3A4O

Lyn kinase domain

• PDB DOI: https://doi.org/10.2210/pdb3A4O/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2009-07-11 Released: 2009-12-08 
• Deposition Author(s): Miyano, N., Kinoshita, T., Tada, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.324 
• R-Value Work: 0.293 

Starting Model: experimental

Literature

Structural basis for the inhibitor recognition of human Lyn kinase domain

Miyano, N., Kinoshita, T., Nakai, R., Kirii, Y., Yokota, K., Tada, T.

(2009) Bioorg Med Chem Lett 19: 6557-6560

• PubMed: 19857964 
• DOI: https://doi.org/10.1016/j.bmcl.2009.10.038
• Primary Citation of Related Structures:  
  3A4O


• PubMed Abstract: 
  

  Human Lyn tyrosine kinase is expressed in hematopoietic tissues and plays crucial roles in the signal transduction of hematopoietic immune system. Its excess activity is involved in several tumors. The crystal structure has revealed that the potent inhibitor staurosporine binds to human Lyn kinase domain at the ATP-binding site. The remarkable structural features of the staurosporine-binding region will offer valuable structural insights for the structure-based design of novel Lyn-selective inhibitors.

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Organizational Affiliation: 

Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 33.46 kDa 
• Atom Count: 2,112 
• Modelled Residue Count: 259 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase Lyn	A [auth X]	286	Homo sapiens	Mutation(s): 0  EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P07948 (Homo sapiens) Explore P07948  Go to UniProtKB:  P07948
PHAROS:  P07948 GTEx:  ENSG00000254087

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STU	B [auth X]	STAUROSPORINE C28 H26 N4 O3 HKSZLNNOFSGOKW-FYTWVXJKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
STU	PDBBind:  3A4O	IC50: 1.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.324 
• R-Value Work: 0.293 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.382	α = 90
b = 128.382	β = 90
c = 54.875	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-08 
Deposition Author(s): Miyano, N., Kinoshita, T., Tada, T.

Revision History  

• Version 1.0: 2009-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description