Project name: mj_TB_wt_dynamic [mutate: RC215A]

Status: done

Started: 2025-02-25 05:50:12
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 RC215A
Energy difference between WT (input) and mutated protein (by FoldX) 0.902848 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                                                       (00:15:14)
[INFO]       CABS:     Running CABS flex simulation                                                (00:15:29)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:45:36)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:45:39)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:45:43)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:45:46)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:45:49)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:45:53)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:45:56)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:45:59)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:46:02)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:46:05)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:46:08)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:46:11)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:46:14)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:46:24)
[INFO]       Main:     Simulation completed successfully.                                          (01:46:27)
Show buried residues

Minimal score value
-3.9029
Maximal score value
2.0285
Average score
-0.6772
Total score value
-303.3778

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 0.2257
2 R A -1.5531
3 E A 0.0000
4 C A -0.4412
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 -0.7802
12 A A -0.4062
13 G A 0.0000
14 V A 0.0000
15 Q A -0.5583
16 M A 0.0000
17 G A 0.0000
18 N A 0.0000
19 A A 0.0000
20 C A 0.0000
21 W A 0.0000
22 E A -0.5905
23 L A 0.0000
24 Y A 0.0000
25 C A 0.0000
26 L A 0.5903
27 E A 0.0000
28 H A 0.0000
29 G A -0.2254
30 I A 0.3392
31 Q A -0.8345
32 P A -0.6407
33 D A -1.3979
34 G A -1.1574
35 Q A -0.6618
36 M A 0.0000
37 P A 0.0000
38 S A -1.3992
39 D A -2.3533
40 K A -1.6315
41 T A -0.9760
42 I A 0.0000
43 G A 0.0000
44 G A -0.7247
45 G A -1.4801
46 D A -1.6611
47 D A -2.1922
48 S A -1.3628
49 F A 0.0000
50 T A -0.5887
51 T A 0.0000
52 F A 0.0000
53 F A 0.1979
54 C A 0.0000
55 E A -0.8058
56 T A -1.1772
57 G A -1.5128
58 A A -1.5304
59 G A -1.8796
60 K A -2.6233
61 H A -1.8220
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 -1.7084
72 P A -1.4556
73 T A -1.2820
74 V A 0.0000
75 I A -1.7647
76 D A -3.0237
77 E A -3.0449
78 I A 0.0000
79 R A -3.2789
80 N A -2.9335
81 G A -2.0416
82 P A -1.4885
83 Y A -1.1869
84 R A -2.2423
85 Q A 0.0000
86 L A 0.0000
87 F A 0.0000
88 H A -1.1958
89 P A -1.4663
90 E A -1.9110
91 Q A 0.0000
92 L A -0.2230
93 I A -0.0954
94 T A -0.4645
95 G A -1.3113
96 K A -2.2404
97 E A -2.0230
98 D A -2.4504
99 A A -1.2448
100 A A -0.6932
101 N A -0.8399
102 N A -0.3133
103 Y A 0.0000
104 A A -0.5225
105 R A 0.0000
106 G A 0.0000
107 H A -0.7246
108 Y A 0.0711
109 T A -0.6222
110 I A -0.8890
111 G A 0.0000
112 K A -2.6326
113 E A -2.9561
114 I A 0.0000
115 I A 0.0000
116 D A -3.0755
117 P A -2.4186
118 V A 0.0000
119 L A -2.3555
120 D A -3.0557
121 R A -2.8859
122 I A 0.0000
123 R A -3.9029
124 K A -3.5719
125 L A 0.0000
126 S A -2.4217
127 D A -3.1950
128 Q A -2.0638
129 C A -0.2681
130 T A 0.0000
131 G A -1.0417
132 L A 0.0000
133 Q A -1.9941
134 G A -1.1388
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 0.0000
144 G A -0.3013
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 -0.8822
153 L A 0.0000
154 M A 0.0000
155 E A -1.0526
156 R A -0.8472
157 L A 0.0000
158 S A -0.5694
159 V A 0.3204
160 D A -1.0706
161 Y A -0.6872
162 G A -1.1593
163 K A -2.6864
164 K A -2.2966
165 S A -1.7313
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 -0.3134
175 P A -0.1898
176 Q A 0.1932
177 V A 1.4109
178 S A 0.5682
179 T A 0.3417
180 A A 0.2392
181 V A -0.2567
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 0.0000
