Project name: VacA-RD4

Status: done

Started: 2026-07-18 02:22:35
Chain sequence(s) A: MTLDLWQSAGLNIIAPPEGGKDTVVNINRINTNADGTIRVGGYKASLTTNAAHLHIGKGGINLSNQASGRSLLVENLTGNITVDGPLRVNNQVGGYALAGSNANFEFKAGTDTKNGTATFNNDISLGRFVNLKVDAHTANFKGIDTGNGGFNTLDFSGVTDKVNINKLITASTNVAIKNFNINELLVKTNGVSVGEYTHFSEDIGSQSRINTVRLETGTRSIFSGGVKFKSGEKLVIDEFYYSPWNYFDARNIKNVEITRKFASSTPENPWGTSKLMFNNLTLGQNAVMDYSQFSNLTIQGDFINNQGTINYLVRGGKVATLNVGNAAAMMFNNDIDSATGFYKPLIKINSAQDLIKNTEHVLLKAKIIGYGNVSTGTNGISNVNLEEQFKERLALYNNNNRMDTCVVRNTDDIKACGMAIGNQSMVNNPDNYKYLIGKAWKNIGISKTANGSKISVYYLGNSTPTENGGNTTNLPTNTTNNARSANYAGGTASPTEHHHHHH
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]                                                (00:00:01)
[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]       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                                          (00:06:00)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/97c60f04763225b/tmp/folded.pdb                (00:06:00)
[INFO]       Main:     Simulation completed successfully.                                          (00:07:53)
Show buried residues

Minimal score value
-3.4929
Maximal score value
1.9732
Average score
-0.7673
Total score value
-385.9675

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 0.1675
2 T A -0.6880
3 L A -0.8406
4 D A -1.8326
5 L A 0.0000
6 W A -0.3784
7 Q A 0.0000
8 S A -0.5621
9 A A -0.4450
10 G A -0.6181
11 L A 0.0876
12 N A -0.4384
13 I A 0.9007
14 I A 1.7577
15 A A 0.0000
16 P A -0.5019
17 P A -1.3105
18 E A -2.5891
19 G A -2.2768
20 G A -2.0278
21 K A -2.8417
22 D A -2.5809
23 T A -1.2110
24 V A 0.3729
25 V A 0.4909
26 N A -1.0194
27 I A 0.0000
28 N A -1.7707
29 R A -2.0533
30 I A 0.0000
31 N A -1.5321
32 T A 0.0000
33 N A -1.3524
34 A A -1.0002
35 D A -1.0224
36 G A -0.6112
37 T A 0.1164
38 I A 1.4315
39 R A 0.5249
40 V A 1.3847
41 G A 0.0895
42 G A 0.0000
43 Y A -0.3756
44 K A -1.3651
45 A A 0.0000
46 S A -0.5377
47 L A 0.0000
48 T A -0.1144
49 T A 0.0000
50 N A 0.0847
51 A A 0.0000
52 A A -0.9581
53 H A -0.6051
54 L A 0.0000
55 H A -0.9156
56 I A 0.0000
57 G A -1.8749
58 K A -2.4629
59 G A -1.7498
60 G A 0.0000
61 I A 0.0000
62 N A 0.0000
63 L A 0.0000
64 S A -1.2788
65 N A 0.0000
66 Q A -0.6912
67 A A 0.1535
68 S A 0.4002
69 G A 0.0000
70 R A 0.0000
71 S A -0.8064
72 L A 0.0000
73 L A -0.5998
74 V A 0.0000
75 E A -0.7291
76 N A 0.0000
77 L A -0.8366
78 T A -1.4245
79 G A 0.0000
80 N A -0.8072
81 I A 0.0000
82 T A -0.6508
83 V A 0.0000
84 D A -1.7252
85 G A 0.0000
86 P A -1.3493
87 L A 0.0000
88 R A -1.3854
89 V A 0.0000
90 N A -1.6686
91 N A -2.2302
92 Q A -1.6370
93 V A -0.2954
94 G A -0.5909
95 G A 0.0000
96 Y A 0.7804
97 A A 0.0000
98 L A 1.3719
99 A A 0.6893
100 G A 0.0334
101 S A 0.4399
102 N A -0.1318
103 A A 0.0000
104 N A -0.7756
105 F A 0.0000
106 E A -1.1368
107 F A 0.0000
108 K A -1.6437
109 A A 0.0000
110 G A 0.0000
111 T A -1.9988
112 D A -2.4992
113 T A -2.1364
114 K A -3.0974
115 N A -2.6947
116 G A 0.0000
117 T A -1.2124
118 A A 0.0000
119 T A -0.6524
120 F A 0.0000
121 N A -1.7879
122 N A -2.1563
123 D A -2.6251
124 I A 0.0000
125 S A -0.9649
126 L A 0.0000
127 G A 0.0000
128 R A -0.3008
