3EZZ

Crystal Structure of human MKP-2

• PDB DOI: https://doi.org/10.2210/pdb3EZZ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-10-24 Released: 2009-08-25 
• Deposition Author(s): Jeong, D.G., Jung, S.K., Ryu, S.E., Kim, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.242 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

Starting Model: experimental

Literature

Crystal structure of the catalytic domain of human MKP-2 reveals a 24-mer assembly.

Jeong, D.G., Jung, S.K., Yoon, T.S., Woo, E.J., Kim, J.H., Park, B.C., Ryu, S.E., Kim, S.J.

(2009) Proteins 76: 763-767

• PubMed: 19415758 
• DOI: https://doi.org/10.1002/prot.22423
• Primary Citation of Related Structures:  
  3EZZ

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Organizational Affiliation: 

Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-Gu, Daejeon, Republic of Korea.

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

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

Macromolecule Content

• Total Structure Weight: 98.99 kDa 
• Atom Count: 6,921 
• Modelled Residue Count: 864 
• Deposited Residue Count: 864 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein phosphatase 4	A, B, C, D, E, F	144	Homo sapiens	Mutation(s): 1  Gene Names: DUSP4, MKP2, VH2 EC: 3.1.3.48 (PDB Primary Data), 3.1.3.16 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13115 (Homo sapiens) Explore Q13115  Go to UniProtKB:  Q13115
PHAROS:  Q13115 GTEx:  ENSG00000120875

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth A], I [auth B], J [auth C], K [auth C], L [auth D], M [auth D], N [auth E], O [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.242 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.557	α = 90
b = 141.557	β = 90
c = 158.532	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-25 
Deposition Author(s): Jeong, D.G., Jung, S.K., Ryu, S.E., Kim, S.J.

Revision History  

• Version 1.0: 2009-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description