3FHY Transferase date Dec 10, 2008
title Crystal Structure Of D235n Mutant Of Human Pyridoxal Kinase
authors M.K.Safo, A.K.Gandhi, F.N.Musayev, M.Ghatge, M.L.Di Salvo, V.Schirch
compound source
Molecule: Pyridoxal Kinase
Chain: A, B
Synonym: Pyridoxine Kinase
Ec: 2.7.1.35
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: C21orf124, C21orf97, Pdxk, Pkh, Pnk
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta (De3)Plyss Competent Cells;
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28
symmetry Space Group: I 2 2 2
R_factor 0.214 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.110 114.643 169.681 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand ATP, MG, MPD, NA, SO4 enzyme Transferase E.C.2.7.1.35 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • pyridoxal kinase activity


  • Primary referenceKinetic and structural studies of the role of the active site residue Asp235 of human pyridoxal kinase., Gandhi AK, Ghatge MS, Musayev FN, Sease A, Aboagye SO, di Salvo ML, Schirch V, Safo MK, Biochem Biophys Res Commun. 2009 Mar 27;381(1):12-5. Epub 2009 Feb 4. PMID:19351586
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (114 Kb) [Save to disk]
  • Biological Unit Coordinates (3fhy.pdb1.gz) 108 Kb
  • LPC: Ligand-Protein Contacts for 3FHY
  • CSU: Contacts of Structural Units for 3FHY
  • Likely Quarternary Molecular Structure file(s) for 3FHY
  • Structure Factors (335 Kb)
  • Retrieve 3FHY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3FHY from S2C, [Save to disk]
  • Re-refined 3fhy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3FHY 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 3FHY
  • 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 3FHY, from MSDmotif at EBI
  • Fold representative 3fhy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3fhy_B] [3fhy_A] [3fhy]
  • SWISS-PROT database: [O00764]
  • Domain organization of [PDXK_HUMAN] by SWISSPFAM
  • Other resources with information on 3FHY
  • Community annotation for 3FHY 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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