7A2X

Crystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R123H mutant in complex with VSL12 at pH 5.0

PDB DOI: https://doi.org/10.2210/pdb7A2X/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-08-18 Released: 2021-08-25
Deposition Author(s): Camara-Artigas, A., Plaza-Garrido, M., Salinas-Garcia, M.C.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.92 Å
R-Value Free: 0.148
R-Value Work: 0.130
R-Value Observed: 0.131

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R123H mutant in complex with VSL12 at pH 5.0

Camara-Artigas, A., Plaza-Garrido, M., Salinas-Garcia, M.C.

To be published.

Macromolecule Content

Total Structure Weight: 8.13 kDa
Atom Count: 827
Modelled Residue Count: 73
Deposited Residue Count: 73
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase Fyn	A	60	Homo sapiens	Mutation(s): 5 Gene Names: FYN EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P06241 (Homo sapiens) Explore P06241 Go to UniProtKB: P06241
PHAROS: P06241 GTEx: ENSG00000010810
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06241
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VSL12 high affinity synthetic peptide acetylated in the amino-terminus	B	13	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.92 Å
R-Value Free: 0.148
R-Value Work: 0.130
R-Value Observed: 0.131
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.897	α = 90
b = 33.1	β = 90
c = 62.624	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-08-25

Deposition Author(s):

Camara-Artigas, A.

Plaza-Garrido, M.

Salinas-Garcia, M.C.

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BIO2016-78020-R

Revision History (Full details and data files)

Version 1.0: 2021-08-25
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.