Project name: XYS1

Status: done

Started: 2025-02-23 21:28:43
Chain sequence(s) A: MRSSLFVLDVENKATVQAAERELTERTWDVQEGTTGVVARRALLDRLMLEEEVPEDDEEDKVPSVLRESPEGRLKVFVYDLPSKYNTKLLEKDSRCLNHMFAAEIFVHRNLLNSSIRTMDPSEADWFYTPVYTTCDLTPNGLPLPFKAPQLMRSAIRWVAEHYPYWNRSEGADHFFTVPHDFGACFHYQEEEAIKRRILPVLQRATLVQTFGQNNHVCLKEGSIVVPPYAPPQKMRSRFIPPDTPRSIFVYFRGMFYDISNDPEGGYYARGARAAIWENFKDNPLFDLSSDHPSTYYEDMQRAVFCLCPLGWAPWSPRIVESVIFGCIPVIIGDDIVLPFSDAIRWDEISVYVAEKDVQNLDTILTAIKPEEIMAMQRKMWKPEVRTAMLFPQPAEPGDSFHQILNGLARKLPHKPEVFVKPGEHPIDWTAGPQQDQDEWRGDDEN
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage Used: no changes made
Dynamic mode Yes
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:      Running AlphaCutter                                                         (00:00:02)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:33)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:33)
[INFO]       CABS:     Running CABS flex simulation                                                (00:07:12)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:14:20)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:14:22)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:14:24)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:14:26)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:14:29)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:14:31)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:14:33)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:14:35)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:14:37)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:14:40)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:14:42)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:14:44)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:14:46)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:14:54)
[INFO]       Main:     Simulation completed successfully.                                          (01:14:56)
Show buried residues

Minimal score value
-3.6961
Maximal score value
2.2001
Average score
-0.6387
Total score value
-284.8766

