3MZ7 Hydrolase date May 11, 2010
title Crystal Structure Of D101l Co2+ Hdac8 Complexed With M344
authors D.P.Dowling, S.G.Gattis, C.A.Fierke, D.W.Christianson
compound source
Molecule: Histone Deacetylase 8
Chain: A
Synonym: Hd8
Ec: 3.5.1.98
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hdac8
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phd2-Xa-His
symmetry Space Group: P 21 21 2
R_factor 0.220 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.799 88.431 52.503 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand B3N, CO, GOL, K enzyme Hydrolase E.C.3.5.1.98 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructures of metal-substituted human histone deacetylase 8 provide mechanistic inferences on biological function ., Dowling DP, Gattis SG, Fierke CA, Christianson DW, Biochemistry. 2010 Jun 22;49(24):5048-56. PMID:20545365
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (3mz7.pdb1.gz) 60 Kb
  • LPC: Ligand-Protein Contacts for 3MZ7
  • CSU: Contacts of Structural Units for 3MZ7
  • Structure Factors (299 Kb)
  • Retrieve 3MZ7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3MZ7 from S2C, [Save to disk]
  • Re-refined 3mz7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3MZ7 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 3MZ7
  • 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 3MZ7, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3mz7] [3mz7_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3MZ7
  • Community annotation for 3MZ7 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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