Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.11 kDa 
• Atom Count: 2286 
• Residue Count: 263 
• Unique protein chains: 1

2DQ7

Crystal Structure of Fyn kinase domain complexed with staurosporine

• DOI: 10.2210/pdb2DQ7/pdb

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


• Deposited: 2006-05-23 Released: 2006-07-04 
• Deposition Author(s): Kinoshita, T., Tada, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.281 
• R-Value Work: 0.255 

Literature

Structure of human Fyn kinase domain complexed with staurosporine.

Kinoshita, T., Matsubara, M., Ishiguro, H., Okita, K., Tada, T.

(2006) Biochem Biophys Res Commun 346: 840-844

• PubMed: 16782058 
• DOI: 10.1016/j.bbrc.2006.05.212
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The tyrosine kinase Fyn is a member of the Src kinase family. Besides the role of Fyn in T cell signal transduction in concert with Lck, its excess activity in the brain is involved with conditions such as Alzheimer's and Parkinson's diseases. Therefore, inhibition of Fyn kinase may help counteract these nervous system disorders. Here, we solved the crystal structure of the human Fyn kinase domain complexed with staurosporine, a potent kinase inhibitor, at 2.8 A resolution. Staurosporine binds to the ATP-binding site of Fyn in a similar manner as in the Lck- and Csk-complexes. The small structural differences in the staurosporine-binding and/or -unbinding region among the three kinase domains may help obtaining the selective inhibitors against the respective kinases.

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Organizational Affiliation: 

Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Gakuencho 1-1, Sakai, Osaka 599-8531, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Proto-oncogene tyrosine-protein kinase Fyn	X	283	Homo sapiens	Mutation(s): 0  Gene Names: FYN EC: 2.7.10.2
Find proteins for P06241 (Homo sapiens) Explore P06241  Go to UniProtKB:  P06241
NIH Common Fund Data Resources
PHAROS  P06241 GTEx  ENSG00000010810

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	X	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
STO	Kd:  49   nM  BindingDB
STO	Kd:  33   nM  BindingDB
STO	IC50:  4.400000095367432   nM  BindingDB
STO	IC50:  2.4000000953674316   nM  BindingDB
STO	Kd:  52   nM  BindingDB
STU	IC50 :  4.800000190734863   nM  PDBBind
STO	IC50:  4.400000095367432   nM  BindingDB
STO	Kd:  51   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.281 
• R-Value Work: 0.255 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.962	α = 90
b = 52.962	β = 90
c = 210.989	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-05-23 
• Released Date: 2006-07-04 
Deposition Author(s): Kinoshita, T., Tada, T.

Revision History 

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2015-04-22
  Changes: Structure summary