Project name: mj_TB_wt_dynamic [mutate: PR173A]

Status: done

Started: 2025-02-26 03:43:33
Chain sequence(s) A: MRECISVHVGQAGVQMGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFTTFFCETGAGKHVPRAVFVDLEPTVIDEIRNGPYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDPVLDRIRKLSDQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIAAIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGIDSYEDEDEGEE
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
Dynamic mode Yes
Automated mutations No
Mutated residues PR173A
Energy difference between WT (input) and mutated protein (by FoldX) -2.29561 kcal/mol
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]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:10:32)
[INFO]       CABS:     Running CABS flex simulation                                                (00:10:50)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:17:06)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:17:09)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:17:11)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:17:13)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:17:16)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:17:18)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:17:20)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:17:22)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:17:25)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:17:27)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:17:29)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:17:31)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:17:34)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:17:40)
[INFO]       Main:     Simulation completed successfully.                                          (01:17:42)
Show buried residues

Minimal score value
-3.9024
Maximal score value
1.2304
Average score
-0.6742
Total score value
-302.0358

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 0.3530
2 R A -0.6676
3 E A 0.0000
4 C A -0.0396
5 I A 0.0000
6 S A 0.0000
7 V A 0.0000
8 H A 0.0000
9 V A 0.0000
10 G A 0.0000
11 Q A -0.5832
12 A A 0.0000
13 G A 0.0000
14 V A 0.0000
15 Q A -0.5759
16 M A 0.0000
17 G A 0.0000
18 N A -0.5778
19 A A 0.0000
20 C A 0.0000
21 W A 0.0000
22 E A -0.0549
23 L A 0.0000
24 Y A 0.0000
25 C A 0.0000
26 L A 1.1451
27 E A 0.0000
28 H A 0.0000
29 G A 0.3767
30 I A 1.2304
31 Q A -0.0866
32 P A -0.5181
33 D A -0.9920
34 G A -1.0561
35 Q A -0.5293
36 M A 0.0000
37 P A 0.0000
38 S A -0.8777
39 D A -1.1438
40 K A -1.8072
41 T A 0.0000
42 I A 0.7134
43 G A 0.1455
44 G A -0.7245
45 G A -1.2185
46 D A -1.5361
47 D A -1.3879
48 S A -0.9140
49 F A 0.0000
50 T A -0.5997
51 T A 0.0000
52 F A 0.0000
53 F A -0.3091
54 C A 0.0000
55 E A -2.2055
56 T A -1.6244
57 G A -1.4232
58 A A -1.1468
59 G A -1.7362
60 K A -2.6237
61 H A 0.0000
62 V A -1.1300
63 P A 0.0000
64 R A 0.0000
65 A A 0.0000
66 V A 0.0000
67 F A 0.0000
68 V A 0.0000
69 D A 0.0000
70 L A 0.0000
71 E A -1.6235
72 P A -1.6561
73 T A -1.1611
74 V A 0.0000
75 I A 0.0000
76 D A -2.6368
77 E A -3.2013
78 I A 0.0000
79 R A -3.6185
80 N A -3.0495
81 G A -2.3030
