Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.82 kDa 
• Atom Count: 2903 
• Modelled Residue Count: 335 
• Deposited Residue Count: 359 
• Unique protein chains: 1

4I5H

Crystal Structure of a Double Mutant Rat Erk2 Complexed With a Type II Quinazoline Inhibitor

• PDB DOI: 10.2210/pdb4I5H/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-11-28 Released: 2013-07-10 
• Deposition Author(s): Hari, S.B., Maly, D.J., Merritt, E.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.257 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

Literature

Sequence determinants of a specific inactive protein kinase conformation.

Hari, S.B., Merritt, E.A., Maly, D.J.

(2013) Chem Biol 20: 806-815

• PubMed: 23790491 
• DOI: 10.1016/j.chembiol.2013.05.005
• Primary Citation of Related Structures:  
  4I5H


• PubMed Abstract: 
  

Only a small percentage of protein kinases have been shown to adopt a distinct inactive ATP-binding site conformation, called the Asp-Phe-Gly-out (DFG-out) conformation. Given the high degree of homology within this enzyme family, we sought to understand the basis of this disparity on a sequence level. We identified two residue positions that sensitize mitogen-activated protein kinases (MAPKs) to inhibitors that stabilize the DFG-out inactive conformation. After characterizing the structure and dynamics of an inhibitor-sensitive MAPK mutant, we demonstrated the generality of this strategy by sensitizing a kinase (apoptosis signal-regulating kinase 1) not in the MAPK family to several DFG-out stabilizing ligands, using the same residue positions. The use of specific inactive conformations may aid the study of noncatalytic roles of protein kinases, such as binding partner interactions and scaffolding effects.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	359	Rattus norvegicus	Mutation(s): 2  Gene Names: Erk2, Mapk, Mapk1, Prkm1 EC: 2.7.11.24
UniProt
Find proteins for P63086 (Rattus norvegicus) Explore P63086  Go to UniProtKB:  P63086

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G17	B [auth A]	N-{3-[2-(cyclopropylamino)quinazolin-6-yl]-4-methylphenyl}-3-(trifluoromethyl)benzamide C26 H21 F3 N4 O BYBFDHQBBWQPTD-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
G17	PDBBind:  4I5H	Ki: 2 (nM) from 1 assay(s)
	Binding MOAD:  4I5H	Ki: 2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.257 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.24	α = 90
b = 77.24	β = 90
c = 121.791	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-28 
• Released Date: 2013-07-10 
Deposition Author(s): Hari, S.B., Maly, D.J., Merritt, E.A.

Revision History  

• Version 1.0: 2013-07-10
  Type: Initial release