Project name: 43c60430d953a9 [mutate: LK89A]

Status: done

Started: 2023-09-25 13:52:38
Settings
Chain sequence(s) A: TCTHGLYKRTPRYPELLELLVSQCS
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) 0.474623 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                                                       (00:00:16)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:32)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:41)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:02:59)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:02:59)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:02:59)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:02:59)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:02:59)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:02:59)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:02:59)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:03:00)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:03:00)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:03:00)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:03:00)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:03:00)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:03:00)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:03:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:03:01)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:03:01)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:01)
Show buried residues

Minimal score value
-2.0541
Maximal score value
1.6566
Average score
-0.1901
Total score value
-4.752

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 0.0315
71 C A 0.2147
72 T A -0.0545
73 H A -0.1471
74 G A 0.7287
75 L A 1.5558
76 Y A 1.2348
77 K A -1.2378
78 R A -2.0541
79 T A -1.6931
80 P A -1.6632
81 R A -1.8131
82 Y A -0.0918
83 P A -0.6886
84 E A -1.7751
85 L A -0.1465
86 L A 0.2115
87 E A 0.0586
88 L A 1.6566
89 K A 0.8258 mutated: LK89A
90 V A 1.5130
91 S A 0.1440
92 Q A -0.9774
93 C A -0.2652
94 S A -0.3195
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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, -0.1901 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_10 -0.1901 View CSV PDB
model_3 -0.214 View CSV PDB
model_8 -0.219 View CSV PDB
model_0 -0.2214 View CSV PDB
model_1 -0.224 View CSV PDB
model_2 -0.2522 View CSV PDB
model_9 -0.3005 View CSV PDB
model_11 -0.3134 View CSV PDB
model_7 -0.3547 View CSV PDB
model_5 -0.3692 View CSV PDB
model_6 -0.4313 View CSV PDB
model_4 -0.5303 View CSV PDB
input -0.5528 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018