Project name: 6H_LkADH_A

Status: done

Started: 2024-03-20 02:54:47
Settings
Chain sequence(s) A: MGSSHHHHHHSSGLVPRGSHMTDRLKGKVAIVTGGTLGIGLAIADKFVEEGAKVVITGRRADVGERAAKSIGGTDVIRFVQHDASDEAGWTKLFDTTEEAFGPVTTVVNNAGIDVVKSVEDTTTEEWRKLLSVNLDGVFFGTRLGIQRMKNKGLGASIINMSSIFGMVGDPNVGAYNASKGAVRIMSKSAALDCALKDYDVRVNTVHPGPIKTPMLDDEEGAEEMWSQRTKTPMGHIGEPNDIAWVCVYLASGESKFATGAEFVIDGGWTAQ
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode No
Automated mutations Yes
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:15)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:15)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:15)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:15)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:15)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:03:05)
[INFO]       Auto_mut: Residue number 14 from chain A and a score of 1.720 (leucine) selected for  
                       automated muatation                                                         (00:03:08)
[INFO]       Auto_mut: Residue number 15 from chain A and a score of 1.716 (valine) selected for   
                       automated muatation                                                         (00:03:08)
[INFO]       Auto_mut: Residue number 37 from chain A and a score of 1.440 (leucine) selected for  
                       automated muatation                                                         (00:03:08)
[INFO]       Auto_mut: Residue number 185 from chain A and a score of 1.257 (isoleucine) selected  
                       for automated muatation                                                     (00:03:08)
[INFO]       Auto_mut: Residue number 264 from chain A and a score of 1.007 (valine) selected for  
                       automated muatation                                                         (00:03:08)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 0.754 (methionine) selected    
                       for automated muatation                                                     (00:03:08)
[INFO]       Auto_mut: Mutating residue number 14 from chain A (leucine) into glutamic acid        (00:03:08)
[INFO]       Auto_mut: Mutating residue number 14 from chain A (leucine) into aspartic acid        (00:03:08)
[INFO]       Auto_mut: Mutating residue number 15 from chain A (valine) into glutamic acid         (00:03:08)
[INFO]       Auto_mut: Mutating residue number 14 from chain A (leucine) into arginine             (00:04:21)
[INFO]       Auto_mut: Mutating residue number 15 from chain A (valine) into lysine                (00:04:22)
[INFO]       Auto_mut: Mutating residue number 14 from chain A (leucine) into lysine               (00:04:24)
[INFO]       Auto_mut: Mutating residue number 15 from chain A (valine) into aspartic acid         (00:05:37)
[INFO]       Auto_mut: Mutating residue number 37 from chain A (leucine) into glutamic acid        (00:05:37)
[INFO]       Auto_mut: Mutating residue number 37 from chain A (leucine) into aspartic acid        (00:05:41)
[INFO]       Auto_mut: Mutating residue number 15 from chain A (valine) into arginine              (00:06:49)
[INFO]       Auto_mut: Mutating residue number 37 from chain A (leucine) into lysine               (00:07:01)
[INFO]       Auto_mut: Mutating residue number 37 from chain A (leucine) into arginine             (00:07:01)
[INFO]       Auto_mut: Mutating residue number 185 from chain A (isoleucine) into glutamic acid    (00:08:11)
[INFO]       Auto_mut: Mutating residue number 185 from chain A (isoleucine) into aspartic acid    (00:08:29)
[INFO]       Auto_mut: Mutating residue number 264 from chain A (valine) into glutamic acid        (00:08:38)
[INFO]       Auto_mut: Mutating residue number 185 from chain A (isoleucine) into lysine           (00:09:31)
[INFO]       Auto_mut: Mutating residue number 185 from chain A (isoleucine) into arginine         (00:09:46)
[INFO]       Auto_mut: Mutating residue number 264 from chain A (valine) into lysine               (00:09:56)
[INFO]       Auto_mut: Mutating residue number 264 from chain A (valine) into aspartic acid        (00:10:53)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into glutamic acid      (00:11:08)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into aspartic acid      (00:11:14)
