Project name: bacillus

Status: done

Started: 2024-04-25 20:33:01
Chain sequence(s) A: ANLNGTLMQYFEWYMPNDGQHWKRLQNDSAYLAEHGITAVWIPPAYKGTSQADVGYGAYDLYDLGEFHQKGTVRTKYGTKGELQSAIKSLHSRDINVYGDVVINHKGGADATEDVTAVEVDPADRNRVISGEHRIKAWTHFHFPGRGSTYSDFKWHWYHFDGTDWDESRKLNRIYKFQGKAWDWEVSNENGNYDYLMYADIDYDHPDVAAEIKRWGTWYANELQLDGFRLDAVKHIKFSFLRDWVNHVREKTGKEMFTVAEYWQNDLGALENYLNKTNFNHSVFDVPLHYQFHAASTQGGGYDMRKLLNSTVVSKHPLKAVTFVDNHDTQPGQSLESTVQTWFKPLAYAFILTRESGYPQVFYGDMYGTKGDSQREIPALKHKIEPILKARKQYAYGAQHDYFDHHDIVGWTREGDSSVANSGLAALITDGPGGAKRMYVGRQNAGETWHDITGNRSEPVVINSEGWGEFHVNGGSVSIYVQR
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage No
Dynamic mode No
Automated mutations No
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]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:05:48)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/3145f86b3480b44/tmp/folded.pdb                (00:05:48)
[INFO]       Main:     Simulation completed successfully.                                          (00:08:29)
Show buried residues

Minimal score value
-3.6662
Maximal score value
1.437
Average score
-0.6964
Total score value
-336.3485

