Aggrescan3D: 8d424639f658f08 [mutate: LK94A, LK75A]

Project name: 8d424639f658f08 [mutate: LK94A, LK75A]

Status: done

Started: 2023-09-25 13:13:45

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Chain sequence(s)	A: PSTHVLLTHTISRIAVSYQTPVNLLSAIRSPCQ input PDB
Selected Chain(s)	A
Distance of aggregation	10 Å
FoldX usage	Yes
Dynamic mode	Yes
Automated mutations	No
Mutated residues	LK94A,LK75A
Energy difference between WT (input) and mutated protein (by FoldX)	0.438142 kcal/mol
Downloads	Download all the data

Simulation log

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[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                                                       (00:00:09)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:22)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:30)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:03:30)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:03:30)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:03:31)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:03:31)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:03:31)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:03:31)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:03:31)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:03:31)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:03:31)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:03:32)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:03:32)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:03:32)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:03:32)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:03:32)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:03:33)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:03:33)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:33)

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Show buried residues

Minimal score value: -1.0244
Maximal score value: 2.1197
Average score: 0.1654
Total score value: 5.4595

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
70	P	A	-0.5886
71	S	A	-0.7396
72	T	A	-0.5557
73	H	A	-0.7144
74	V	A	0.5936
75	K	A	-0.2999	mutated: LK75A
76	L	A	1.0116
77	T	A	0.7288
78	H	A	0.0801
79	T	A	0.1370
80	I	A	0.2052
81	S	A	-0.3002
82	R	A	-0.3913
83	I	A	1.4598
84	A	A	1.5225
85	V	A	2.1197
86	S	A	1.2415
87	Y	A	1.6127
88	Q	A	0.2892
89	T	A	0.2916
90	P	A	0.2392
91	V	A	0.5138
92	N	A	-0.4712
93	L	A	0.2940
94	K	A	-0.7835	mutated: LK94A
95	S	A	-0.5188
96	A	A	0.1204
97	I	A	1.1443
98	R	A	-0.6808
99	S	A	-0.5021
100	P	A	-0.3067
101	C	A	-0.2683
102	Q	A	-1.0244

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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, 0.1654 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_2	0.1654	View	CSV	PDB
model_11	0.1249	View	CSV	PDB
model_9	0.1033	View	CSV	PDB
model_4	0.0327	View	CSV	PDB
model_0	0.0116	View	CSV	PDB
model_6	-0.003	View	CSV	PDB
model_3	-0.0375	View	CSV	PDB
model_7	-0.0924	View	CSV	PDB
model_8	-0.1212	View	CSV	PDB
model_5	-0.1557	View	CSV	PDB
model_10	-0.2365	View	CSV	PDB
input	-0.276	View	CSV	PDB
model_1	-0.3653	View	CSV	PDB

Project name: 8d424639f658f08 [mutate: LK94A, LK75A]

Status: done

Started: 2023-09-25 13:13:45

CABS-flex predictions of flexibility of input structure

Model

Average A3D Score