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 0.2279
2 R A -1.6479
3 S A -0.6297
4 S A 0.0306
5 L A -0.0516
6 F A 0.0000
7 V A 0.1305
8 L A 0.0000
9 D A -0.3578
10 V A -0.0183
11 E A -1.4414
12 N A 0.0000
13 K A -0.5490
14 A A -0.5600
15 T A -0.5752
16 V A 0.0000
17 Q A -1.2004
18 A A -0.9931
19 A A 0.0000
20 E A 0.0000
21 R A -3.6626
22 E A -3.4709
23 L A -2.8726
24 T A -2.7430
25 E A -3.2352
26 R A -3.2036
27 T A -1.4524
28 W A -0.1876
29 D A -0.4837
30 V A 0.8764
31 Q A -0.8759
32 E A -1.9474
33 G A -0.7882
34 T A -0.1478
35 T A 0.0498
36 G A -0.2765
37 V A -0.0042
38 V A 1.0810
39 A A 0.2950
40 R A 0.0000
41 R A -1.4592
42 A A -0.8130
43 L A -1.3364
44 L A 0.0000
45 D A -1.7771
46 R A -2.5324
47 L A 0.0000
48 M A 0.0000
49 L A -1.1871
50 E A -2.3951
51 E A -1.8245
52 E A -1.4621
53 V A -1.0528
54 P A -1.5410
55 E A -2.3126
56 D A -3.3641
57 D A -2.9416
58 E A -3.0383
59 E A -1.9349
60 D A -1.1771
61 K A -1.2578
62 V A 0.7903
63 P A 0.1222
64 S A -0.1573
65 V A 0.0707
66 L A 0.0000
67 R A -1.3202
68 E A -1.1164
69 S A -1.3149
70 P A -1.6961
71 E A -2.8242
72 G A -2.6259
73 R A -3.0641
74 L A -1.4273
75 K A -0.5953
76 V A 0.0000
77 F A 0.0572
78 V A 0.0000
79 Y A 0.0000
80 D A -0.2115
81 L A 0.5302
82 P A 0.1302
83 S A -0.4317
84 K A -1.5113
85 Y A 0.0000
86 N A 0.0000
87 T A -1.1447
88 K A -2.1390
89 L A 0.0000
90 L A -1.5160
91 E A -2.7255
92 K A -3.0359
93 D A -2.0454
94 S A -1.3143
95 R A -1.2343
96 C A 0.0000
97 L A 0.4581
98 N A -0.6770
99 H A -0.4513
100 M A 0.0201
101 F A 0.0000
102 A A 0.0000
103 A A 0.0000
104 E A 0.0000
105 I A 0.0000
106 F A -0.1794
107 V A 0.0000
108 H A 0.0000
109 R A -2.0075
110 N A 0.0000
111 L A 0.0000
112 L A -0.8229
113 N A -1.6101
114 S A 0.0000
115 S A -0.5870
116 I A -0.2606
117 R A -0.5672
118 T A -0.4755
119 M A -0.1091
120 D A -1.4881
121 P A -0.7229
122 S A -0.3118
123 E A -0.1097
124 A A 0.0000
125 D A 0.0000
126 W A 0.0000
127 F A 0.0000
128 Y A 0.0000
129 T A 0.0000
130 P A 0.0000
131 V A 0.0000
132 Y A 0.0000
133 T A 0.0000
134 T A -0.7701
135 C A 0.0000
136 D A -1.5487
137 L A 0.0000
138 T A 0.0000
139 P A -0.1377
140 N A 0.0000
141 G A 0.0000
142 L A 0.0000
143 P A 0.0000
144 L A 0.0000
145 P A 0.0000
146 F A 1.2481
147 K A -0.3434
148 A A 0.0000
149 P A 0.0000
150 Q A 0.0000
151 L A 0.0000
152 M A 0.0000
153 R A 0.0000
154 S A 0.0000
155 A A 0.0000
156 I A 0.0000
157 R A -1.8251
158 W A -1.1031
159 V A 0.0000
160 A A 0.0000
161 E A -1.9815
162 H A -0.7367
163 Y A 0.0854
164 P A 0.1043
165 Y A -0.0845
166 W A 0.0000
167 N A 0.0000
168 R A 0.5117
169 S A 0.0942
170 E A 0.0000
171 G A -0.5739
172 A A -0.6060
173 D A 0.0000
174 H A 0.0000
175 F A 0.0000
176 F A 0.0000
177 T A 0.0000
178 V A 0.0000
179 P A 0.0000
180 H A 0.0000
181 D A 0.0000
182 F A 0.0000
183 G A 0.0000
184 A A 0.0000
185 C A 0.0000
186 F A 0.0000
187 H A 0.0000
188 Y A 0.0000
189 Q A -1.0671
190 E A -0.8359
191 E A -1.3145
192 E A 0.0000
193 A A 0.0000
194 I A 0.7581
195 K A -0.4982
196 R A 0.0000
197 R A -1.2104
198 I A 0.0000
199 L A 0.0000
200 P A -1.1744
201 V A 0.0000
202 L A 0.0000
203 Q A -1.5138
204 R A -1.1386
205 A A 0.0000
206 T A -0.9647
207 L A 0.0000
208 V A 0.0000
209 Q A 0.0000
210 T A 0.0000
211 F A 0.0000
212 G A -0.5647
213 Q A 0.0000
214 N A -1.9749
215 N A -1.9214
216 H A 0.0000
217 V A 0.8979
218 C A 0.0414
219 L A -1.0962
220 K A -2.0289
221 E A -1.7643
222 G A -1.2133
223 S A 0.0000
224 I A 0.0000
225 V A 0.0000
226 V A 0.0000
227 P A 0.0000
228 P A 0.0000
229 Y A 0.0000
230 A A 0.0000
231 P A -1.1111
232 P A 0.0000
233 Q A -3.0810
234 K A -3.3831
235 M A 0.0000
236 R A -3.3023
237 S A -2.7005
238 R A -2.7053
239 F A -1.7189
240 I A -0.2930
241 P A 0.0000
242 P A 0.0000
243 D A 0.0000
244 T A 0.0000
245 P A -2.1448
246 R A -2.4213
247 S A -1.5246
248 I A 0.0000
249 F A 0.0000
