3PKJ Hydrolase date Nov 11, 2010
title Human Sirt6 Crystal Structure In Complex With 2'-N-Acetyl Ad
authors P.W.Pan, A.Dong, W.Qiu, P.Loppnau, J.Wang, M.Ravichandran, J.R.Wal C.Bountra, J.Weigelt, C.H.Arrowsmith, J.Min, A.M.Edwards, Struct Genomics Consortium (Sgc)
compound source
Molecule: Nad-Dependent Deacetylase Sirtuin-6
Chain: A, B, C, D, E, F
Synonym: Sir2-Like Protein 6
Ec: 3.5.1.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sirt6, Sir2l6
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon(+) Prare
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28-Lic
symmetry Space Group: P 1 21 1
R_factor 0.234 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
89.042 135.780 89.105 90.00 120.02 90.00
method X-Ray Diffractionresolution 2.12 Å
ligand A2N, SO4, UNX, ZN enzyme Hydrolase E.C.3.5.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B
  • NAD-dependent histone deacet...


  • Primary referenceStructure and biochemical functions of SIRT6., Pan PW, Feldman JL, Devries MK, Dong A, Edwards AM, Denu JM, J Biol Chem. 2011 Apr 22;286(16):14575-87. Epub 2011 Mar 1. PMID:21362626
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (271 Kb) [Save to disk]
  • Biological Unit Coordinates (3pkj.pdb1.gz) 47 Kb
  • Biological Unit Coordinates (3pkj.pdb2.gz) 49 Kb
  • Biological Unit Coordinates (3pkj.pdb3.gz) 48 Kb
  • Biological Unit Coordinates (3pkj.pdb4.gz) 48 Kb
  • Biological Unit Coordinates (3pkj.pdb5.gz) 48 Kb
  • Biological Unit Coordinates (3pkj.pdb6.gz) 47 Kb
  • Biological Unit Coordinates (3pkj.pdb7.gz) 264 Kb
  • LPC: Ligand-Protein Contacts for 3PKJ
  • CSU: Contacts of Structural Units for 3PKJ
  • Structure Factors (2106 Kb)
  • Retrieve 3PKJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PKJ from S2C, [Save to disk]
  • Re-refined 3pkj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PKJ 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 3PKJ
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3PKJ, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pkj_C] [3pkj_B] [3pkj_F] [3pkj_E] [3pkj_A] [3pkj_D] [3pkj]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3PKJ
  • Community annotation for 3PKJ 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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