Project name: NKAB

Status: done

Started: 2025-02-17 13:16:03
Settings
Chain sequence(s) A: STTQIPQIQKTEISFRPNDPKSYEAYVLNIVRFLEKYKDSAQRDDMIFEDCGDSPSEPKERGDFNHERGERKVCRFKLEWLGNCSGLNDETYGYKEGKPCIIIKLNRVLGFKPKPPKNESLETYTSMKYNPNVLPVDCTGKRDEDKDKVGNVEYFGLGNSPGFPLQYYPYYGKLLQPKYLQPLLAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIEVKS
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]                                                (00:00:00)
[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 minimalization                                        (00:00:00)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:05:35)
[INFO]       Auto_mut: Residue number 109 from chain A and a score of 0.947 (leucine) selected for 
                       automated muatation                                                         (00:05:36)
[INFO]       Auto_mut: Residue number 124 from chain A and a score of 0.480 (tyrosine) selected    
                       for automated muatation                                                     (00:05:36)
[INFO]       Auto_mut: Residue number 174 from chain A and a score of 0.096 (leucine) selected for 
                       automated muatation                                                         (00:05:36)
[INFO]       Auto_mut: Residue number 110 from chain A and a score of -0.020 (glycine) selected    
                       for automated muatation                                                     (00:05:36)
[INFO]       Auto_mut: Mutating residue number 109 from chain A (leucine) into glutamic acid       (00:05:36)
[INFO]       Auto_mut: Mutating residue number 109 from chain A (leucine) into aspartic acid       (00:05:36)
[INFO]       Auto_mut: Mutating residue number 124 from chain A (tyrosine) into glutamic acid      (00:05:36)
[INFO]       Auto_mut: Mutating residue number 109 from chain A (leucine) into lysine              (00:07:59)
[INFO]       Auto_mut: Mutating residue number 109 from chain A (leucine) into arginine            (00:08:00)
[INFO]       Auto_mut: Mutating residue number 124 from chain A (tyrosine) into lysine             (00:08:01)
[INFO]       Auto_mut: Mutating residue number 124 from chain A (tyrosine) into aspartic acid      (00:10:33)
[INFO]       Auto_mut: Mutating residue number 174 from chain A (leucine) into glutamic acid       (00:10:34)
[INFO]       Auto_mut: Mutating residue number 174 from chain A (leucine) into aspartic acid       (00:10:44)
[INFO]       Auto_mut: Mutating residue number 174 from chain A (leucine) into lysine              (00:12:57)
[INFO]       Auto_mut: Mutating residue number 124 from chain A (tyrosine) into arginine           (00:13:01)
[INFO]       Auto_mut: Mutating residue number 174 from chain A (leucine) into arginine            (00:13:17)
[INFO]       Auto_mut: Mutating residue number 110 from chain A (glycine) into glutamic acid       (00:15:36)
[INFO]       Auto_mut: Mutating residue number 110 from chain A (glycine) into aspartic acid       (00:15:45)
[INFO]       Auto_mut: Mutating residue number 110 from chain A (glycine) into lysine              (00:17:52)
[INFO]       Auto_mut: Mutating residue number 110 from chain A (glycine) into arginine            (00:18:02)
[INFO]       Auto_mut: Effect of mutation residue number 109 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.4514 kcal/mol, Difference in average score from  
                       the base case: -0.0551                                                      (00:20:22)
[INFO]       Auto_mut: Effect of mutation residue number 109 from chain A (leucine) into lysine:   
                       Energy difference: 0.4290 kcal/mol, Difference in average score from the    
                       base case: -0.0546                                                          (00:20:22)
[INFO]       Auto_mut: Effect of mutation residue number 109 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.1733 kcal/mol, Difference in average score from  
                       the base case: -0.0507                                                      (00:20:22)