[INFO]       Auto_mut: Mutating residue number 264 from chain A (valine) into arginine             (00:12:06)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into lysine             (00:12:18)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into arginine           (00:12:25)
[INFO]       Auto_mut: Effect of mutation residue number 14 from chain A (leucine) into glutamic   
                       acid: Energy difference: -0.2388 kcal/mol, Difference in average score from 
                       the base case: -0.0348                                                      (00:13:39)
[INFO]       Auto_mut: Effect of mutation residue number 14 from chain A (leucine) into lysine:    
                       Energy difference: 0.0188 kcal/mol, Difference in average score from the    
                       base case: -0.0346                                                          (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 14 from chain A (leucine) into aspartic   
                       acid: Energy difference: 0.4066 kcal/mol, Difference in average score from  
                       the base case: -0.0349                                                      (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 14 from chain A (leucine) into arginine:  
                       Energy difference: -0.1001 kcal/mol, Difference in average score from the   
                       base case: -0.0361                                                          (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 15 from chain A (valine) into glutamic    
                       acid: Energy difference: -0.8510 kcal/mol, Difference in average score from 
                       the base case: -0.0241                                                      (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 15 from chain A (valine) into lysine:     
                       Energy difference: -0.5197 kcal/mol, Difference in average score from the   
                       base case: -0.0228                                                          (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 15 from chain A (valine) into aspartic    
                       acid: Energy difference: -0.5749 kcal/mol, Difference in average score from 
                       the base case: -0.0242                                                      (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 15 from chain A (valine) into arginine:   
                       Energy difference: -0.5584 kcal/mol, Difference in average score from the   
                       base case: -0.0254                                                          (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 37 from chain A (leucine) into glutamic   
                       acid: Energy difference: -0.1455 kcal/mol, Difference in average score from 
                       the base case: -0.0248                                                      (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 37 from chain A (leucine) into lysine:    
                       Energy difference: -0.0585 kcal/mol, Difference in average score from the   
                       base case: -0.0309                                                          (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 37 from chain A (leucine) into aspartic   
                       acid: Energy difference: -0.5129 kcal/mol, Difference in average score from 
                       the base case: -0.0248                                                      (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 37 from chain A (leucine) into arginine:  
                       Energy difference: -0.7614 kcal/mol, Difference in average score from the   
                       base case: -0.0354                                                          (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 185 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.1281 kcal/mol, Difference in average   
                       score from the base case: -0.0343                                           (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 185 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.2990 kcal/mol, Difference in average score    
