3F0R Hydrolase date Oct 25, 2008
title Crystal Structure Analysis Of Human Hdac8 Complexed With Tri A In A New Monoclinic Crystal Form
authors D.P.Dowling, S.L.Gantt, S.G.Gattis, C.A.Fierke, D.W.Christianson
compound source
Molecule: Histone Deacetylase 8
Chain: A, B, C
Synonym: Hd8
Ec: 3.5.1.98
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cda07, Hdac8, Hdacl1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phd2-Xa-His
symmetry Space Group: P 1 21 1
R_factor 0.210 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
87.895 90.705 92.141 90.00 94.63 90.00
method X-Ray Diffractionresolution 2.54 Å
ligand K, TSN, ZN BindingDB enzyme Hydrolase E.C.3.5.1.98 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceStructural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors., Dowling DP, Gantt SL, Gattis SG, Fierke CA, Christianson DW, Biochemistry. 2008 Dec 23;47(51):13554-63. PMID:19053282
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (181 Kb) [Save to disk]
  • Biological Unit Coordinates (3f0r.pdb1.gz) 61 Kb
  • Biological Unit Coordinates (3f0r.pdb2.gz) 61 Kb
  • Biological Unit Coordinates (3f0r.pdb3.gz) 59 Kb
  • LPC: Ligand-Protein Contacts for 3F0R
  • CSU: Contacts of Structural Units for 3F0R
  • Likely Quarternary Molecular Structure file(s) for 3F0R
  • Structure Factors (338 Kb)
  • Retrieve 3F0R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3F0R from S2C, [Save to disk]
  • Re-refined 3f0r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3F0R 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 3F0R
  • 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 3F0R, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3f0r] [3f0r_A] [3f0r_C] [3f0r_B]
  • SWISS-PROT database: [Q9BY41]
  • Domain organization of [HDAC8_HUMAN] by SWISSPFAM
  • Other resources with information on 3F0R
  • Community annotation for 3F0R 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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