4KGD High-resolution crystal structure of pyruvate oxidase from L. plantarum in complex with phosphate date
authors Neumann, P., Tittmann, K.
compound source
symmetry
R_factor
R_Free 0.1505
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.06
ligand FAD, GOL, K, MG, PO4, TDP, TPP enzyme
Gene JDM1
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceObservation of a stable carbene at the active site of a thiamin enzyme., Meyer D, Neumann P, Ficner R, Tittmann K, Nat Chem Biol. 2013 Jun 9. doi: 10.1038/nchembio.1275. PMID:23748673
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (470 Kb) [Save to disk]
  • Biological Unit Coordinates (4kgd.pdb1.gz) 921 Kb
  • LPC: Ligand-Protein Contacts for 4KGD
  • CSU: Contacts of Structural Units for 4KGD
  • Structure Factors (6847 Kb)
  • Retrieve 4KGD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KGD from S2C, [Save to disk]
  • Re-refined 4kgd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4KGD 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 4KGD
  • 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 4KGD, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4kgd] [4kgd_A] [4kgd_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4KGD
  • Community annotation for 4KGD at PDBWiki (http://pdbwiki.org)

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