2YXT Transferase date Apr 27, 2007
title Human Pyridoxal Kinase
authors M.K.Safo, F.N.Musayev, T.P.Ko, V.Schirch
compound source
Molecule: Pyridoxal Kinase
Chain: A, B
Synonym: Pyridoxine Kinase
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pdxk, Pkh, Pnk
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet 22b
symmetry Space Group: I 2 2 2
R_factor 0.206 R_Free 0.245
length a length b length c angle alpha angle beta angle gamma
90.630 115.286 172.403 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand MPD, NA, PO4 enzyme Transferase E.C. BRENDA
note 2YXT is a representative structure
A, B
  • pyridoxal kinase activity

  • Primary referenceCrystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation., Musayev FN, di Salvo ML, Ko TP, Gandhi AK, Goswami A, Schirch V, Safo MK, Protein Sci. 2007 Oct;16(10):2184-94. Epub 2007 Aug 31. PMID:17766369
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (118 Kb) [Save to disk]
  • Biological Unit Coordinates (2yxt.pdb1.gz) 111 Kb
  • Biological Unit Coordinates (2yxt.pdb2.gz) 220 Kb
  • LPC: Ligand-Protein Contacts for 2YXT
  • CSU: Contacts of Structural Units for 2YXT
  • Likely Quarternary Molecular Structure file(s) for 2YXT
  • Structure Factors (616 Kb)
  • Retrieve 2YXT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YXT from S2C, [Save to disk]
  • Re-refined 2yxt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YXT 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 2YXT
  • 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 2YXT, from MSDmotif at EBI
  • Fold representative 2yxt from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yxt_A] [2yxt_B] [2yxt]
  • SWISS-PROT database: [O00764]
  • Domain organization of [PDXK_HUMAN] by SWISSPFAM
  • Other resources with information on 2YXT
  • Community annotation for 2YXT 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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