0.0000
473 K A -0.6157
474 D A 0.0000
475 P A -0.3994
476 A A -0.2216
477 V A 0.0177
478 G A -0.5419
479 F A -0.8540
480 L A 0.0000
481 E A -1.4097
482 T A -0.3378
483 I A 0.0764
484 S A 0.0000
485 P A -1.1459
486 G A -1.4376
487 Y A -0.9725
488 S A 0.0000
489 I A 0.0000
490 H A 0.0000
491 T A 0.0000
492 Y A 0.0000
493 L A 0.0000
494 W A 0.0000
495 H A -0.2214
496 R A -0.7019
497 Q A -1.4141
Download PDB file
View in 3Dmol

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 -0.2497 5.9484 View CSV PDB
4.5 -0.2856 5.9095 View CSV PDB
5.0 -0.3291 5.868 View CSV PDB
5.5 -0.3722 5.8256 View CSV PDB
6.0 -0.4064 5.783 View CSV PDB
6.5 -0.4256 5.7404 View CSV PDB
7.0 -0.4293 5.6982 View CSV PDB
7.5 -0.4224 5.6573 View CSV PDB
8.0 -0.4092 5.6199 View CSV PDB
8.5 -0.391 5.5905 View CSV PDB
9.0 -0.3673 5.5724 View CSV PDB