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 A A -0.2616
2 N A -0.7397
3 L A 0.6342
4 N A -0.2134
5 G A -0.0914
6 T A 0.0000
7 L A 0.0000
8 M A 0.0000
9 Q A 0.0000
10 Y A 0.0000
11 F A 0.0000
12 E A 0.0000
13 W A 0.0293
14 Y A -0.5205
15 M A 0.0000
16 P A -1.0070
17 N A -1.2719
18 D A -1.6209
19 G A 0.0000
20 Q A -1.6905
21 H A 0.0000
22 W A 0.0000
23 K A -1.8182
24 R A -1.6895
25 L A 0.0000
26 Q A -1.7648
27 N A -1.7120
28 D A -0.8017
29 S A -1.1353
30 A A -0.5927
31 Y A 0.3395
32 L A 0.0000
33 A A -1.2703
34 E A -1.7848
35 H A -1.2516
36 G A 0.0000
37 I A 0.0000
38 T A -0.9506
39 A A 0.0000
40 V A 0.0000
41 W A 0.0000
42 I A 0.0000
43 P A 0.0000
44 P A 0.0000
45 A A 0.0000
46 Y A 0.0000
47 K A 0.0000
48 G A 0.0000
49 T A -0.6520
50 S A -0.8758
51 Q A -0.9906
52 A A -0.6298
53 D A -0.5287
54 V A -0.0423
55 G A 0.0000
56 Y A 0.0000
57 G A 0.0000
58 A A 0.0000
59 Y A 0.0000
60 D A 0.0000
61 L A 0.1572
62 Y A 0.0000
63 D A 0.0000
64 L A 0.0000
65 G A 0.0000
66 E A -0.4711
67 F A -0.2376
68 H A -0.9066
69 Q A 0.0000
70 K A -1.5860
71 G A -1.1654
72 T A -0.6633
73 V A -0.0278
74 R A -0.5950
75 T A 0.0000
76 K A 0.0000
77 Y A 0.0000
78 G A 0.0000
79 T A -0.7659
80 K A -0.8376
81 G A -1.0485
82 E A -1.3974
83 L A 0.0000
84 Q A -1.3915
85 S A -1.3752
86 A A 0.0000
87 I A 0.0000
88 K A -2.6642
89 S A -2.0490
90 L A 0.0000
91 H A -2.6262
92 S A -2.3396
93 R A -3.4135
94 D A -3.1991
95 I A 0.0000
96 N A -1.6197
97 V A 0.0000
98 Y A 0.0000
99 G A 0.0000
100 D A 0.0000
101 V A 0.0000
102 V A 0.0000
103 I A 0.0000
104 N A 0.0000
105 H A 0.0000
106 K A 0.0000
107 G A 0.0000
108 G A 0.0000
109 A A -0.4891
110 D A -1.1484
111 A A -0.6982
112 T A -1.1041
113 E A -1.8397
114 D A -2.8996
115 V A 0.0000
116 T A -2.1035
117 A A 0.0000
118 V A 0.0000
119 E A 0.0000
120 V A 0.0000
121 D A -0.8529
122 P A -0.9554
123 A A -1.1965
124 D A -2.1169
125 R A 0.0000
126 N A -2.0990
127 R A -1.7681
128 V A 0.5080
129 I A 1.4370
130 S A 0.1843
131 G A -0.9052
132 E A -2.6645
133 H A -2.2497
134 R A -3.0251
135 I A 0.0000
136 K A -2.5405
137 A A 0.0000
138 W A -0.2892
139 T A 0.0000
140 H A -0.6018
141 F A 0.0000
142 H A -1.3317
143 F A 0.0000
144 P A -0.8915
145 G A -0.6675
146 R A 0.0000
147 G A -0.8290
148 S A -1.1276
149 T A -0.3820
150 Y A -0.0058
151 S A -0.9751
152 D A -1.9366
153 F A -1.1489
154 K A -1.1216
155 W A 0.0000
156 H A -0.0914
157 W A 0.1990
158 Y A 0.7049
159 H A 0.0000
160 F A 0.0000
161 D A 0.0000
162 G A 0.0000
163 T A 0.0000
164 D A -0.6112
165 W A -1.0054
166 D A 0.0000
167 E A -1.7540
168 S A -1.7907
169 R A -1.9336
170 K A -2.3462
171 L A -1.3482
172 N A -2.0428
173 R A -2.1192
174 I A -0.7865
175 Y A 0.0000
176 K A -0.7596
177 F A 0.0000
178 Q A -1.2025
179 G A -0.7096
180 K A -0.7405
181 A A -0.5411
182 W A 0.0000
183 D A 0.0000
184 W A 0.4651
185 E A -0.2985
186 V A 0.0000
187 S A 0.0000
188 N A -1.7174
189 E A -1.5516
190 N A -1.6958
191 G A -1.9578
192 N A 0.0000
193 Y A -0.5678
194 D A 0.0000
195 Y A 0.0000
196 L A 0.9183
197 M A 0.8756
198 Y A 0.7421
199 A A 0.0000
200 D A 0.0000
201 I A 0.0000
202 D A 0.0000
203 Y A 0.0000
204 D A -2.0195
205 H A -1.4841
206 P A -1.4969
207 D A -1.8257
208 V A 0.0000
209 A A -1.4261
210 A A -1.1783
211 E A 0.0000
212 I A 0.0000
213 K A -1.6948
214 R A -2.0813
215 W A 0.0000
216 G A 0.0000
217 T A -1.4514
218 W A -0.4980
219 Y A 0.0000
220 A A 0.0000
221 N A -1.8160
222 E A -1.0960
223 L A 0.0000
224 Q A -2.0843
225 L A 0.0000
226 D A -1.3727
227 G A 0.0000
228 F A 0.0000
229 R A 0.0000
230 L A 0.0000
231 D A -0.2367
232 A A -0.0483
233 V A 0.0000
234 K A -0.4376
235 H A 0.0000
236 I A 0.0000
237 K A -0.4612
238 F A 0.0000
239 S A -0.9055
240 F A 0.0000
241 L A 0.0000
242 R A -1.7321
243 D A -2.1637
244 W A 0.0000
245 V A 0.0000
246 N A -2.5623
247 H A -2.5633
248 V A 0.0000
249 R A -3.1323
250 E A -3.6662
251 K A -3.5346
252 T A -2.6739
253 G A -2.6241
254 K A -2.8157
255 E A -2.7503
256 M A 0.0000
257 F A -0.5557
258 T A 0.0000
259 V A 0.0000
260 A A 0.0000
261 E A 0.0000