82 P A -2.0061
83 Y A -2.0791
84 R A -2.2923
85 Q A -1.2811
86 L A 0.0000
87 F A 0.0000
88 H A -1.1347
89 P A -1.4346
90 E A -2.0655
91 Q A 0.0000
92 L A -0.9393
93 I A 0.0000
94 T A -0.6333
95 G A -1.4843
96 K A -2.6263
97 E A -2.2529
98 D A -2.5911
99 A A -1.2633
100 A A -0.7618
101 N A -0.4859
102 N A 0.0000
103 Y A 0.0000
104 A A 0.0000
105 R A -0.6578
106 G A 0.0000
107 H A -0.7709
108 Y A 0.2548
109 T A -0.2944
110 I A -0.4057
111 G A 0.0000
112 K A -2.3231
113 E A -2.3776
114 I A -1.1957
115 I A 0.0000
116 D A -1.8804
117 P A -1.6893
118 V A 0.0000
119 L A -1.1706
120 D A -2.0155
121 R A -1.9760
122 I A 0.0000
123 R A -3.0692
124 K A -2.6228
125 L A 0.0000
126 S A -1.7745
127 D A -2.7076
128 Q A -1.6744
129 C A -0.2663
130 T A -0.4866
131 G A -0.3650
132 L A -0.3178
133 Q A -0.9396
134 G A 0.0000
135 F A 0.0000
136 L A 0.0000
137 V A 0.0000
138 F A 0.0000
139 H A 0.0000
140 S A 0.0000
141 F A 0.0000
142 G A 0.0000
143 G A -0.4046
144 G A 0.0000
145 T A 0.0000
146 G A 0.0000
147 S A 0.0000
148 G A 0.0000
149 F A 0.0000
150 T A 0.0000
151 S A 0.0000
152 L A -0.5734
153 L A 0.0000
154 M A 0.0000
155 E A -0.9292
156 R A 0.0000
157 L A 0.0000
158 S A 0.0000
159 V A 0.1510
160 D A -0.9780
161 Y A -0.9607
162 G A -1.4587
163 K A -2.7194
164 K A -2.7014
165 S A 0.0000
166 K A 0.0000
167 L A 0.0000
168 E A 0.0000
169 F A 0.0000
170 S A 0.0000
171 I A 0.0000
172 Y A 0.0000
173 R A -0.2825 mutated: PR173A
174 A A 0.0000
175 P A 0.0000
176 Q A -0.3430
177 V A 0.4527
178 S A 0.0819
179 T A 0.0501
180 A A 0.0886
181 V A 0.0000
182 V A 0.0000
183 E A 0.0000
184 P A 0.0000
185 Y A 0.0000
186 N A 0.0000
187 S A 0.0000
188 I A 0.0000
189 L A 0.0000
190 T A 0.0000
191 T A 0.0000
192 H A -1.4514
193 T A -0.7632
194 T A 0.0000
195 L A 0.0000
196 E A -1.6993
197 H A -1.7541
198 S A 0.0000
199 D A 0.0000
200 C A 0.0000
201 A A 0.0000
202 F A 0.0000
203 M A 0.0000
204 V A 0.0000
205 D A 0.0000
206 N A -0.5722
207 E A -1.1351
208 A A 0.0000
209 I A 0.0000
210 Y A -1.0729
211 D A -1.9001
212 I A 0.0000
213 C A 0.0000
214 R A -2.1156
215 R A -2.5753
216 N A -1.1457
217 L A 0.0016
218 D A -0.6961
219 I A -0.2560
220 E A -1.6771
221 R A -1.7637
222 P A -1.0311
223 T A -0.4422
224 Y A 0.1315
225 T A -0.2841
226 N A 0.0000
227 L A 0.0000
228 N A 0.0000
229 R A -0.4025
230 L A 0.0000
231 I A 0.0000
232 S A 0.0000
233 Q A 0.0000
234 I A 0.0000
235 V A 0.0000
236 S A 0.0000
237 S A 0.0000
238 I A 0.0000
239 T A 0.0031
240 A A 0.0000
241 S A 0.0000
242 L A 0.0000
243 R A 0.0000
244 F A 0.0000
245 D A -1.7963
246 G A -0.8370
247 A A 0.1746
248 L A 0.8546
249 N A 0.0620
250 V A -0.0708
251 D A 0.0000
252 L A 0.0000
253 T A -0.4236
254 E A -0.8940
255 F A 0.0000
256 Q A -0.8064
257 T A -1.1114
258 N A -1.1335
259 L A 0.0000
260 V A 0.0000
261 P A 0.0000
262 Y A 0.0000
263 P A 0.0000
264 R A -2.1139
265 I A 0.0000
266 H A 0.0000
267 F A 0.0000
268 P A 0.0000
269 L A 0.0000
270 A A 0.0000
271 T A 0.0000
272 Y A 0.0000
273 A A 0.0000
274 P A 0.0000
275 V A 0.0000
276 I A 0.0000
277 S A -0.4940
278 A A 0.0000
279 E A -0.9647
280 K A -1.1408
281 A A 0.0000
282 Y A -0.1616
283 H A -1.2226
284 E A -1.5407