193 T A -0.7340
194 T A 0.0000
195 L A 0.0000
196 E A -1.4583
197 H A -1.3165
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 0.0000
207 E A -0.7503
208 A A -0.8021
209 I A 0.0000
210 Y A 0.3112
211 D A -0.8185
212 I A -0.4433
213 C A 0.0000
214 R A -0.9741
215 C A -0.6188 mutated: RC215A
216 N A -1.4943
217 L A 0.0000
218 D A -1.0656
219 I A -0.0137
220 E A -1.8445
221 R A -1.6487
222 P A -0.6998
223 T A -0.1571
224 Y A 0.2789
225 T A -0.0652
226 N A 0.0000
227 L A 0.0000
228 N A 0.0000
229 R A -0.9046
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 -0.6799
243 R A 0.0000
244 F A -1.1010
245 D A -2.3370
246 G A -1.4403
247 A A -0.3787
248 L A 0.2316
249 N A -0.7158
250 V A 0.0000
251 D A -1.0732
252 L A 0.0000
253 T A -1.0766
254 E A -1.1938
255 F A 0.0000
256 Q A 0.0000
257 T A 0.0000
258 N A -0.7531
259 L A 0.0000
260 V A 0.0000
261 P A 0.0000
262 Y A 0.0000
263 P A -1.9424
264 R A -1.2796
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 0.0000
278 A A -1.8090
279 E A -2.4207
280 K A -1.9070
281 A A 0.0000
282 Y A -0.7769
283 H A -1.5236
284 E A -1.6679
285 Q A -1.4798
286 L A 0.0000
287 S A -0.9762
288 V A 0.0000
289 A A -1.3710
290 E A -2.1047
291 I A 0.0000
292 T A 0.0000
293 N A -1.3148
294 A A -0.9435
295 C A 0.0000
296 F A 0.0000
297 E A -1.3694
298 P A -1.2177
299 A A -1.2852
300 N A -1.6861
301 Q A 0.0000
302 M A 0.0000
303 V A 0.0000
304 K A -1.3123
305 C A 0.0000
306 D A -2.2372
307 P A -2.0015
308 R A -2.3128
309 H A -1.6650
310 G A -1.1304
311 K A -0.8948
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 R A 0.0000
321 G A 0.0000
322 D A 0.1044
323 V A 1.4079
324 V A 0.0000
325 P A -1.0610
326 K A -2.6105
327 D A -1.7495
328 V A 0.0000
329 N A -2.0278
330 A A -1.3421
331 A A 0.0000
332 I A -0.5413
333 A A -0.7489
334 A A -1.2024
335 I A 0.0000
336 K A -1.3899
337 T A -1.6257
338 K A -2.5094
339 R A -2.1644
340 S A -1.3948
341 I A 0.0000
342 Q A -1.3406
343 F A 0.0000
344 V A 0.5164
345 D A 0.7750
346 W A 1.2824
347 C A -0.4879
348 P A 0.0000
349 T A 0.9040
350 G A 0.0000
351 F A 2.0285
352 K A 0.5337
353 V A 0.2740
354 G A 0.0000
355 I A 0.6265
356 N A 0.0000
357 Y A 0.8085
358 Q A -0.0946
359 P A 0.0000
360 P A -0.2450
361 T A 0.0000
362 V A 0.0447
363 V A -0.3464
364 P A -0.6914
365 G A -1.1242
366 G A -1.1918
367 D A -2.0039
368 L A 0.0000
369 A A -1.4011
370 K A -1.5514
371 V A 0.0000
372 Q A -0.9322
373 R A -0.8338
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 -1.3276
387 A A 0.0000
388 W A 0.0000
389 A A -1.1056
390 R A -1.5248
391 L A 0.0000
392 D A -1.7298
393 H A -2.0103
394 K A -1.7270
395 F A 0.0000
396 D A -1.6500
397 L A -0.6160
398 M A 0.0000
399 Y A -0.0525
400 A A -0.4775
401 K A -1.5718
402 R A -0.9709
403 A A -0.5262
404 F A 0.0535
405 V A 0.0000
406 H A -1.4618
407 W A 0.0942
408 Y A 0.0000
409 V A -1.8812
410 G A -1.9127
411 E A -2.0214
412 G A -1.7039
413 M A 0.0000
414 E A -3.5270
415 E A -3.2371
416 G A -2.5200
417 E A -2.7787
418 F A 0.0000
419 S A -2.4727
420 E A -3.1981
421 A A 0.0000
422 R A -2.4689
423 E A -2.8099
424 D A -2.1626
425 M A 0.0000
426 A A -1.6374
427 A A -1.5765
428 L A 0.0000
429 E A -1.8091
430 K A -2.2057
431 D A -1.5958
432 Y A 0.0000
433 E A -1.8838
434 E A -1.3090
435 V A 0.0000
436 G A -0.9921
437 I A 0.2232
438 D A -1.2270
439 S A -0.8753
440 Y A -0.8902
441 E A -2.6815
442 D A -3.1312
443 E A -3.4822
444 D A -2.8270
445 E A -2.4669
446 G A -2.1526
447 E A -2.6188
448 E A -3.0944
Download PDB file
View in 3Dmol

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, -0.6772 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_2 -0.6772 View CSV PDB
model_7 -0.6956 View CSV PDB
model_4 -0.7005 View CSV PDB
model_1 -0.7274 View CSV PDB
input -0.7302 View CSV PDB
CABS_average -0.7332 View CSV PDB
model_8 -0.7344 View CSV PDB
model_5 -0.7374 View CSV PDB
model_6 -0.7376 View CSV PDB
model_3 -0.7385 View CSV PDB
model_9 -0.7396 View CSV PDB
model_11 -0.7519 View CSV PDB
model_0 -0.7727 View CSV PDB
model_10 -0.7854 View CSV PDB