› 5h5s

X-ray diffraction
1.85Å resolution

Crystal structure of human GPX4 in complex with GXpep-3

Released:
DOI: 10.2210/pdb5h5s/pdb
PDB entry 5h5s coloured by chain, front view.
PDB entry 5h5s coloured by chain, side view.
PDB entry 5h5s coloured by chain, top view.
Source organisms:
Primary publication:
Discovery of GPX4 inhibitory peptides from random peptide T7 phage display and subsequent structural analysis.
Sakamoto K, Sogabe S, Kamada Y, Matsumoto SI, Kadotani A, Sakamoto JI, Tani A
Biochem Biophys Res Commun 482 195-201 (2017)
PMID: 27836545

Function and Biology Details

Reactions catalysed: 
2 glutathione + a hydroperoxy-fatty-acyl-[lipid] = glutathione disulfide + a hydroxy-fatty-acyl-[lipid] + H(2)O
2 glutathione + H(2)O(2) = glutathione disulfide + 2 H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153275 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Phospholipid hydroperoxide glutathione peroxidase GPX4 Chain: A
Molecule details ›
Chain: A
Length: 169 amino acids
Theoretical weight: 19.4 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P36969 (Residues: 29-197; Coverage: 86%)
Gene name: GPX4
Sequence domains: Glutathione peroxidase
Structure domains: Glutaredoxin
GXpep-3 Chain: B
Molecule details ›
Chain: B
Length: 14 amino acids
Theoretical weight: 1.56 KDa
Source organism: Escherichia phage T7
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand GOL 1 x GOL
1 modified residue:
Ligand CSD 1 x CSD

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P21
Unit cell:
a: 35.017Å b: 39.077Å c: 59.394Å
α: 90° β: 97.84° γ: 90°
R-values:
R R work R free
0.168 0.166 0.204
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

T7 Phage as an Emerging Nanobiomaterial with Genetically Tunable Target Specificity.
Yue et al. (2022)
2 more

3 mentions without citation

Development of therapies for rare genetic disorders of GPX4: roadmap and opportunities.
Cheff et al. (2021)
2 more