129 F A 0.5641
130 V A 0.0000
131 N A -0.5630
132 L A 0.0000
133 K A -1.4700
134 V A 0.0000
135 D A -1.8606
136 A A 0.0000
137 H A -1.9476
138 T A -1.3068
139 A A 0.0000
140 N A -0.9704
141 F A 0.0000
142 K A -2.4579
143 G A 0.0000
144 I A 0.0000
145 D A -1.1793
146 T A 0.0000
147 G A -1.1624
148 N A -1.6393
149 G A 0.0000
150 G A 0.0000
151 F A 0.9714
152 N A 0.0000
153 T A -0.1468
154 L A 0.0000
155 D A -0.9782
156 F A 0.0000
157 S A -1.0386
158 G A -1.1453
159 V A 0.0000
160 T A -1.4936
161 D A -1.4903
162 K A -1.4310
163 V A 0.0000
164 N A -1.3313
165 I A 0.0000
166 N A -2.5233
167 K A -2.0402
168 L A 0.0000
169 I A -0.5306
170 T A 0.0000
171 A A 0.0000
172 S A 0.0000
173 T A 0.0000
174 N A -0.4124
175 V A 0.0000
176 A A -1.1050
177 I A 0.0000
178 K A -1.9852
179 N A -1.8680
180 F A 0.0000
181 N A -1.4961
182 I A 0.0000
183 N A -2.1443
184 E A -1.6358
185 L A 0.0000
186 L A -0.5762
187 V A 0.0000
188 K A -0.9925
189 T A -0.1834
190 N A 0.0822
191 G A 0.4817
192 V A 1.8435
193 S A 1.4861
194 V A 1.9732
195 G A 0.5392
196 E A 0.4936
197 Y A 0.1856
198 T A 0.0000
199 H A -0.9115
200 F A 0.0000
201 S A -1.4830
202 E A -1.9930
203 D A -2.5606
204 I A 0.0000
205 G A -1.8820
206 S A -2.1075
207 Q A -2.0769
208 S A 0.0000
209 R A -1.7146
210 I A 0.0000
211 N A -1.5086
212 T A -1.4275
213 V A 0.0000
214 R A -1.1009
215 L A 0.0000
216 E A -1.0685
217 T A -0.8264
218 G A -0.4853
219 T A -0.5138
220 R A -1.5102
221 S A -0.6706
222 I A 0.7647
223 F A 0.7934
224 S A 0.0000
225 G A 0.0000
226 G A 0.0000
227 V A 0.0000
228 K A -1.4110
229 F A 0.0000
230 K A -2.6055
231 S A -2.7769
232 G A -2.8720
233 E A -2.8739
234 K A -2.4998
235 L A 0.0000
236 V A -0.8545
237 I A 0.0000
238 D A -1.6130
239 E A -1.5526
240 F A 0.0000
241 Y A 0.0000
242 Y A 0.0000
243 S A 0.0000
244 P A 0.0000
245 W A -0.2621
246 N A 0.0000
247 Y A -0.2952
248 F A 0.0000
249 D A 0.0000
250 A A 0.0000
251 R A -2.8286
252 N A -3.2422
253 I A 0.0000
254 K A -2.9435
255 N A -2.1888
256 V A 0.0000
257 E A -0.9255
258 I A 0.0000
259 T A -1.6240
260 R A -2.4374
261 K A -1.6457
262 F A 0.0000
263 A A 0.0000
264 S A 0.0000
265 S A -0.8516
266 T A -1.0718
267 P A -1.5733
268 E A -2.5326
269 N A -2.1003
270 P A 0.0000
271 W A -0.0462
272 G A -0.3171
273 T A -0.5149
274 S A 0.0000
275 K A -0.9069
276 L A 0.0000
277 M A -1.0506
278 F A 0.0000
279 N A -2.2844
280 N A -1.7889
281 L A 0.0000
282 T A -0.3825
283 L A 0.0000
284 G A 0.0000
285 Q A -1.9872
286 N A -2.1205
287 A A 0.0000
288 V A -0.7976
289 M A 0.0000
290 D A -0.4830
291 Y A 0.0000
292 S A 0.0000
293 Q A -1.0492
294 F A -0.4558
295 S A 0.0000
296 N A -1.5353
297 L A -0.9637
298 T A -1.1560
299 I A 0.0000
300 Q A -2.1111
301 G A -1.7490
302 D A -1.1566
303 F A 0.0000
304 I A 0.1455
305 N A 0.0000
306 N A -0.6533
307 Q A -0.8715
308 G A 0.0000
309 T A 0.0000
310 I A 0.0000
311 N A -0.7183
312 Y A 0.0000
313 L A -0.8331
314 V A 0.0000
315 R A -1.8530
316 G A -1.4112
317 G A -1.5983
318 K A -1.7780
319 V A -0.6237
320 A A -0.6754
321 T A -0.6154
322 L A 0.0000
323 N A -1.8454
324 V A 0.0000
325 G A -1.8980
326 N A -1.5572
327 A A -0.5875
328 A A 0.0000
329 A A 0.3214
330 M A 0.0000
331 M A 0.2688
