3CYN | pdb_00003cyn

The structure of human GPX8

• PDB DOI: https://doi.org/10.2210/pdb3CYN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-04-25 Released: 2008-08-12 
• Deposition Author(s): Kavanagh, K.L., Johansson, C., Yue, W.W., Kochan, G., Pike, A.C.W., Murray, J., Roos, A.K., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Wikstrom, M., Edwards, A.M., Bountra, C., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

The structure of human GPX8

Kavanagh, K.L., Johansson, C., Yue, W.W., Kochan, G., Oppermann, U.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.51 kDa 
• Atom Count: 4,506 
• Modeled Residue Count: 523 
• Deposited Residue Count: 567 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable glutathione peroxidase 8	A, B, C	189	Homo sapiens	Mutation(s): 0  Gene Names: LOC493869 EC: 1.11.1.9
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TED1 (Homo sapiens) Explore Q8TED1  Go to UniProtKB:  Q8TED1
PHAROS:  Q8TED1 GTEx:  ENSG00000164294

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], F [auth B], G [auth B], H [auth B], I [auth B], K [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], J [auth B], L [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.688	α = 90
b = 120.854	β = 119.38
c = 75.603	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: 2008-08-12 
Deposition Author(s): Kavanagh, K.L., Johansson, C., Yue, W.W., Kochan, G., Pike, A.C.W., Murray, J., Roos, A.K., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Wikstrom, M., Edwards, A.M., Bountra, C., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2018-01-31
  Changes: Structure summary
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description