                       from the base case: -0.0342                                                 (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 185 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.4545 kcal/mol, Difference in average    
                       score from the base case: -0.0324                                           (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 185 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.2058 kcal/mol, Difference in average score   
                       from the base case: -0.0353                                                 (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 264 from chain A (valine) into glutamic   
                       acid: Energy difference: 1.1098 kcal/mol, Difference in average score from  
                       the base case: -0.0213                                                      (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 264 from chain A (valine) into lysine:    
                       Energy difference: 0.0537 kcal/mol, Difference in average score from the    
                       base case: -0.0207                                                          (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 264 from chain A (valine) into aspartic   
                       acid: Energy difference: 1.8742 kcal/mol, Difference in average score from  
                       the base case: -0.0221                                                      (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 264 from chain A (valine) into arginine:  
                       Energy difference: -0.0341 kcal/mol, Difference in average score from the   
                       base case: -0.0089                                                          (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into glutamic 
                       acid: Energy difference: -0.0176 kcal/mol, Difference in average score from 
                       the base case: -0.0068                                                      (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into lysine:  
                       Energy difference: 0.0024 kcal/mol, Difference in average score from the    
                       base case: -0.0061                                                          (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into aspartic 
                       acid: Energy difference: -0.0176 kcal/mol, Difference in average score from 
                       the base case: -0.0067                                                      (00:13:40)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into          
                       arginine: Energy difference: 0.0104 kcal/mol, Difference in average score   
                       from the base case: -0.0078                                                 (00:13:40)
[INFO]       Main:     Simulation completed successfully.                                          (00:13:59)
Show buried residues
Minimal score value
-4.0118
Maximal score value
1.7201
Average score
-0.8887
Total score value
-241.7391
Download the table (csv)

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
1 M A 0.7543
2 G A -0.2448
3 S A -0.6412
4 S A -1.1703
5 H A -2.0664
6 H A -2.4182
7 H A -2.6436
8 H A -2.6454
9 H A -2.4406
10 H A -2.1082
11 S A -1.1078
12 S A -0.3041
13 G A 0.4631
14 L A 1.7201
15 V A 1.7164
16 P A -0.0648
17 R A -1.6804
18 G A -1.2905
19 S A -1.0891
20 H A -1.0539
21 M A 0.1546
22 T A -0.8713
23 D A -1.7643
24 R A -1.6591
25 L A 0.0000
26 K A -2.6443
27 G A -1.6409
28 K A -1.2435
29 V A 0.0000
30 A A 0.0000
31 I A 0.0000
32 V A 0.0000
33 T A 0.0000
34 G A -0.3214
35 G A 0.0000
36 T A -0.3660
37 L A 1.4401
38 G A 0.3399
39 I A -0.1295
40 G A 0.0000
41 L A 0.5099
42 A A -0.2482
43 I A 0.0000
44 A A 0.0000
45 D A -1.0065
46 K A -1.0594
47 F A 0.0000
48 V A -1.3244
49 E A -2.3390
50 E A 0.0000
51 G A -1.9056
52 A A 0.0000
53 K A -1.4439
54 V A 0.0000
55 V A 0.0000
56 I A 0.0000
57 T A 0.0000
58 G A -2.0490
59 R A -3.3317
60 R A -3.4115
61 A A -2.6442
62 D A -2.5194
63 V A -1.8283
64 G A 0.0000
65 E A -3.7655
66 R A -3.3505
67 A A 0.0000
68 A A 0.0000
69 K A -3.1096
70 S A -1.8068
71 I A -1.1965
72 G A -1.4753
73 G A -1.6290
74 T A -1.6498
75 D A -2.0961