[INFO]       Auto_mut: Effect of mutation residue number 109 from chain A (leucine) into arginine: 
                       Energy difference: -0.3176 kcal/mol, Difference in average score from the   
                       base case: -0.0587                                                          (00:20:22)
[INFO]       Auto_mut: Effect of mutation residue number 124 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.2135 kcal/mol, Difference in average score from  
                       the base case: -0.0471                                                      (00:20:22)
[INFO]       Auto_mut: Effect of mutation residue number 124 from chain A (tyrosine) into lysine:  
                       Energy difference: -0.0462 kcal/mol, Difference in average score from the   
                       base case: -0.0501                                                          (00:20:22)
[INFO]       Auto_mut: Effect of mutation residue number 124 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 0.6302 kcal/mol, Difference in average score from  
                       the base case: -0.0480                                                      (00:20:22)
[INFO]       Auto_mut: Effect of mutation residue number 124 from chain A (tyrosine) into          
                       arginine: Energy difference: -0.1709 kcal/mol, Difference in average score  
                       from the base case: -0.0391                                                 (00:20:22)
[INFO]       Auto_mut: Effect of mutation residue number 174 from chain A (leucine) into glutamic  
                       acid: Energy difference: -0.9767 kcal/mol, Difference in average score from 
                       the base case: -0.0394                                                      (00:20:22)
[INFO]       Auto_mut: Effect of mutation residue number 174 from chain A (leucine) into lysine:   
                       Energy difference: -0.3320 kcal/mol, Difference in average score from the   
                       base case: -0.0430                                                          (00:20:22)
[INFO]       Auto_mut: Effect of mutation residue number 174 from chain A (leucine) into aspartic  
                       acid: Energy difference: -1.4251 kcal/mol, Difference in average score from 
                       the base case: -0.0400                                                      (00:20:22)
[INFO]       Auto_mut: Effect of mutation residue number 174 from chain A (leucine) into arginine: 
                       Energy difference: -0.0818 kcal/mol, Difference in average score from the   
                       base case: -0.0400                                                          (00:20:22)
[INFO]       Auto_mut: Effect of mutation residue number 110 from chain A (glycine) into glutamic  
                       acid: Energy difference: 2.2317 kcal/mol, Difference in average score from  
                       the base case: -0.0226                                                      (00:20:22)
[INFO]       Auto_mut: Effect of mutation residue number 110 from chain A (glycine) into lysine:   
                       Energy difference: 2.3254 kcal/mol, Difference in average score from the    
                       base case: -0.0222                                                          (00:20:22)
[INFO]       Auto_mut: Effect of mutation residue number 110 from chain A (glycine) into aspartic  
                       acid: Energy difference: 3.3119 kcal/mol, Difference in average score from  
                       the base case: -0.0076                                                      (00:20:22)
[INFO]       Auto_mut: Effect of mutation residue number 110 from chain A (glycine) into arginine: 
                       Energy difference: 2.3582 kcal/mol, Difference in average score from the    
                       base case: -0.0279                                                          (00:20:22)
[INFO]       Main:     Simulation completed successfully.                                          (00:20:27)
