2VL3 Oxidoreductase date Jan 08, 2008
title Oxidized And Reduced Forms Of Human Peroxiredoxin 5
authors A.Smeets, J.P.Declercq
compound source
Molecule: Peroxiredoxin-5
Chain: A, B, C
Fragment: Residues 2-162
Synonym: Prx-V, Peroxisomal Antioxidant Enzyme, Plp, Thiore Reductase, Thioredoxin Peroxidase Pmp20, Antioxidant Enzyme Aoeb166, Tpx Type Vi, Liver Tissue 2d-Page Spot 71b, Alu Co 1, Human Peroxiredoxin 5;
Ec: 1.11.1.15
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Lung
Expression_system: Escherichia Coli M15
Expression_system_taxid: 1007065
Expression_system_plasmid: Pqe-30
symmetry Space Group: C 2 2 21
R_factor 0.235 R_Free 0.289
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.350 102.120 146.490 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.83 Å
ligand
enzyme Oxidoreductase E.C.1.11.1.15 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceThe crystal structures of oxidized forms of human peroxiredoxin 5 with an intramolecular disulfide bond confirm the proposed enzymatic mechanism for atypical 2-Cys peroxiredoxins., Smeets A, Marchand C, Linard D, Knoops B, Declercq JP, Arch Biochem Biophys. 2008 Sep 1;477(1):98-104. Epub 2008 May 4. PMID:18489898
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (84 Kb) [Save to disk]
  • Biological Unit Coordinates (2vl3.pdb1.gz) 53 Kb
  • Biological Unit Coordinates (2vl3.pdb2.gz) 53 Kb
  • CSU: Contacts of Structural Units for 2VL3
  • Likely Quarternary Molecular Structure file(s) for 2VL3
  • Structure Factors (707 Kb)
  • Retrieve 2VL3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VL3 from S2C, [Save to disk]
  • Re-refined 2vl3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VL3 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2VL3
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2VL3, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vl3] [2vl3_C] [2vl3_B] [2vl3_A]
  • SWISS-PROT database: [P30044]
  • Domain organization of [PRDX5_HUMAN] by SWISSPFAM
  • Other resources with information on 2VL3
  • Community annotation for 2VL3 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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