3C0Y Hydrolase date Jan 21, 2008
title Crystal Structure Of Catalytic Domain Of Human Histone Deacetylase Hdac7
authors J.R.Min, A.Schuetz, A.Allali-Hassani, P.Loppnau, N.P.Kwiatkowski, R.Mazitschek, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, M.Vedadi, A.Bochkarev, A.N.Plotnikov, Structural Genomics Consortium (Sgc)
compound source
Molecule: Histone Deacetylase 7a
Chain: A, B, C
Fragment: Catalytic Domain: Residues 482-903
Synonym: Hd7a, Hdac7
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hdac7a, Hdac7
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Codon Plus Ril (Stratagen);
Expression_system_vector_type: Plasmid
Expression_system_plasmid: P28a-Lic
symmetry Space Group: P 32
R_factor 0.202 R_Free 0.264
length a length b length c angle alpha angle beta angle gamma
81.750 81.750 148.895 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand K, ZN enzyme
note 3C0Y supersedes 2NVR, 2I4Y
Primary referenceHuman HDAC7 harbors a class IIa histone deacetylase-specific zinc binding motif and cryptic deacetylase activity., Schuetz A, Min J, Allali-Hassani A, Schapira M, Shuen M, Loppnau P, Mazitschek R, Kwiatkowski NP, Lewis TA, Maglathin RL, McLean TH, Bochkarev A, Plotnikov AN, Vedadi M, Arrowsmith CH, J Biol Chem. 2008 Apr 25;283(17):11355-63. Epub 2008 Feb 19. PMID:18285338
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (185 Kb) [Save to disk]
  • Biological Unit Coordinates (3c0y.pdb1.gz) 65 Kb
  • Biological Unit Coordinates (3c0y.pdb2.gz) 62 Kb
  • Biological Unit Coordinates (3c0y.pdb3.gz) 60 Kb
  • LPC: Ligand-Protein Contacts for 3C0Y
  • CSU: Contacts of Structural Units for 3C0Y
  • Likely Quarternary Molecular Structure file(s) for 3C0Y
  • Structure Factors (952 Kb)
  • Retrieve 3C0Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3C0Y from S2C, [Save to disk]
  • Re-refined 3c0y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3C0Y 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 3C0Y
  • 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 3C0Y, from MSDmotif at EBI
  • Fold representative 3c0y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3c0y] [3c0y_B] [3c0y_A] [3c0y_C]
  • SWISS-PROT database: [Q8WUI4]
  • Domain organization of [HDAC7_HUMAN] by SWISSPFAM
  • Other resources with information on 3C0Y
  • Community annotation for 3C0Y 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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