3RQD Hydrolase Hydrolase Inhibitor date Apr 28, 2011
title Ideal Thiolate-Zinc Coordination Geometry In Depsipeptide Bi Histone Deacetylase 8
authors K.E.Cole, D.P.Dowling, D.W.Christianson
compound source
Molecule: Histone Deacetylase 8
Chain: A, B
Synonym: Hd8
Ec: 3.5.1.98
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hdac8, Hdacl1, Cda07
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Largazole
Chain: C, D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Symploca
Organism_taxid: 105591
symmetry Space Group: P 1 21 1
R_factor 0.202 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.059 88.302 93.660 90.00 101.62 90.00
method X-Ray Diffractionresolution 2.14 Å
ligand 02G, 03Y, BB9, K, ZN enzyme Hydrolase E.C.3.5.1.98 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural basis of the antiproliferative activity of largazole, a depsipeptide inhibitor of the histone deacetylases., Cole KE, Dowling DP, Boone MA, Phillips AJ, Christianson DW, J Am Chem Soc. 2011 Aug 17;133(32):12474-7. Epub 2011 Jul 26. PMID:21790156
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (129 Kb) [Save to disk]
  • Biological Unit Coordinates (3rqd.pdb1.gz) 62 Kb
  • Biological Unit Coordinates (3rqd.pdb2.gz) 63 Kb
  • Biological Unit Coordinates (3rqd.pdb3.gz) 122 Kb
  • LPC: Ligand-Protein Contacts for 3RQD
  • CSU: Contacts of Structural Units for 3RQD
  • Structure Factors (596 Kb)
  • Retrieve 3RQD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RQD from S2C, [Save to disk]
  • Re-refined 3rqd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RQD 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 3RQD
  • 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 3RQD, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rqd_C] [3rqd_D] [3rqd_A] [3rqd_B] [3rqd]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3RQD
  • Community annotation for 3RQD at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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