2I3Y

Crystal structure of human glutathione peroxidase 5

Structural Biology Knowledgebase: 2I3Y SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.175

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2I3Y

Classification: oxidoreductase

Total Structure Weight: 24648.34

Macromolecule Entities
Molecule Chains Length Organism Details
Epididymal secretory glutathione peroxidase A 215 Homo sapiens EC#: 1.11.1.9 IUBMB
Gene Name(s): GPX5 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.175
  • Space Group: P 62 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 104.54 α = 90.00
b = 104.54 β = 90.00
c = 71.66 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-08-21
  • Released Date: 2006-09-12
  • Deposition author(s): Kavanagh, K.L., Johansson, C., Rojkova, A., Umeano, C., Bunkoczi, G., Gileadi, O., Von Delft, F., Weigelt, J., Arrowsmith, C., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor