4I5I Crystal structure of the SIRT1 catalytic domain bound to NAD and an EX527 analog date 2012-11-28
authors Zhao, X., Allison, D., Condon, B., Zhang, F., Gheyi, T., Zhang, A., Ashok, S., Russell, M., Macewan, I., Qian, Y., Jamison, J.A., Luz, J.G.
compound source
symmetry
R_factor
R_Free 0.19532
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.50
ligand 4I5, NAD, ZN BindingDB enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceThe 2.5 A crystal structure of the SIRT1 catalytic domain bound to nicotinamide adenine dinucleotide (NAD+) and an indole (EX527 analogue) reveals a novel mechanism of histone deacetylase inhibition., Zhao X, Allison D, Condon B, Zhang F, Gheyi T, Zhang A, Ashok S, Russell M, MacEwan I, Qian Y, Jamison JA, Luz JG, J Med Chem. 2013 Feb 14;56(3):963-9. doi: 10.1021/jm301431y. Epub 2013 Jan 29. PMID:23311358
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (97 Kb) [Save to disk]
  • Biological Unit Coordinates (4i5i.pdb1.gz) 47 Kb
  • Biological Unit Coordinates (4i5i.pdb2.gz) 47 Kb
  • Biological Unit Coordinates (4i5i.pdb3.gz) 91 Kb
  • LPC: Ligand-Protein Contacts for 4I5I
  • CSU: Contacts of Structural Units for 4I5I
  • Structure Factors (502 Kb)
  • Retrieve 4I5I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4I5I from S2C, [Save to disk]
  • Re-refined 4i5i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4I5I 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 4I5I
  • 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 4I5I, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4i5i] [4i5i_A] [4i5i_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4I5I
  • Community annotation for 4I5I at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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