Project name: f71c487ed6b3f55 [mutate: MI46A]

Status: done

Started: 2020-04-05 14:01:34
Settings
Chain sequence(s) A: LTQPPSTSGTPGQRVTISCSGSSSNIETNTVNWYQQLPGTAPKLVMHTNNQRPSGVPDRFSGSRSGTSASLAIGGLQSEDEADYFCAAWDDNLNGVIFGGGTKLTVL
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Mutated residues MI46A
Energy difference between WT (input) and mutated protein (by FoldX) 1.94006 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure

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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]       FoldX:    Building mutant model                                                       (00:00:37)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:38)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:53)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:21:38)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:21:39)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:21:39)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:21:39)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:21:40)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:21:40)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:21:41)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:21:41)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:21:42)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:21:42)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:21:42)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:21:43)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:21:43)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:21:45)
[INFO]       Movie:    Creting movie with webm format                                              (00:23:28)
[INFO]       Main:     Simulation completed successfully.                                          (00:23:31)
Show buried residues

Minimal score value
-2.4057
Maximal score value
2.9772
Average score
-0.5519
Total score value
-59.0519

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 L A 1.9721
2 T A 0.9591
3 Q A 0.0000
4 P A -0.6621
5 P A -0.6664
6 S A -0.8759
7 T A -0.9103
8 S A -0.8197
9 G A -0.8183
10 T A -0.5383
11 P A -0.6238
12 G A -1.2300
13 Q A -1.7028
14 R A -2.2616
15 V A 0.0000
16 T A -0.8254
17 I A 0.0000
18 S A -0.6103
19 C A 0.0000
20 S A -0.1003
21 G A 0.1653
22 S A 0.1521
23 S A -0.0926
24 S A -0.7593
25 N A -0.6524
26 I A 0.4434
27 E A -1.6312
28 T A -1.1569
29 N A -1.1331
30 T A -0.7592
31 V A 0.0000
32 N A 0.5833
33 W A 0.0000
34 Y A 0.5938
35 Q A 0.0000
36 Q A -0.7602
37 L A 0.0000
38 P A -1.3364
39 G A -1.0176
40 T A -0.5418
41 A A -0.3630
42 P A -0.4099
43 K A -0.4672
44 L A -0.1809
45 V A 0.0000
46 I A 0.0000 mutated: MI46A
47 H A -1.1760
48 T A -1.3496
49 N A -1.9527
50 N A -2.2343
51 Q A -2.1470
52 R A -2.4057
53 P A -1.6715
54 S A -1.1212
55 G A -0.9280
56 V A -1.2055
57 P A -1.5403
58 D A -2.2688
59 R A -2.0501
60 F A -0.3020
61 S A -0.3660
62 G A 0.0000
63 S A -0.9152
64 R A -1.6148
65 S A -1.0423
66 G A -0.9988
67 T A -0.4597
68 S A -0.6109
69 A A 0.0000
70 S A -0.6966
71 L A 0.0000
72 A A -0.2998
73 I A 0.0000
74 G A -1.5415
75 G A -1.5073
76 L A 0.0000
77 Q A -1.6021
78 S A -1.0247
79 E A 0.0000
80 D A -2.3409
81 E A -2.3221
82 A A 0.0000
83 D A -1.1389
84 Y A 0.0000
85 F A 0.8803
86 C A 0.0000
87 A A 0.0000
88 A A 0.0000
89 W A 0.9085
90 D A -0.8469
91 D A -1.6984
92 N A -1.5819
93 L A -0.1483
94 N A -1.0484
95 G A -0.3514
96 V A 1.3466
97 I A 2.2373
98 F A 2.9772
99 G A 1.3317
100 G A 0.0000
101 G A -0.6264
102 T A 0.0000
103 K A -1.4898
104 L A 0.0000
105 T A -1.2751
106 V A 0.0000
107 L A 0.2052
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CABS-flex predictions of flexibility of input structure

In dynamic mode, A3D 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 A3D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A3D score, -0.5519 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 A3D Score
model_1 -0.5519 View CSV PDB
model_5 -0.5979 View CSV PDB
model_10 -0.6061 View CSV PDB
model_2 -0.6222 View CSV PDB
model_9 -0.6406 View CSV PDB
model_6 -0.6496 View CSV PDB
model_3 -0.6548 View CSV PDB
input -0.6615 View CSV PDB
model_4 -0.7021 View CSV PDB
model_7 -0.7355 View CSV PDB
model_11 -0.7421 View CSV PDB
model_8 -0.7996 View CSV PDB
model_0 -0.8407 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018