Project name: d2ea3f2bd10e2 [mutate: LK89A]

Status: done

Started: 2023-09-25 14:10:34
Settings
Chain sequence(s) A: TCTHGLYKRTPRYPEELLLLVSQCS
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Mutated residues LK89A
Energy difference between WT (input) and mutated protein (by FoldX) 0.64132 kcal/mol
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]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:00:13)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:27)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:37)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:02:54)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:02:54)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:02:54)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:02:54)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:02:54)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:02:54)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:02:54)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:02:54)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:02:55)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:02:55)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:02:55)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:02:55)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:02:55)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:02:56)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:56)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:02:56)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:56)
Show buried residues

Minimal score value
-2.8236
Maximal score value
2.2787
Average score
-0.21
Total score value
-5.2503

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
70 T A 0.0796
71 C A 0.3052
72 T A -0.1813
73 H A -0.2382
74 G A 0.8022
75 L A 1.8037
76 Y A 1.9681
77 K A -0.4587
78 R A -1.6346
79 T A -1.8406
80 P A -1.7556
81 R A -2.5659
82 Y A -0.6474
83 P A -1.5293
84 E A -2.8236
85 E A -1.8885
86 L A 0.3959
87 L A 1.9334
88 L A 2.2787
89 K A 0.5242 mutated: LK89A
90 V A 1.2435
91 S A -0.0361
92 Q A -0.8416
93 C A 0.0534
94 S A -0.1968
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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, -0.21 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 -0.21 View CSV PDB
model_9 -0.2466 View CSV PDB
model_11 -0.2819 View CSV PDB
input -0.289 View CSV PDB
model_0 -0.3342 View CSV PDB
model_3 -0.3382 View CSV PDB
model_10 -0.3393 View CSV PDB
model_5 -0.3793 View CSV PDB
model_2 -0.383 View CSV PDB
model_7 -0.4148 View CSV PDB
model_6 -0.4199 View CSV PDB
model_8 -0.4414 View CSV PDB
model_4 -0.5431 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018