262 Y A 0.0000
263 W A -0.5081
264 Q A -1.3211
265 N A -2.1530
266 D A -2.5559
267 L A -1.7124
268 G A -1.4356
269 A A -1.5960
270 L A 0.0000
271 E A -1.9413
272 N A -1.8318
273 Y A 0.0000
274 L A 0.0000
275 N A -1.8759
276 K A -1.8054
277 T A 0.0000
278 N A -1.7464
279 F A -0.6448
280 N A -1.0542
281 H A 0.0000
282 S A 0.0000
283 V A 0.0000
284 F A 0.0000
285 D A 0.0000
286 V A 0.0000
287 P A 0.0000
288 L A 0.0000
289 H A 0.0000
290 Y A -0.1380
291 Q A -0.6368
292 F A 0.0000
293 H A -0.5868
294 A A -0.6883
295 A A 0.0000
296 S A 0.0000
297 T A -1.0185
298 Q A -1.7035
299 G A -1.2611
300 G A -1.3651
301 G A -1.4040
302 Y A 0.0000
303 D A -1.9995
304 M A 0.0000
305 R A -2.9768
306 K A -2.6430
307 L A 0.0000
308 L A -1.3172
309 N A -2.0828
310 S A -1.6766
311 T A 0.0000
312 V A 0.0000
313 V A 0.0000
314 S A -1.1330
315 K A -1.9746
316 H A -0.7976
317 P A -0.2841
318 L A 1.0968
319 K A 0.0808
320 A A 0.0000
321 V A 0.0000
322 T A 0.0000
323 F A 0.0000
324 V A 0.0000
325 D A 0.0000
326 N A 0.0000
327 H A 0.0000
328 D A -0.4733
329 T A 0.0000
330 Q A 0.0000
331 P A 0.0000
332 G A -1.4240
333 Q A -0.6538
334 S A -0.4365
335 L A -0.1333
336 E A -0.7310
337 S A 0.0000
338 T A -0.8114
339 V A 0.0000
340 Q A -0.9352
341 T A 0.0118
342 W A 0.8405
343 F A 0.0000
344 K A 0.0000
345 P A -0.1956
346 L A 0.0000
347 A A 0.0000
348 Y A 0.0000
349 A A 0.0000
350 F A 0.0000
351 I A 0.0000
352 L A 0.0000
353 T A 0.0000
354 R A -1.3143
355 E A -1.9877
356 S A -0.7360
357 G A -0.0911
358 Y A 0.1609
359 P A 0.0000
360 Q A 0.0000
361 V A 0.0000
362 F A 0.0000
363 Y A 0.2116
364 G A 0.0000
365 D A 0.0000
366 M A 0.0000
367 Y A -0.0347
368 G A 0.0000
369 T A 0.0000
370 K A -1.9604
371 G A -2.2649
372 D A -2.8493
373 S A -2.6046
374 Q A -2.6927
375 R A -3.0991
376 E A -2.4286
377 I A 0.0000
378 P A -0.6559
379 A A -0.3603
380 L A 0.0000
381 K A -1.5312
382 H A -2.1080
383 K A -2.2290
384 I A 0.0000
385 E A -2.2278
386 P A -1.4755
387 I A 0.0000
388 L A 0.0000
389 K A -1.7747
390 A A 0.0000
391 R A 0.0000
392 K A -1.1229
393 Q A -1.1064
394 Y A -0.8524
395 A A 0.0000
396 Y A 0.0000
397 G A -0.9008
398 A A -0.6938
399 Q A -1.2824
400 H A -1.2276
401 D A -1.9921
402 Y A -1.7776
403 F A 0.0000
404 D A -2.8622
405 H A -2.5278
406 H A -2.7663
407 D A -2.1254
408 I A 0.0000
409 V A 0.0000
410 G A 0.0000
411 W A 0.0000
412 T A 0.0000
413 R A 0.0000
414 E A -1.0052
415 G A 0.0000
416 D A -1.0635
417 S A -0.9909
418 S A -0.7963
419 V A -0.5884
420 A A -0.7410
421 N A -1.7210
422 S A 0.0000
423 G A 0.0000
424 L A 0.0000
425 A A 0.0000
426 A A 0.0000
427 L A 0.0000
428 I A 0.0000
429 T A 0.0000
430 D A 0.0000
431 G A -1.1402
432 P A -0.8802
433 G A -1.0339
434 G A -0.7836
435 A A -1.3071
436 K A -2.1024
437 R A -2.6970
438 M A 0.0000
439 Y A -1.2805
440 V A 0.0000
441 G A 0.0000
442 R A -3.1491
443 Q A -2.5307
444 N A 0.0000
445 A A -1.6496
446 G A -0.9608
447 E A -0.6885
448 T A -0.3298
449 W A 0.0000
450 H A -1.2202
451 D A 0.0000
452 I A -0.4645
453 T A -1.0475
454 G A -1.3249
455 N A -1.6646
456 R A -1.7344
457 S A -1.5674
458 E A -2.1409
459 P A -1.0359
460 V A 0.0000
461 V A 1.0073
462 I A 0.0000
463 N A -1.5031
464 S A -1.8882
465 E A -2.7892
466 G A 0.0000
467 W A -1.4105
468 G A 0.0000
469 E A -2.4904
470 F A 0.0000
471 H A -1.4722
472 V A 0.0000
473 N A -1.2325
474 G A -1.0058
475 G A 0.0000
476 S A -0.3627
477 V A 0.0000
478 S A 0.0000
479 I A 0.0000
480 Y A 0.0000
481 V A 0.0000
482 Q A -1.3784
483 R A -2.2404
Download PDB file
View in 3Dmol

Calculations for various pH values

This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is globular. Max score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -0.6151 3.2847 View CSV PDB
4.5 -0.6597 3.2847 View CSV PDB
5.0 -0.7125 3.2847 View CSV PDB
5.5 -0.7638 3.2847 View CSV PDB
6.0 -0.8038 3.2847 View CSV PDB
6.5 -0.8276 3.2847 View CSV PDB
7.0 -0.8373 3.2847 View CSV PDB
7.5 -0.838 3.2847 View CSV PDB
8.0 -0.833 3.2847 View CSV PDB
8.5 -0.8221 3.2847 View CSV PDB
9.0 -0.8039 3.2847 View CSV PDB