4FV3 | pdb_00004fv3

Crystal Structure of the ERK2 complexed with EK6

• PDB DOI: https://doi.org/10.2210/pdb4FV3/pdb

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


• Deposited: 2012-06-29 Released: 2012-08-29 
• Deposition Author(s): Kang, Y.N., Stuckey, J.A., Xie, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.236 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6DMG

Literature

Crystal Structure of the ERK2 complexed with EK6

Kang, Y.N., Stuckey, J.A., Xie, X.

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)

Macromolecule Content

• Total Structure Weight: 42.57 kDa 
• Atom Count: 3,058 
• Modelled Residue Count: 347 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	360	Homo sapiens	Mutation(s): 0  Gene Names: ERK2, MAPK1, PRKM1, PRKM2 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens) Explore P28482  Go to UniProtKB:  P28482
PHAROS:  P28482 GTEx:  ENSG00000100030

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EK6	B [auth A]	ethyl N-{2-chloro-4-[5-(5-{[(1S)-1-(3-chloro-4-fluorophenyl)-2-hydroxyethyl]carbamoyl}-1H-pyrrol-3-yl)-1H-pyrazol-4-yl]benzyl}glycinate C27 H26 Cl2 F N5 O4 VVRLXUNPTACSJC-XMMPIXPASA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.236 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.78	α = 90
b = 70.7	β = 110.11
c = 60.86	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Kang, Y.N., Stuckey, J.A., Xie, X.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Structure summary
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary