3OEZ

crystal structure of the L317I mutant of the chicken c-Src tyrosine kinase domain complexed with imatinib

• PDB DOI: https://doi.org/10.2210/pdb3OEZ/pdb

• Classification: TRANSFERASE
• Organism(s): Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-08-13 Released: 2011-08-17 
• Deposition Author(s): Boubeva, R., Pernot, L., Perozzo, R., Scapozza, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.240 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Starting Model: experimental

Literature

a single amino-acid dictates the dynamics of the switch between active and inactive C-Src conformation

Boubeva, R., Pernot, L., Cristiani, A., Moretti, L., Berteotti, A., Perozzo, R., Gervasio, F., Scapozza, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.59 kDa 
• Atom Count: 4,576 
• Modelled Residue Count: 522 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A, B	286	Gallus gallus	Mutation(s): 1  Gene Names: SRC EC: 2.7.10.2
UniProt
Find proteins for P00523 (Gallus gallus) Explore P00523  Go to UniProtKB:  P00523

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STI	C [auth A], F [auth B]	4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE C29 H31 N7 O KTUFNOKKBVMGRW-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
STI	BindingDB:  3OEZ	Ki: min: 1.00e+4, max: 3.10e+4 (nM) from 2 assay(s)
		Kd: min: 1.00e+4, max: 3.98e+4 (nM) from 3 assay(s)
		IC50: min: 2784, max: 1.00e+5 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.240 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.895	α = 79.16
b = 63.426	β = 90.02
c = 74.145	γ = 90.19

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-17 
Deposition Author(s): Boubeva, R., Pernot, L., Perozzo, R., Scapozza, L.

Revision History  

• Version 1.0: 2011-08-17
  Type: Initial release
  
• Version 1.1: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary