Project name: mj_TB_wt_dynamic [mutate: EK415A]

Status: done

Started: 2025-02-26 03:44:05
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 EK415A
Energy difference between WT (input) and mutated protein (by FoldX) -0.635922 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                                          (00:00:00)
[INFO]       FoldX:    Building mutant model                                                       (00:10:15)
[INFO]       CABS:     Running CABS flex simulation                                                (00:11:18)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:15:50)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:15:53)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:15:55)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:15:57)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:15:59)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:16:01)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:16:04)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:16:06)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:16:08)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:16:11)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:16:13)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:16:15)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:16:17)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:16:24)
[INFO]       Main:     Simulation completed successfully.                                          (01:16:26)
Show buried residues

Minimal score value
-4.0991
Maximal score value
1.5664
Average score
-0.6642
Total score value
-297.5411

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 0.0935
2 R A -1.3698
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 -0.6838
12 A A -0.3392
13 G A 0.0000
14 V A 0.0000
15 Q A -0.7263
16 M A 0.0000
17 G A 0.0000
18 N A -0.7892
19 A A 0.0000
20 C A 0.0000
21 W A 0.0000
22 E A -0.3913
23 L A 0.0000
24 Y A 0.0000
25 C A 0.0000
26 L A 0.3539
27 E A -0.5056
28 H A 0.0000
29 G A -0.5063
30 I A 0.2805
31 Q A -1.0580
32 P A -0.9639
33 D A -1.5819
34 G A 0.0000
35 Q A -0.6010
36 M A 0.0000
37 P A 0.0000
38 S A -1.5829
39 D A -2.1027
40 K A -2.3069
41 T A -0.6532
42 I A 0.8728
43 G A 0.3525
44 G A 0.3073
45 G A 0.1089
46 D A 0.0000
47 D A -1.4553
48 S A -1.5055
49 F A 0.0000
50 T A -0.1922
51 T A 0.0000
52 F A 0.0000
53 F A 0.1029
54 C A 0.0000
55 E A -1.4978
56 T A -1.3003
57 G A -1.4790
58 A A -1.3468
59 G A -1.5419
60 K A -2.0533
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 -2.0104
72 P A -2.0208
73 T A -1.5274
74 V A 0.0000
75 I A 0.0000
76 D A -3.6597
77 E A -3.8554
78 I A 0.0000
79 R A -3.9948
80 N A -3.2498
81 G A -2.3882
82 P A -2.1024
83 Y A -1.6149
84 R A -2.2999
85 Q A 0.0000
86 L A 0.0000
87 F A -0.6286
88 H A 0.0000
89 P A -1.4922
90 E A -1.8830
91 Q A 0.0000
92 L A -0.6927
93 I A -0.3223
94 T A -1.0203
95 G A -1.8847
96 K A -3.2414
97 E A -3.3344
98 D A -2.6953
99 A A -1.4223
100 A A -0.8507
101 N A -0.2757
102 N A 0.0000
103 Y A -0.5187
104 A A 0.0000
105 R A 0.0000
106 G A 0.0000
107 H A -1.0890
108 Y A -0.0768
109 T A -0.3527
110 I A -0.6537
111 G A 0.0000
112 K A -1.4493
113 E A -1.5417
114 I A 0.0000
115 I A 0.0000
116 D A -1.8133
117 P A -1.6671
118 V A 0.0000
119 L A 0.0000
120 D A -2.3331
121 R A -2.3877
122 I A 0.0000
123 R A -4.0991
124 K A -3.7226
125 L A 0.0000
126 S A -2.5546
127 D A -3.2241
128 Q A -1.6834
129 C A -0.1613
130 T A -0.7090
131 G A -1.1546
132 L A 0.0000
133 Q A -1.1001
134 G A -0.6759
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 0.1360
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 -0.7235
153 L A 0.0000
154 M A 0.0000
155 E A -1.7608
156 R A -2.2453
157 L A 0.0000
158 S A 0.0000
159 V A -0.3093
160 D A -1.7904
161 Y A -0.9054
162 G A -1.0585
163 K A -1.7270
164 K A -1.8253
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 P A 0.0000
174 A A 0.0931
175 P A 0.0647
176 Q A 0.4483
177 V A 1.5664
178 S A 0.7183
179 T A 0.4620
180 A A 0.5622
181 V A 0.2060
