7A2W

Crystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R123H mutant in complex with VSL12 at pH 3.0

PDB DOI: https://doi.org/10.2210/pdb7A2W/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: 0.99 Å
R-Value Free: 0.151
R-Value Work: 0.131
R-Value Observed: 0.132

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 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 3.0

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

To be published.

Macromolecule Content

Total Structure Weight: 8.38 kDa
Atom Count: 769
Modelled Residue Count: 74
Deposited Residue Count: 74
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase Fyn	A	61	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	B	13	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.99 Å
R-Value Free: 0.151
R-Value Work: 0.131
R-Value Observed: 0.132
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.905	α = 90
b = 32.884	β = 90
c = 62.796	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
Version 1.2: 2024-10-23
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.