4Y92

Crystal structure of the intertwined form of the Src tyrosine kinase SH3 domain E97T-Q128R mutant

• PDB DOI: https://doi.org/10.2210/pdb4Y92/pdb

• Classification: TRANSFERASE
• Organism(s): Avian sarcoma virus PR2257/16
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-02-16 Released: 2016-03-02 
• Deposition Author(s): Camara-Artigas, A., Bacarizo, J.
• Funding Organization(s): Junta de Andalucia, Spanish Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.233 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Literature

Crystal structure of the intertwined form of the Src tyrosine kinase SH3 domain E97T-Q128R mutant

Camara-Artigas, A., Bacarizo, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 7.52 kDa 
• Atom Count: 481 
• Modelled Residue Count: 56 
• Deposited Residue Count: 61 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-tyrosine kinase	A	61	Avian sarcoma virus PR2257/16	Mutation(s): 2  Gene Names: src
UniProt
Find proteins for Q64817 (Avian sarcoma virus PR2257/16) Explore Q64817  Go to UniProtKB:  Q64817

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	B [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.233 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.29	α = 90
b = 46.29	β = 90
c = 126.55	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Camara-Artigas, A., Bacarizo, J.

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Funding Organization	Location	Grant Number
Junta de Andalucia	Spain	P09-CVI-5063
Spanish Ministry of Economy and Competitiveness	Spain	BIO2012-39922-C02-02

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 2.0: 2017-09-13
  Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description