Project name: mj_TB_wt_dynamic [mutate: RH320A]

Status: done

Started: 2025-02-25 05:52:58
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 RH320A
Energy difference between WT (input) and mutated protein (by FoldX) 2.60054 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure

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]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:15:13)
[INFO]       CABS:     Running CABS flex simulation                                                (00:17:06)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:48:56)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:48:59)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:49:02)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:49:05)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:49:08)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:49:11)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:49:14)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:49:17)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:49:20)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:49:23)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:49:26)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:49:29)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:49:32)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:49:40)
[INFO]       Main:     Simulation completed successfully.                                          (01:49:43)
Show buried residues

Minimal score value
-3.7792
Maximal score value
1.3681
Average score
-0.6938
Total score value
-310.8245

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 -0.1093
2 R A -1.5542
3 E A 0.0000
4 C A 0.0000
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 -1.5024
12 A A 0.0000
13 G A 0.0000
14 V A 0.0000
15 Q A -1.0024
16 M A 0.0000
17 G A 0.0000
18 N A -0.8696
19 A A 0.0000
20 C A 0.0000
21 W A 0.0000
22 E A -0.9287
23 L A 0.0000
24 Y A 0.0000
25 C A 0.0000
26 L A 1.3248
27 E A 0.0000
28 H A 0.0000
29 G A 0.4256
30 I A 1.3097
31 Q A -0.6428
32 P A -1.1573
33 D A -2.2056
34 G A 0.0000
35 Q A -0.6692
36 M A 0.0000
37 P A 0.0000
38 S A -0.5213
39 D A 0.0000
40 K A -1.5897
41 T A 0.0000
42 I A 0.9735
43 G A 0.0000
44 G A -0.8362
45 G A -1.5250
46 D A -1.5098
47 D A -1.7565
48 S A -1.0497
49 F A 0.0000
50 T A 0.0000
51 T A 0.0000
52 F A 0.0000
53 F A -0.3025
54 C A 0.0000
55 E A -1.9497
56 T A -1.3237
57 G A -1.3217
58 A A -1.0280
59 G A -1.5018
60 K A -1.7589
61 H A 0.0000
62 V A 0.0000
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 -2.5161
72 P A -2.0394
73 T A -1.8908
74 V A 0.0000
75 I A 0.0000
76 D A -2.9463
77 E A -3.0569
78 I A 0.0000
79 R A -3.5388
80 N A -3.1713
81 G A -2.2832
82 P A -1.9530
83 Y A -1.3493
84 R A -1.8027
85 Q A -1.1326
86 L A 0.0000
87 F A 0.0000
88 H A 0.0000
89 P A -1.0920
90 E A -1.6454
91 Q A 0.0000
92 L A -0.3897
93 I A -0.1135
94 T A -0.7890
95 G A -1.8010
96 K A -2.9326
97 E A -3.0340
98 D A -2.6380
99 A A 0.0000
100 A A -1.0810
101 N A -0.5477
102 N A 0.0000
103 Y A 0.0000
104 A A 0.0000
105 R A -0.8733
106 G A 0.0000
107 H A -0.7871
108 Y A 0.0140
109 T A -0.6093
110 I A -1.2580
111 G A 0.0000
112 K A -2.5502
113 E A -2.6731
114 I A 0.0000
115 I A 0.0000
116 D A -2.1776
117 P A -1.7083
118 V A 0.0000
119 L A 0.0000
120 D A -1.9636
121 R A -2.2721
122 I A 0.0000
123 R A -3.1646
124 K A -2.9675
125 L A 0.0000
126 S A -2.0988
127 D A -2.7893
128 Q A -1.8294
129 C A -1.0755
130 T A -0.8290
131 G A -0.8851
132 L A -0.4107
133 Q A -1.1295
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 -0.3139
144 G A 0.0000
145 T A -0.7378
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 -0.6868
153 L A 0.0000
154 M A 0.0000
155 E A -1.1342
156 R A -0.8402
157 L A 0.0000
158 S A -0.6077
159 V A 0.2596
160 D A -1.0193
161 Y A -0.3160
162 G A -0.9843
163 K A -2.0695
164 K A -1.7400
165 S A -0.9741
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 P A 0.0000
174 A A -0.1023
175 P A -0.0488
176 Q A 0.2677
177 V A 1.3681
178 S A 0.4724
179 T A 0.2136
180 A A 0.1168
181 V A 0.0000
182 V A 0.0000
183 E A -0.1969
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 -1.1974
193 T A -0.7713
194 T A 0.0000
195 L A 0.0000