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 -0.9433
193 T A -0.5681
194 T A 0.0000
195 L A 0.0000
196 E A -0.9751
197 H A -1.3170
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 -0.9274
208 A A 0.0000
209 I A 0.0000
210 Y A -0.7276
211 D A -1.5660
212 I A -1.0219
213 C A 0.0000
214 R A -2.2326
215 R A -2.1366
216 N A -0.8365
217 L A 0.0233
218 D A -1.2440
219 I A -0.7498
220 E A -2.1548
221 R A -2.4532
222 P A -1.2424
223 T A -0.6821
224 Y A -0.1180
225 T A -0.4216
226 N A -0.8853
227 L A 0.0000
228 N A -0.2803
229 R A -0.4443
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 0.5583
243 R A 0.0000
244 F A 0.7750
245 D A 0.0000
246 G A -0.1398
247 A A 0.0883
248 L A -0.2352
249 N A -0.9186
250 V A 0.2882
251 D A 0.0000
252 L A 0.0000
253 T A -0.5620
254 E A -0.9745
255 F A 0.0000
256 Q A 0.0000
257 T A -0.8227
258 N A -0.9318
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 -1.2150
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 -0.0077
276 I A 0.0000
277 S A -1.0198
278 A A -1.2497
279 E A -1.7044
280 K A -2.1670
281 A A 0.0000
282 Y A -1.1823
283 H A -2.2399
284 E A -2.8685
285 Q A -2.2386
286 L A 0.0000
287 S A -1.1171
288 V A -1.0544
289 A A -0.6396
290 E A -1.7762
291 I A 0.0000
292 T A 0.0000
293 N A 0.0000
294 A A -1.0336
295 C A 0.0000
296 F A 0.0000
297 E A -1.3699
298 P A -1.2724
299 A A -0.9413
300 N A -0.8116
301 Q A 0.0000
302 M A 0.0000
303 V A 0.0000
304 K A -1.9058
305 C A 0.0000
306 D A -2.8432
307 P A -2.7713
308 R A -2.9419
309 H A -2.2149
310 G A 0.0000
311 K A -1.1999
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 -1.1891
323 V A 0.4462
324 V A 0.0000
325 P A -0.9954
326 K A -2.1010
327 D A -1.4649
328 V A 0.0000
329 N A -1.8219
330 A A -1.0618
331 A A 0.0000
332 I A -0.7018
333 A A -0.7383
334 A A -1.0519
335 I A 0.0000
336 K A -1.8651
337 T A -1.4063
338 K A -1.9223
339 R A -2.5677
340 S A -1.3440
341 I A -1.0412
342 Q A -0.9649
343 F A -0.0067
344 V A 0.2795
345 D A -0.3405
346 W A 0.5846
347 C A 0.0000
348 P A -0.0795
349 T A -0.2040
350 G A -0.5119
351 F A -0.5208
352 K A -1.5401
353 V A 0.0000
354 G A 0.0000
355 I A 0.0000
356 N A 0.0000
357 Y A 0.2978
358 Q A 0.0723
359 P A 0.0000
360 P A -0.6228
361 T A 0.0000
362 V A -0.4518
363 V A 0.0000
364 P A -1.1543
365 G A -1.1810
366 G A -1.6587
367 D A -2.3247
368 L A 0.0000
369 A A -1.1212
370 K A -0.9798
371 V A 0.0000
372 Q A -0.7040
373 R A -0.8429
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 -1.8231
387 A A 0.0000
388 W A 0.0000
389 A A -1.3464
390 R A -1.8821
391 L A 0.0000
392 D A -1.8087
393 H A -1.8665
394 K A -0.9521
395 F A 0.0000
396 D A -1.7487
397 L A -0.0024
398 M A 0.0000
399 Y A -0.2359
400 A A -0.5561
401 K A -1.9368
402 R A -1.7824
403 A A -0.9564
404 F A -0.1224
405 V A 0.0000
406 H A -0.9588
407 W A 0.3901
408 Y A 0.0000
409 V A -0.6221
410 G A -0.7486
411 E A -1.2629
412 G A -1.2093
413 M A 0.0000
414 E A -2.8799
415 K A -2.3186 mutated: EK415A
416 G A -2.1173
417 E A -2.2708
418 F A 0.0000
419 S A -2.2474
420 E A -2.7454
421 A A 0.0000
422 R A -3.2931
423 E A -3.1562
424 D A -2.3901
425 M A 0.0000
426 A A -1.8927
427 A A -1.7871
428 L A 0.0000
429 E A -1.9024
430 K A -2.3269
431 D A 0.0000
432 Y A 0.0000
433 E A -2.1835
434 E A -1.8530
435 V A 0.0000
436 G A 0.0000
437 I A 0.1041
438 D A -1.3730
439 S A -1.5543
440 Y A -1.9112
441 E A -3.3978
442 D A -3.6744
443 E A -3.6228
444 D A 0.0000
445 E A -2.1728
446 G A -1.9867
447 E A -2.2177
448 E A -1.9858
Download PDB file
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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, -0.6642 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_9 -0.6642 View CSV PDB
model_11 -0.6897 View CSV PDB
model_5 -0.6982 View CSV PDB
model_0 -0.6987 View CSV PDB
model_7 -0.7023 View CSV PDB
model_2 -0.7206 View CSV PDB
CABS_average -0.7216 View CSV PDB
model_1 -0.7257 View CSV PDB
model_10 -0.731 View CSV PDB
model_8 -0.7341 View CSV PDB
input -0.7399 View CSV PDB
model_4 -0.7469 View CSV PDB
model_3 -0.7578 View CSV PDB
model_6 -0.7906 View CSV PDB