Show buried residues
Minimal score value
-4.5192
Maximal score value
0.9473
Average score
-1.2872
Total score value
-293.488
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 S A -1.6201
2 T A 0.0000
3 T A -0.6554
4 Q A 0.0000
5 I A 0.0000
6 P A 0.0000
7 Q A -1.6861
8 I A -1.6134
9 Q A -2.3009
10 K A -2.7714
11 T A -2.0492
12 E A -2.2401
13 I A 0.0000
14 S A -1.1920
15 F A 0.0000
16 R A -3.1601
17 P A -3.0972
18 N A -2.9913
19 D A -2.7775
20 P A -2.6758
21 K A -2.9256
22 S A -2.1992
23 Y A 0.0000
24 E A -2.3823
25 A A -1.0672
26 Y A -0.6615
27 V A 0.0000
28 L A -0.6090
29 N A -1.0521
30 I A 0.0000
31 V A -1.1833
32 R A -2.3248
33 F A -1.5295
34 L A 0.0000
35 E A -3.4445
36 K A -3.1144
37 Y A 0.0000
38 K A -3.7012
39 D A -3.8271
40 S A -2.5663
41 A A -2.6023
42 Q A 0.0000
43 R A -3.3625
44 D A -2.5832
45 D A -2.5856
46 M A -0.5267
47 I A -0.8679
48 F A 0.0000
49 E A -2.2220
50 D A -2.8133
51 C A -1.5755
52 G A -1.8376
53 D A -2.6340
54 S A -1.5439
55 P A -1.3661
56 S A -1.5062
57 E A -2.3335
58 P A -2.0773
59 K A -2.1493
60 E A -2.7858
61 R A -2.2431
62 G A -2.1873
63 D A -2.6365
64 F A -0.6364
65 N A -2.0127
66 H A -2.9337
67 E A -3.7757
68 R A -3.8638
69 G A -2.8946
70 E A -2.7499
71 R A 0.0000
72 K A -1.6545
73 V A 0.0000
74 C A 0.0000
75 R A -2.1500
76 F A 0.0000
77 K A -2.2792
78 L A 0.0000
79 E A -2.3362
80 W A -1.6554
81 L A 0.0000
82 G A -1.4196
83 N A -1.8580
84 C A 0.0000
85 S A 0.0000
86 G A -1.0884
87 L A -0.3260
88 N A -1.6971
89 D A -2.1781
90 E A -2.2174
91 T A -2.0861
92 Y A 0.0000
93 G A 0.0000
94 Y A 0.0000
95 K A -3.5773
96 E A -3.2277
97 G A -2.3732
98 K A -1.9149
99 P A 0.0000
100 C A 0.0000
101 I A 0.0000
102 I A 0.0000
103 I A 0.0000
104 K A -0.6137
105 L A 0.0000
106 N A -1.2990
107 R A -1.5355
108 V A -0.2557
109 L A 0.9473
110 G A -0.0202
111 F A -0.4879
112 K A -1.6718
113 P A 0.0000
114 K A -2.5918
115 P A -1.8958
116 P A 0.0000
117 K A -3.2230
118 N A -2.8050
119 E A -2.9099
120 S A -2.0509
121 L A 0.0000
122 E A -2.4862
123 T A -0.7790
124 Y A 0.4796
125 T A 0.0000
126 S A -0.7458
127 M A -0.9164
128 K A -1.8075
129 Y A -1.3556
130 N A -1.0239
131 P A -1.2693
132 N A -1.1453
133 V A 0.0000
134 L A 0.0000
135 P A 0.0000
136 V A 0.0000
137 D A -0.3462
138 C A 0.0000
139 T A -1.8566
140 G A 0.0000
141 K A -3.2431
142 R A -3.4691
143 D A -4.1626
144 E A -4.2239
145 D A 0.0000
146 K A -4.5192
147 D A -3.8946
148 K A -3.2005
149 V A 0.0000
150 G A -2.1950
151 N A -1.8404
152 V A -0.8670
153 E A -0.8669
154 Y A -0.4537
155 F A -0.7642
156 G A 0.0000
157 L A 0.0000
158 G A -1.6213
159 N A -1.6197
160 S A 0.0000
161 P A -0.6494
162 G A 0.0000
163 F A 0.0000
164 P A 0.0000
165 L A 0.0000
166 Q A 0.0000
167 Y A 0.0000
168 Y A 0.0000
169 P A 0.0000
170 Y A 0.0000
171 Y A 0.0000
172 G A 0.0000
173 K A -1.3443
174 L A 0.0956
175 L A 0.0000
176 Q A 0.0000
177 P A -1.1278
178 K A -1.3451
179 Y A 0.0000
180 L A 0.0000
181 Q A -0.7106
182 P A 0.0000
183 L A 0.0000
184 L A 0.0000
185 A A 0.0000
186 V A 0.0000
187 Q A 0.0000
188 F A 0.0000
189 T A -1.5107
190 N A -1.7381
191 L A -1.5191
192 T A -1.2812
193 M A -1.1785
194 D A -2.3933
195 T A -1.9776
196 E A -2.7200
197 I A 0.0000
198 R A -3.1182
199 I A 0.0000
200 E A 0.0000
201 C A 0.0000
202 K A -0.9124
203 A A 0.0000
204 Y A -0.6476
205 G A -1.7393
206 E A -2.6746
207 N A -1.7518
208 I A 0.0000
209 G A -1.2883
210 Y A -0.8992
211 S A -1.9960
212 E A -3.2283
213 K A -3.3297
214 D A -2.8830
215 R A -2.7774
216 F A -1.6711
217 Q A -1.9009
218 G A 0.0000
219 R A -1.3802
220 F A 0.0000
221 D A -2.4412
222 V A 0.0000
223 K A -2.2262
224 I A 0.0000
225 E A -2.0137
226 V A 0.0000
227 K A -2.3150
228 S A -1.5235
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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
LD174A -1.4251 -0.04 View CSV PDB
LE174A -0.9767 -0.0394 View CSV PDB
LR109A -0.3176 -0.0587 View CSV PDB
YK124A -0.0462 -0.0501 View CSV PDB
YR124A -0.1709 -0.0391 View CSV PDB
LK109A 0.429 -0.0546 View CSV PDB
GR110A 2.3582 -0.0279 View CSV PDB
GE110A 2.2317 -0.0226 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018