1Y9D Oxidoreductase date Dec 15, 2004
title Pyruvate Oxidase Variant V265a From Lactobacillus Plantarum
authors G.Wille, M.Ritter, M.S.Weiss, S.Konig, W.Mantele, G.Hubner
compound source
Molecule: Pyruvate Oxidase
Chain: A, B, C, D
Synonym: Pyruvic Oxidase, Pox
Ec: 1.2.3.3
Engineered: Yes
Mutation: Yes
Organism_scientific: Lactobacillus Plantarum
Organism_taxid: 1590
Gene: Pox5
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: C600
symmetry Space Group: P 1 21 1
R_factor 0.178 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
94.660 155.780 100.750 90.00 92.92 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand FAD, MG, NA, SO4, TPP enzyme Oxidoreductase E.C.1.2.3.3 BRENDA
related structures by homologous chain: 1POW, 1POX
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceThe role of Val-265 for flavin adenine dinucleotide (FAD) binding in pyruvate oxidase: FTIR, kinetic, and crystallographic studies on the enzyme variant V265A., Wille G, Ritter M, Weiss MS, Konig S, Mantele W, Hubner G, Biochemistry 2005 Apr 5;44(13):5086-94. PMID:15794646
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (392 Kb) [Save to disk]
  • Biological Unit Coordinates (1y9d.pdb1.gz) 382 Kb
  • LPC: Ligand-Protein Contacts for 1Y9D
  • CSU: Contacts of Structural Units for 1Y9D
  • Likely Quarternary Molecular Structure file(s) for 1Y9D
  • Structure Factors (2255 Kb)
  • Retrieve 1Y9D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y9D from S2C, [Save to disk]
  • Re-refined 1y9d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Y9D 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 1Y9D
  • 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 1Y9D, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y9d_B] [1y9d] [1y9d_D] [1y9d_C] [1y9d_A]
  • SWISS-PROT database: [P37063]
  • Domain organization of [POXB_LACPL] by SWISSPFAM
  • Other resources with information on 1Y9D
  • Community annotation for 1Y9D 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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