2VQJ Hydrolase date Mar 17, 2008
title Structure Of Hdac4 Catalytic Domain Bound To A Trifluoromethylketone Inhbitor
authors M.J.Bottomley, P.Lo Surdo, P.Di Giovine, A.Cirillo, R.Scarpelli, F.Ferrigno, P.Jones, P.Neddermann, R.De Francesco, C.Steinkuhler, P.Gallinari, A.Carfi
compound source
Molecule: Histone Deacetylase 4
Chain: A
Fragment: Catalytic Domain, Residues 648-1057
Synonym: Hd4
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Petm-11 (Obtained From Embl- Heidelberg)
symmetry Space Group: C 2 2 21
R_factor 0.225 R_Free 0.276
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.770 137.562 68.993 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.1 Å
ligand DIO, K, SO4, TFG, ZN enzyme
Primary referenceStructural and functional analysis of the human HDAC4 catalytic domain reveals a regulatory structural zinc-binding domain., Bottomley MJ, Lo Surdo P, Di Giovine P, Cirillo A, Scarpelli R, Ferrigno F, Jones P, Neddermann P, De Francesco R, Steinkuhler C, Gallinari P, Carfi A, J Biol Chem. 2008 Jul 8. PMID:18614528
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (2vqj.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 2VQJ
  • CSU: Contacts of Structural Units for 2VQJ
  • Likely Quarternary Molecular Structure file(s) for 2VQJ
  • Structure Factors (487 Kb)
  • Retrieve 2VQJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VQJ from S2C, [Save to disk]
  • Re-refined 2vqj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VQJ 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 2VQJ
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2VQJ, from MSDmotif at EBI
  • Fold representative 2vqj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vqj] [2vqj_A]
  • SWISS-PROT database: [P56524]
  • Domain organization of [HDAC4_HUMAN] by SWISSPFAM
  • Other resources with information on 2VQJ
  • Community annotation for 2VQJ 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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