Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 70.18 kDa 
• Atom Count: 4499 
• Modelled Residue Count: 556 
• Deposited Residue Count: 604 
• Unique protein chains: 1

4EQU

Human STK-10 (LOK) kinase domain in DFG-out conformation with inhibitor DSA-7

• PDB DOI: 10.2210/pdb4EQU/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-19 Released: 2012-11-07 
• Deposition Author(s): Merritt, E.A., Larson, E.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.246 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 

Literature

Affinity-Based Probes Based on Type II Kinase Inhibitors.

Ranjitkar, P., Perera, B.G., Swaney, D.L., Hari, S.B., Larson, E.T., Krishnamurty, R., Merritt, E.A., Villen, J., Maly, D.J.

(2012) J Am Chem Soc 134: 19017-19025

• PubMed: 23088519 
• DOI: 10.1021/ja306035v
• Primary Citation of Related Structures:  
  4EQU


• PubMed Abstract: 
  

Protein kinases are key components of most mammalian signal transduction networks and are therapeutically relevant drug targets. Efforts to study protein kinase function would benefit from new technologies that are able to profile kinases in complex proteomes. Here, we describe active site-directed probes for profiling kinases in whole cell extracts and live cells. These probes contain general ligands that stabilize a specific inactive conformation of the ATP-binding sites of protein kinases, as well as trifluoromethylphenyl diazirine and alkyne moieties that allow covalent modification and enrichment of kinases, respectively. A diverse group of serine/threonine and tyrosine kinases were identified as specific targets of these probes in whole cell extracts. In addition, a number of kinase targets were selectively labeled in live cells. Our chemical proteomics approach should be valuable for interrogating protein kinase active sites in physiologically relevant environments.

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Organizational Affiliation: 

Department of Chemistry, University of Washington, Seattle, Washington 98195, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase 10	A, B	302	Homo sapiens	Mutation(s): 0  Gene Names: STK10, LOK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O94804 (Homo sapiens) Explore O94804  Go to UniProtKB:  O94804
PHAROS:  O94804 GTEx:  ENSG00000072786

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G6I	C [auth A], F [auth B]	N-{3-[(3-{4-[(4-methoxyphenyl)amino]-1,3,5-triazin-2-yl}pyridin-2-yl)amino]-4-methylphenyl}-3-(trifluoromethyl)benzamide C30 H24 F3 N7 O2 FLZNVZVIUIDCOF-UHFFFAOYSA-N
1PE	J [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
CA	D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.246 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.81	α = 90
b = 49.04	β = 101.42
c = 133.76	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-19 
• Released Date: 2012-11-07 
Deposition Author(s): Merritt, E.A., Larson, E.T.

Revision History  

• Version 1.0: 2012-11-07
  Type: Initial release
  
• Version 1.1: 2012-11-14
  Changes: Structure summary
• Version 1.2: 2012-12-19
  Changes: Database references