› 5ykw

X-ray diffraction
2.08Å resolution

Structural basis of the thiol resolving mechanism in yeast mitochondrial 1-Cys peroxiredoxin via glutathione/thioredoxin systems

Released:
DOI: 10.2210/pdb5ykw/pdb
PDB entry 5ykw coloured by chain, front view.
PDB entry 5ykw coloured by chain, side view.
PDB entry 5ykw coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Entry authors: Li CC, Yang J, Yang MJ, Liu L, Peng CT, Li T, He LH, Song YJ, Zhu YB, Zhao NL, Zhao C, Bao R

Function and Biology Details

Reactions catalysed: 
Glutaredoxin + ROOH = glutaredoxin disulfide + H(2)O + ROH
2 glutathione + ROOH = glutathione disulfide + H(2)O + ROH
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-150449 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Thioredoxin-3, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 106 amino acids
Theoretical weight: 11.84 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P25372 (Residues: 22-127; Coverage: 84%)
Gene names: TRX3, YCR083W, YCR83W
Sequence domains: Thioredoxin
Structure domains: Glutaredoxin
Peroxiredoxin PRX1, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 8 amino acids
Theoretical weight: 849 Da
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P34227 (Residues: 88-95; Coverage: 3%)
Gene names: PRX1, YBL0503, YBL0524, YBL064C

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P32
Unit cell:
a: 49.333Å b: 49.333Å c: 50.612Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.178 0.175 0.21
Expression system: Escherichia coli BL21(DE3)

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