285 Q A -1.5809
286 L A 0.0000
287 S A -1.3789
288 V A -1.5706
289 A A -1.1596
290 E A -2.3011
291 I A 0.0000
292 T A 0.0000
293 N A 0.0000
294 A A -1.3226
295 C A 0.0000
296 F A 0.0000
297 E A -1.7998
298 P A -0.8123
299 A A -0.7363
300 N A -1.1297
301 Q A -0.8086
302 M A 0.0000
303 V A 0.0000
304 K A -1.1350
305 C A -0.8003
306 D A -1.0242
307 P A 0.0000
308 R A -1.4548
309 H A -1.3197
310 G A -0.7897
311 K A 0.0000
312 Y A 0.0000
313 M A 0.0000
314 A A 0.0000
315 C A 0.0000
316 C A -0.3561
317 L A 0.0000
318 L A 0.0000
319 Y A 0.0000
320 R A 0.0000
321 G A 0.0000
322 D A -1.4734
323 V A 0.4759
324 V A -0.7328
325 P A -1.3831
326 K A -2.5868
327 D A -2.6082
328 V A 0.0000
329 N A -2.1600
330 A A -1.3766
331 A A 0.0000
332 I A -0.7709
333 A A -0.6644
334 A A -0.9924
335 I A 0.0000
336 K A -1.9890
337 T A -1.6127
338 K A -2.0495
339 R A -2.7258
340 S A 0.0000
341 I A -0.2482
342 Q A -1.0234
343 F A -0.5056
344 V A -0.5167
345 D A -1.6876
346 W A -1.0491
347 C A 0.0000
348 P A -0.7389
349 T A -0.5982
350 G A -0.9030
351 F A -0.5531
352 K A -0.8076
353 V A 0.0000
354 G A 0.0000
355 I A 0.0000
356 N A 0.0000
357 Y A 0.5705
358 Q A -0.3084
359 P A 0.0000
360 P A -0.9308
361 T A 0.0000
362 V A -0.3136
363 V A -0.1868
364 P A -0.5542
365 G A -0.8844
366 G A -0.8507
367 D A -1.0156
368 L A 0.0000
369 A A -1.0287
370 K A -2.2365
371 V A 0.0000
372 Q A -1.9039
373 R A -2.3554
374 A A 0.0000
375 V A 0.0000
376 C A 0.0000
377 M A 0.0000
378 L A 0.0000
379 S A 0.0000
380 N A 0.0000
381 T A 0.0000
382 T A 0.0000
383 A A 0.0000
384 I A 0.0000
385 A A 0.0000
386 E A -1.5248
387 A A 0.0000
388 W A 0.0000
389 A A -1.1466
390 R A -1.3044
391 L A 0.0000
392 D A -1.9243
393 H A -1.8453
394 K A -1.0335
395 F A 0.0000
396 D A -2.0339
397 L A -0.6269
398 M A 0.0000
399 Y A -0.5029
400 A A -0.8269
401 K A -2.1266
402 R A -2.3244
403 A A -0.9840
404 F A -0.1470
405 V A -0.9224
406 H A -1.0255
407 W A 0.5143
408 Y A 0.0000
409 V A -0.2062
410 G A -0.5660
411 E A -0.9465
412 G A -0.8950
413 M A 0.0000
414 E A -2.7301
415 E A -3.0198
416 G A -2.6496
417 E A -3.0141
418 F A 0.0000
419 S A -2.9954
420 E A -3.8973
421 A A 0.0000
422 R A -3.9024
423 E A -3.7414
424 D A -3.1107
425 M A 0.0000
426 A A -2.2441
427 A A -2.0429
428 L A 0.0000
429 E A -2.2154
430 K A -2.4476
431 D A -1.9976
432 Y A 0.0000
433 E A -1.7654
434 E A -1.6059
435 V A 0.0000
436 G A 0.0000
437 I A 0.4221
438 D A -1.1573
439 S A -0.9931
440 Y A -1.5690
441 E A -3.0290
442 D A -2.9488
443 E A -3.3214
444 D A -3.3887
445 E A -3.2390
446 G A 0.0000
447 E A -2.9779
448 E A -3.1145
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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, -0.6742 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_6 -0.6742 View CSV PDB
model_2 -0.6773 View CSV PDB
model_9 -0.6825 View CSV PDB
model_1 -0.6982 View CSV PDB
model_8 -0.715 View CSV PDB
CABS_average -0.7167 View CSV PDB
model_3 -0.7181 View CSV PDB
model_10 -0.731 View CSV PDB
model_5 -0.7339 View CSV PDB
model_11 -0.7394 View CSV PDB
model_7 -0.7399 View CSV PDB
input -0.7408 View CSV PDB
model_0 -0.745 View CSV PDB
model_4 -0.7453 View CSV PDB