2HE3 | pdb_00002he3

Crystal structure of the selenocysteine to cysteine mutant of human glutathionine peroxidase 2 (GPX2)

• PDB DOI: https://doi.org/10.2210/pdb2HE3/pdb

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


• Deposited: 2006-06-21 Released: 2006-07-25 
• Deposition Author(s): Johansson, C., Kavanagh, K.L., Rojkova, A., Gileadi, O., von Delft, F., Arrowsmith, C., Weigelt, J., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.205 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the selenocysteine to cysteine mutant of human glutathionine peroxidase 2 (GPX2)

Kavanagh, K.L., Oppermann, U.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 24.19 kDa 
• Atom Count: 1,657 
• Modeled Residue Count: 185 
• Deposited Residue Count: 208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione peroxidase 2	A	208	Homo sapiens	Mutation(s): 1  Gene Names: GPX2 EC: 1.11.1.9 (PDB Primary Data), 1.11.1.12 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P18283 (Homo sapiens) Explore P18283  Go to UniProtKB:  P18283
PHAROS:  P18283 GTEx:  ENSG00000176153

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.205 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.308	α = 90
b = 117.212	β = 90
c = 120.157	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-25 
Deposition Author(s): Johansson, C., Kavanagh, K.L., Rojkova, A., Gileadi, O., von Delft, F., Arrowsmith, C., Weigelt, J., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-07-25
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2018-01-31
  Changes: Structure summary
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-08-30
  Changes: Data collection, Refinement description