4DY6 Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 2'-phosphate bis(adenosine)-5'-diphosphate date 2012-02-28
authors Poncet-Montange, G., Assairi, L., Arold, S., Pochet, S., Labesse, G.
compound source
symmetry
R_factor
R_Free 0.2504
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.20
ligand A22, CIT enzyme
note 4DY6 supersedes 2I2E
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceNAD kinases use substrate-assisted catalysis for specific recognition of NAD., Poncet-Montange G, Assairi L, Arold S, Pochet S, Labesse G, J Biol Chem. 2007 Nov 23;282(47):33925-34. Epub 2007 Aug 8. PMID:17686780
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (99 Kb) [Save to disk]
  • Biological Unit Coordinates (4dy6.pdb1.gz) 365 Kb
  • LPC: Ligand-Protein Contacts for 4DY6
  • CSU: Contacts of Structural Units for 4DY6
  • Structure Factors (214 Kb)
  • Retrieve 4DY6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DY6 from S2C, [Save to disk]
  • Re-refined 4dy6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4DY6 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 4DY6
  • 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 4DY6, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dy6_A] [4dy6]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4DY6
  • Community annotation for 4DY6 at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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