3HY8 Oxidoreductase date Jun 22, 2009
title Crystal Structure Of Human Pyridoxine 5'-Phosphate Oxidase R Mutant
authors M.K.Safo, F.N.Musayev, M.L.Di Salvo, M.K.Saavedra, V.Schirch
compound source
Molecule: Pyridoxine-5'-Phosphate Oxidase
Chain: A
Synonym: Pyridoxamine-Phosphate Oxidase
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pnpo
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta(Lambdade3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: P 31 2 1
R_factor 0.226 R_Free 0.287
length a length b length c angle alpha angle beta angle gamma
82.270 82.270 58.788 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand FMN, PLP, PO4 enzyme Oxidoreductase E.C. BRENDA

Primary referenceMolecular basis of reduced pyridoxine 5'-phosphate oxidase catalytic activity in neonatal epileptic encephalopathy disorder., Musayev FN, Di Salvo ML, Saavedra MA, Contestabile R, Ghatge MS, Haynes A, Schirch V, Safo MK, J Biol Chem. 2009 Nov 6;284(45):30949-56. Epub 2009 Sep 15. PMID:19759001
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (43 Kb) [Save to disk]
  • Biological Unit Coordinates (3hy8.pdb1.gz) 76 Kb
  • LPC: Ligand-Protein Contacts for 3HY8
  • CSU: Contacts of Structural Units for 3HY8
  • Likely Quarternary Molecular Structure file(s) for 3HY8
  • Structure Factors (79 Kb)
  • Retrieve 3HY8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HY8 from S2C, [Save to disk]
  • Re-refined 3hy8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3HY8 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 3HY8
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3HY8, from MSDmotif at EBI
  • Fold representative 3hy8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3hy8] [3hy8_A]
  • SWISS-PROT database: [Q9NVS9]
  • Domain organization of [PNPO_HUMAN] by SWISSPFAM
  • Other resources with information on 3HY8
  • Community annotation for 3HY8 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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