5YKJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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

Li, C.C.Yang, J.Yang, M.J.Liu, L.Peng, C.T.Li, T.He, L.H.Song, Y.J.Zhu, Y.B.Zhao, N.L.Zhao, C.Bao, R.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxiredoxin PRX1, mitochondrialA214Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRX1YBL064CYBL0503YBL0524
EC: 1.11.1.15 (PDB Primary Data), 1.11.1.25 (UniProt), 1.11.1.27 (UniProt)
UniProt
Find proteins for P34227 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P34227 
Go to UniProtKB:  P34227
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
AL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.03α = 90
b = 84.03β = 90
c = 62.784γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references