196 E A -1.7388
197 H A -1.6940
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 -0.5324
206 N A 0.0000
207 E A -0.7901
208 A A 0.0000
209 I A 0.0000
210 Y A -0.2377
211 D A -1.3894
212 I A 0.0000
213 C A 0.0000
214 R A -1.6316
215 R A -2.1114
216 N A 0.0000
217 L A 0.1656
218 D A 0.0000
219 I A 0.4493
220 E A -1.4500
221 R A -1.6196
222 P A -0.6377
223 T A -0.0020
224 Y A 0.4948
225 T A -0.1963
226 N A 0.0000
227 L A 0.0000
228 N A 0.0000
229 R A 0.0000
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 0.0000
240 A A 0.0000
241 S A 0.0000
242 L A -0.8544
243 R A 0.0000
244 F A 0.0000
245 D A -2.6564
246 G A -1.8753
247 A A -0.8472
248 L A -0.4133
249 N A -1.8903
250 V A 0.0000
251 D A -1.5010
252 L A 0.0000
253 T A -1.2814
254 E A -2.0117
255 F A 0.0000
256 Q A 0.0000
257 T A -1.0913
258 N A -0.8313
259 L A 0.0000
260 V A 0.0000
261 P A 0.0000
262 Y A 0.1678
263 P A -0.5262
264 R A -0.8880
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 -0.0699
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 0.0000
278 A A -1.2723
279 E A -1.9702
280 K A 0.0000
281 A A 0.0000
282 Y A -0.4695
283 H A -1.8808
284 E A -2.4165
285 Q A -1.5682
286 L A 0.0000
287 S A -1.1348
288 V A 0.0000
289 A A -1.8272
290 E A -2.2448
291 I A 0.0000
292 T A 0.0000
293 N A -1.8657
294 A A -1.5294
295 C A 0.0000
296 F A 0.0000
297 E A -2.3841
298 P A -1.5463
299 A A -1.1345
300 N A -1.2875
301 Q A 0.0000
302 M A 0.0000
303 V A 0.0000
304 K A -2.0036
305 C A 0.0000
306 D A -2.8684
307 P A -2.3372
308 R A -2.8136
309 H A -1.6114
310 G A -1.0802
311 K A -0.6790
312 Y A 0.0000
313 M A 0.0000
314 A A 0.0000
315 C A 0.0000
316 C A 0.0000
317 L A 0.0000
318 L A 0.0000
319 Y A 0.0000
320 H A 0.0000 mutated: RH320A
321 G A 0.0000
322 D A -0.6083
323 V A 0.2874
324 V A -0.4933
325 P A -1.1705
326 K A -2.7163
327 D A -2.8701
328 V A 0.0000
329 N A -2.3053
330 A A -1.6723
331 A A 0.0000
332 I A -1.3525
333 A A -1.1504
334 A A -1.4727
335 I A 0.0000
336 K A -2.3773
337 T A -2.1579
338 K A -3.2835
339 R A -3.1620
340 S A 0.0000
341 I A -0.9963
342 Q A -1.3161
343 F A -0.3116
344 V A -0.4587
345 D A -1.9162
346 W A -1.3080
347 C A -1.4452
348 P A 0.0000
349 T A -0.4767
350 G A -0.4082
351 F A -0.3702
352 K A -1.3104
353 V A -0.5105
354 G A 0.0000
355 I A 0.0000
356 N A 0.0000
357 Y A 0.3635
358 Q A -0.2914
359 P A 0.0000
360 P A -0.0726
361 T A 0.0000
362 V A 0.6976
363 V A 0.0000
364 P A -0.5762
365 G A -0.9052
366 G A -1.1866
367 D A -0.8552
368 L A 0.0000
369 A A -0.7422
370 K A -0.6230
371 V A 0.0000
372 Q A -1.0465
373 R A -1.5704
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 -1.2259
386 E A 0.0000
387 A A 0.0000
388 W A 0.0000
389 A A -0.9149
390 R A -1.2910
391 L A -0.9596
392 D A -1.4584
393 H A -1.7442
394 K A -1.4231
395 F A 0.0000
396 D A -1.3587
397 L A -0.5025
398 M A 0.0000
399 Y A -0.2202
400 A A -0.6609
401 K A -2.0212
402 R A -1.9732
403 A A -0.8682
404 F A -0.0364
405 V A -0.8151
406 H A -1.1834
407 W A 0.6219
408 Y A 0.0000
409 V A -0.5155
410 G A -0.6199
411 E A -0.7311
412 G A -0.8948
413 M A 0.0000
414 E A -2.6247
415 E A -2.7678
416 G A -2.3286
417 E A -2.4193
418 F A -1.9648
419 S A -2.3591
420 E A -3.3131
421 A A 0.0000
422 R A -2.4478
423 E A -2.7559
424 D A -2.1977
425 M A 0.0000
426 A A -1.7152
427 A A -1.7604
428 L A 0.0000
429 E A -2.3146
430 K A -2.9328
431 D A 0.0000
432 Y A 0.0000
433 E A -3.0724
434 E A -2.0484
435 V A -1.1103
436 G A -1.0338
437 I A 0.6291
438 D A -0.8882
439 S A -1.2243
440 Y A -1.8330
441 E A -3.4558
442 D A -3.7792
443 E A -3.5902
444 D A -3.1670
445 E A -1.9561
446 G A -1.2604
447 E A -1.3613
448 E A -2.0104
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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, -0.6938 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_1 -0.6938 View CSV PDB
model_5 -0.6959 View CSV PDB
model_9 -0.7014 View CSV PDB
model_10 -0.7126 View CSV PDB
model_11 -0.7151 View CSV PDB
model_0 -0.7161 View CSV PDB
model_8 -0.7163 View CSV PDB
model_6 -0.7204 View CSV PDB
model_2 -0.7219 View CSV PDB
CABS_average -0.7237 View CSV PDB
input -0.7434 View CSV PDB
model_7 -0.7521 View CSV PDB
model_3 -0.7671 View CSV PDB
model_4 -0.7717 View CSV PDB