2VQQ Hydrolase date Mar 18, 2008
title Structure Of Hdac4 Catalytic Domain (A Double Cysteine-To- Alanine Mutant) 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, B
Fragment: Catalytic Domain, Residues 648-1057
Synonym: Hd4
Engineered: Yes
Mutation: 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: P 1 21 1
R_factor 0.194 R_Free 0.221
length a length b length c angle alpha angle beta angle gamma
85.605 70.673 88.201 90.00 108.08 90.00
method X-Ray Diffractionresolution 1.9 Å
ligand 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] (132 Kb) [Save to disk]
  • Biological Unit Coordinates (2vqq.pdb1.gz) 64 Kb
  • Biological Unit Coordinates (2vqq.pdb2.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 2VQQ
  • CSU: Contacts of Structural Units for 2VQQ
  • Likely Quarternary Molecular Structure file(s) for 2VQQ
  • Structure Factors (1594 Kb)
  • Retrieve 2VQQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VQQ from S2C, [Save to disk]
  • Re-refined 2vqq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VQQ 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 2VQQ
  • 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 2VQQ, from MSDmotif at EBI
  • Fold representative 2vqq from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vqq] [2vqq_A] [2vqq_B]
  • SWISS-PROT database: [P56524]
  • Domain organization of [HDAC4_HUMAN] by SWISSPFAM
  • Other resources with information on 2VQQ
  • Community annotation for 2VQQ 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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