5EEF Hydrolase Hydrolase Inhibitor date Oct 22, 2015
title Crystal Structure Of Danio Rerio Histone Deacetylase 6 Catal Domain 1 In Complex With Trichostatin A
authors Y.Hai, D.W.Christianson
compound source
Molecule: Hdac6
Chain: A, B
Fragment: Catalytic Domain 1 (Unp Residues 60-419)
Engineered: Yes
 Organism_scientific: Danio Rerio
Organism_common: Zebrafish
Organism_taxid: 7955
Gene: Hdac6
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
symmetry Space Group: P 1 21 1
R_factor 0.211 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.876 123.717 55.186 90.00 113.85 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand EDO, NH4, SO4, TSN, ZN enzyme
Primary referenceHistone deacetylase 6 structure and molecular basis of catalysis and inhibition., Hai Y, Christianson DW, Nat Chem Biol. 2016 Jul 25. doi: 10.1038/nchembio.2134. PMID:27454933
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (236 Kb) [Save to disk]
  • Biological Unit Coordinates (5eef.pdb1.gz) 115 Kb
  • Biological Unit Coordinates (5eef.pdb2.gz) 118 Kb
  • LPC: Ligand-Protein Contacts for 5EEF
  • CSU: Contacts of Structural Units for 5EEF
  • Structure Factors (1953 Kb)
  • Retrieve 5EEF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EEF from S2C, [Save to disk]
  • Re-refined 5eef structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5EEF 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 5EEF
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5eef_A] [5eef_B] [5eef]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5EEF
  • Community annotation for 5EEF at PDBWiki (http://pdbwiki.org)

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