250 V A 0.0000
251 Y A 0.0000
252 F A 0.0000
253 R A 0.0000
254 G A 0.0000
255 M A 0.0000
256 F A 0.0000
257 Y A 0.4818
258 D A 0.0000
259 I A 0.9636
260 S A -0.0337
261 N A 0.1492
262 D A 0.0000
263 P A 0.0000
264 E A -0.8206
265 G A -0.5838
266 G A 0.4412
267 Y A 1.5516
268 Y A 1.4551
269 A A 0.0000
270 R A 0.7577
271 G A 0.0424
272 A A -0.6417
273 R A 0.0000
274 A A -0.4065
275 A A -1.6152
276 I A 0.0000
277 W A 0.0000
278 E A -2.5322
279 N A -1.8048
280 F A 0.0000
281 K A -2.1305
282 D A -2.3748
283 N A 0.0000
284 P A -0.9581
285 L A -0.4928
286 F A 0.0000
287 D A -0.8023
288 L A -0.7300
289 S A 0.0000
290 S A -0.3317
291 D A 0.0000
292 H A -0.4870
293 P A -0.2614
294 S A -0.5109
295 T A -0.5594
296 Y A -0.4901
297 Y A 0.0000
298 E A -1.5588
299 D A 0.0000
300 M A 0.0000
301 Q A 0.0000
302 R A -1.3695
303 A A 0.0000
304 V A 0.0000
305 F A 0.0000
306 C A 0.0000
307 L A 0.0000
308 C A 0.0000
309 P A 0.0000
310 L A 0.0000
311 G A 0.0000
312 W A 0.2610
313 A A 0.0000
314 P A 0.0000
315 W A 0.0000
316 S A 0.0000
317 P A 0.0000
318 R A 0.0000
319 I A 0.0000
320 V A 0.0000
321 E A 0.0000
322 S A 0.0000
323 V A 0.0000
324 I A 0.0000
325 F A 0.0000
326 G A 0.0000
327 C A 0.0000
328 I A 0.0000
329 P A 0.0000
330 V A 0.0000
331 I A 0.0000
332 I A 0.0000
333 G A -0.8871
334 D A -2.2096
335 D A 0.0000
336 I A 0.0000
337 V A 0.0344
338 L A 0.0000
339 P A 0.0000
340 F A 0.0000
341 S A -1.0233
342 D A -1.5232
343 A A 0.0000
344 I A 0.0000
345 R A -1.7140
346 W A 0.0000
347 D A -1.9590
348 E A -2.2157
349 I A 0.0000
350 S A -0.4303
351 V A 0.6339
352 Y A 1.0619
353 V A 0.0000
354 A A -1.9567
355 E A -3.4842
356 K A -3.6961
357 D A -2.9636
358 V A 0.0000
359 Q A -3.3169
360 N A -2.9328
361 L A 0.0000
362 D A -1.0460
363 T A -0.7554
364 I A -0.7522
365 L A 0.0000
366 T A -0.6527
367 A A -0.4703
368 I A 0.0000
369 K A -2.8329
370 P A -2.6895
371 E A -3.3371
372 E A -3.0981
373 I A 0.0000
374 M A -1.5565
375 A A -1.5035
376 M A 0.0000
377 Q A 0.0000
378 R A -1.7123
379 K A -1.6381
380 M A 0.0000
381 W A 0.0000
382 K A 0.0000
383 P A -1.6996
384 E A 0.0000
385 V A 0.0000
386 R A -0.6549
387 T A -0.4102
388 A A 0.0000
389 M A 0.0000
390 L A 0.0000
391 F A 0.0000
392 P A 0.0000
393 Q A -1.7553
394 P A -1.2639
395 A A -1.3923
396 E A -2.1710
397 P A -1.3599
398 G A -1.3466
399 D A 0.0000
400 S A 0.0000
401 F A 0.0000
402 H A -0.7434
403 Q A 0.0000
404 I A 0.0000
405 L A -0.7384
406 N A 0.0000
407 G A 0.0000
408 L A 0.0000
409 A A -1.7079
410 R A -1.9658
411 K A -1.6747
412 L A -1.2606
413 P A -1.0490
414 H A -2.1924
415 K A -1.7903
416 P A -0.9697
417 E A -0.9499
418 V A 1.4930
419 F A 2.1815
420 V A 2.2001
421 K A 0.2681
422 P A -0.3139
423 G A -1.1608
424 E A -2.0791
425 H A 0.0000
426 P A -0.9977
427 I A -0.6956
428 D A -1.4617
429 W A -1.0023
430 T A -0.8459
431 A A 0.0000
432 G A -0.8639
433 P A -1.0666
434 Q A -1.3078
435 Q A -1.3620
436 D A -1.3919
437 Q A -2.1923
438 D A -2.3070
439 E A -2.8726
440 W A 0.0000
441 R A -2.9131
442 G A -2.7215
443 D A -3.6223
444 D A -3.6215
445 E A -3.6142
446 N A -3.1096
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CABS-flex predictions of flexibility of input structure

In dynamic mode, A4D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A4D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A4D score, -0.6387 in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

Model
Average A4D Score
model_0 -0.6387 View CSV PDB
model_6 -0.6726 View CSV PDB
model_11 -0.6759 View CSV PDB
model_8 -0.6797 View CSV PDB
model_2 -0.705 View CSV PDB
CABS_average -0.7113 View CSV PDB
model_7 -0.7148 View CSV PDB
model_5 -0.7197 View CSV PDB
model_10 -0.7262 View CSV PDB
model_9 -0.73 View CSV PDB
model_1 -0.7366 View CSV PDB
model_3 -0.7482 View CSV PDB
model_4 -0.7882 View CSV PDB
input -0.8798 View CSV PDB