332 F A 0.0000
333 N A -0.6661
334 N A -1.3773
335 D A -2.3400
336 I A -1.4140
337 D A -1.3608
338 S A -0.8442
339 A A -0.3323
340 T A -0.4532
341 G A -0.7557
342 F A 0.0000
343 Y A -0.9857
344 K A -1.5022
345 P A 0.0000
346 L A 0.0000
347 I A 0.0000
348 K A -0.9962
349 I A 0.0000
350 N A -2.3067
351 S A -2.1309
352 A A 0.0000
353 Q A -1.9044
354 D A -2.5829
355 L A 0.0000
356 I A -0.8443
357 K A -1.7948
358 N A -1.6310
359 T A -1.2783
360 E A -1.3937
361 H A 0.0000
362 V A -0.4517
363 L A 0.0000
364 L A 0.0000
365 K A -1.7578
366 A A 0.0000
367 K A -1.5064
368 I A 0.4024
369 I A 0.0000
370 G A 0.1082
371 Y A -0.2812
372 G A 0.1767
373 N A 0.5997
374 V A 1.3474
375 S A -0.1165
376 T A 0.1588
377 G A -0.3118
378 T A -0.5002
379 N A -0.9893
380 G A -0.3086
381 I A 1.0623
382 S A -0.0264
383 N A -0.7364
384 V A -0.5670
385 N A -1.2634
386 L A -0.9924
387 E A -1.9375
388 E A -2.2987
389 Q A -1.5303
390 F A 0.0000
391 K A -1.5455
392 E A -1.5667
393 R A 0.0000
394 L A 0.0000
395 A A 0.0000
396 L A 0.0000
397 Y A -1.5375
398 N A -1.9157
399 N A -2.2949
400 N A -2.3659
401 N A -1.4148
402 R A -0.9417
403 M A 0.0000
404 D A 0.0000
405 T A 0.0000
406 C A 0.0000
407 V A -0.5656
408 V A 0.0000
409 R A -1.8597
410 N A -2.4957
411 T A -2.6262
412 D A -2.5655
413 D A -1.6542
414 I A 0.0000
415 K A -1.8720
416 A A -0.7478
417 C A 0.0000
418 G A 0.0000
419 M A 0.0852
420 A A 0.0000
421 I A 0.0000
422 G A -0.6895
423 N A -1.0203
424 Q A -1.7623
425 S A -1.8467
426 M A 0.0000
427 V A -1.6747
428 N A -2.5890
429 N A -3.1852
430 P A 0.0000
431 D A -3.4929
432 N A -3.2295
433 Y A -2.2329
434 K A -2.8018
435 Y A -1.3090
436 L A 0.0000
437 I A -0.7952
438 G A -0.9679
439 K A -1.3697
440 A A 0.0000
441 W A 0.0000
442 K A -1.3942
443 N A 0.0000
444 I A 0.8228
445 G A 0.0000
446 I A 0.0000
447 S A 0.0791
448 K A -0.6391
449 T A -0.9104
450 A A -1.2119
451 N A -1.2538
452 G A -0.8293
453 S A -0.9245
454 K A -1.2346
455 I A 0.0000
456 S A 0.0000
457 V A 0.0000
458 Y A -0.3735
459 Y A 0.0000
460 L A 0.1944
461 G A -0.2415
462 N A -0.3802
463 S A -0.1599
464 T A -0.3554
465 P A 0.0000
466 T A -1.6083
467 E A -2.8891
468 N A -2.5386
469 G A -1.9773
470 G A -1.8798
471 N A -1.4718
472 T A -1.6890
473 T A -1.2093
474 N A -1.3288
475 L A -0.7250
476 P A -0.7583
477 T A -1.2184
478 N A -1.8488
479 T A -1.9560
480 T A -2.0387
481 N A -2.7869
482 N A -2.8484
483 A A -2.1723
484 R A -2.8174
485 S A -1.8075
486 A A -1.3705
487 N A -1.5794
488 Y A 0.0109
489 A A -0.2894
490 G A -0.6308
491 G A -0.6036
492 T A -0.2908
493 A A -0.3653
494 S A -0.6502
495 P A -1.0085
496 T A -1.5062
497 E A -2.8237
498 H A -2.7894
499 H A -2.8469
500 H A -2.8441
501 H A -2.6117
502 H A -2.3527
503 H A -1.8716
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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 -0.6481 3.721 View CSV PDB
4.5 -0.6876 3.721 View CSV PDB
5.0 -0.734 3.721 View CSV PDB
5.5 -0.7778 3.721 View CSV PDB
6.0 -0.8084 3.721 View CSV PDB
6.5 -0.8187 3.721 View CSV PDB
7.0 -0.8113 3.721 View CSV PDB
7.5 -0.7938 3.721 View CSV PDB
8.0 -0.7709 3.721 View CSV PDB
8.5 -0.743 3.721 View CSV PDB
9.0 -0.7083 3.721 View CSV PDB