2R37

Crystal structure of human glutathione peroxidase 3 (selenocysteine to glycine mutant)

• PDB DOI: https://doi.org/10.2210/pdb2R37/pdb

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


• Deposited: 2007-08-29 Released: 2007-09-11 
• Deposition Author(s): Pilka, E.S., Guo, K., Gileadi, O., Rojkowa, A., von Delft, F., Pike, A.C.W., Kavanagh, K.L., Johannson, C., Sundstrom, M., Arrowsmith, C.H., Weigelt, J., Edwards, A.M., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.183 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 

Starting Model: experimental

Literature

Crystal structure of human glutathione peroxidase 3 (selenocysteine to glycine mutant).

Pilka, E.S., Guo, K., Gileadi, O., Rojkowa, A., von Delft, F., Pike, A.C.W., Kavanagh, K.L., Johannson, C., Sundstrom, M., Arrowsmith, C.H., Weigelt, J., Edwards, A.M., Oppermann, U.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 47.22 kDa 
• Atom Count: 3,462 
• Modelled Residue Count: 379 
• Deposited Residue Count: 414 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione peroxidase 3	A, B	207	Homo sapiens	Mutation(s): 1  Gene Names: GPX3, GPXP EC: 1.11.1.9
UniProt & NIH Common Fund Data Resources
Find proteins for P22352 (Homo sapiens) Explore P22352  Go to UniProtKB:  P22352
PHAROS:  P22352 GTEx:  ENSG00000211445

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.183 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.72	α = 90
b = 61.308	β = 90
c = 100.4	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-11 
Deposition Author(s): Pilka, E.S., Guo, K., Gileadi, O., Rojkowa, A., von Delft, F., Pike, A.C.W., Kavanagh, K.L., Johannson, C., Sundstrom, M., Arrowsmith, C.H., Weigelt, J., Edwards, A.M., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-09-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description