76 V A -1.2764
77 I A 0.0000
78 R A -1.7880
79 F A -1.3816
80 V A -1.4249
81 Q A -2.5208
82 H A 0.0000
83 D A -2.2568
84 A A 0.0000
85 S A -1.5899
86 D A -2.3267
87 E A -2.6465
88 A A -1.5736
89 G A -1.7855
90 W A 0.0000
91 T A -1.6497
92 K A -2.4776
93 L A 0.0000
94 F A 0.0000
95 D A -2.8787
96 T A -2.0539
97 T A 0.0000
98 E A -2.1268
99 E A -2.5023
100 A A -1.7200
101 F A 0.0000
102 G A -1.2253
103 P A -1.2086
104 V A 0.0000
105 T A 0.0000
106 T A 0.0000
107 V A 0.0000
108 V A 0.0000
109 N A 0.0000
110 N A -0.1146
111 A A -0.0382
112 G A -0.2120
113 I A -0.4141
114 D A -1.0452
115 V A -0.4598
116 V A 0.2745
117 K A -1.2776
118 S A -1.1044
119 V A -0.0097
120 E A -2.1577
121 D A -2.4294
122 T A -1.3660
123 T A -1.7838
124 T A -1.9625
125 E A -3.0580
126 E A -2.7675
127 W A -1.6667
128 R A -3.3286
129 K A -3.2820
130 L A 0.0000
131 L A -1.3170
132 S A -1.5732
133 V A 0.0000
134 N A 0.0000
135 L A -0.1949
136 D A -1.2041
137 G A 0.0000
138 V A 0.0000
139 F A 0.1643
140 F A -0.5311
141 G A 0.0000
142 T A 0.0000
143 R A -1.2804
144 L A -1.0027
145 G A 0.0000
146 I A 0.0000
147 Q A -2.2166
148 R A -2.4208
149 M A 0.0000
150 K A -3.0006
151 N A -3.5275
152 K A -2.8942
153 G A -2.0135
154 L A -1.2875
155 G A -1.5368
156 A A 0.0000
157 S A 0.0000
158 I A 0.0000
159 I A 0.0000
160 N A 0.0000
161 M A 0.0000
162 S A 0.0000
163 S A 0.0000
164 I A 0.0000
165 F A 0.3687
166 G A 0.4190
167 M A 0.6060
168 V A 0.6878
169 G A -0.3870
170 D A -0.8253
171 P A -1.0034
172 N A -1.4319
173 V A 0.0000
174 G A -0.3250
175 A A 0.0000
176 Y A -0.0320
177 N A -0.3758
178 A A 0.0324
179 S A 0.0000
180 K A 0.0000
181 G A 0.4893
182 A A 0.6240
183 V A 0.0000
184 R A 0.2204
185 I A 1.2572
186 M A 0.6640
187 S A 0.0000
188 K A -0.8446
189 S A -0.2821
190 A A 0.0000
191 A A 0.0000
192 L A 0.2059
193 D A -0.5066
194 C A 0.0000
195 A A -0.5017
196 L A 0.2299
197 K A -1.9004
198 D A -2.7393
199 Y A -2.8987
200 D A -3.3580
201 V A 0.0000
202 R A 0.0000
203 V A 0.0000
204 N A 0.0000
205 T A 0.0000
206 V A 0.0000
207 H A 0.0000
208 P A 0.0000
209 G A -0.2358
210 P A 0.0000
211 I A 0.0000
212 K A -2.5103
213 T A 0.0000
214 P A -0.9234
215 M A -0.5017
216 L A -2.2852
217 D A -3.8317
218 D A -3.5649
219 E A -4.0118
220 E A -3.9600
221 G A -2.9233
222 A A 0.0000
223 E A -3.7507
224 E A -3.0609
225 M A -1.9214
226 W A -1.7737
227 S A -2.3446
228 Q A -2.5369
229 R A -2.4353
230 T A -1.5686
231 K A -1.6510
232 T A 0.0000
233 P A -1.1487
234 M A -0.1368
235 G A -1.5096
236 H A -2.2253
237 I A 0.0000
238 G A -1.9365
239 E A -2.7646
240 P A -1.5221
241 N A -1.7410
242 D A -1.6906
243 I A 0.0000
244 A A 0.0000
245 W A 0.2026
246 V A 0.6210
247 C A 0.0000
248 V A 0.0000
249 Y A 0.0768
250 L A 0.0000
251 A A 0.0000
252 S A 0.0000
253 G A -1.6359
254 E A -2.1199
255 S A 0.0000
256 K A -1.6542
257 F A 0.7543
258 A A 0.0383
259 T A -0.0128
260 G A 0.0000
261 A A -0.3762
262 E A -0.5199
263 F A 0.4628
264 V A 1.0069
265 I A 0.4579
266 D A 0.0108
267 G A -0.2272
268 G A -0.3394
269 W A -0.4544
270 T A -0.0812
271 A A -0.4699
272 Q A -1.2510
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Automated mutations analysis

In the automated mutations mode, the server selects aggregation prone resides and each selected residue is mutated to glutamic acid, lysine, aspartic acid and arginine. The table below shows 2 best scored mutants for each mutated residue. Protein variants are ordered according to the mutation effect they had on protein stability (energetic effect) together with the difference in the average per-residue aggregation score between the wild type and the mutant (in the table green values indicate a positive change, grey are neutral, and orange/red mean destabilizing or more aggregation prone mutants).
Summary for all the mutants can be found in this CSV file.

Mutant
Energetic effect
Score comparison
LR37A -0.7614 -0.0354 View CSV PDB
VE15A -0.851 -0.0241 View CSV PDB
IK185A -0.299 -0.0342 View CSV PDB
VR15A -0.5584 -0.0254 View CSV PDB
LE14A -0.2388 -0.0348 View CSV PDB
LD37A -0.5129 -0.0248 View CSV PDB
LR14A -0.1001 -0.0361 View CSV PDB
IE185A -0.1281 -0.0343 View CSV PDB
VR264A -0.0341 -0.0089 View CSV PDB
ME1A -0.0176 -0.0068 View CSV PDB
MD1A -0.0176 -0.0067 View CSV PDB
VK264A 0.0537 -0.0207 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018