3C0Z Hydrolase date Jan 21, 2008
title Crystal Structure Of Catalytic Domain Of Human Histone Deacetylase Hdac7 In Complex With Saha
authors J.Min, A.Schuetz, P.Loppnau, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, 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 Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a-Mhl
symmetry Space Group: P 32
R_factor 0.197 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
81.825 81.825 148.867 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand K, SHH, ZN BindingDB enzyme
note 3C0Z supersedes 2PQO
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] (184 Kb) [Save to disk]
  • Biological Unit Coordinates (3c0z.pdb1.gz) 64 Kb
  • Biological Unit Coordinates (3c0z.pdb2.gz) 62 Kb
  • Biological Unit Coordinates (3c0z.pdb3.gz) 60 Kb
  • LPC: Ligand-Protein Contacts for 3C0Z
  • CSU: Contacts of Structural Units for 3C0Z
  • Likely Quarternary Molecular Structure file(s) for 3C0Z
  • Structure Factors (944 Kb)
  • Retrieve 3C0Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3C0Z from S2C, [Save to disk]
  • Re-refined 3c0z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3C0Z 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 3C0Z
  • 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 3C0Z, from MSDmotif at EBI
  • Fold representative 3c0z from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3c0z_A] [3c0z_B] [3c0z] [3c0z_C]
  • SWISS-PROT database: [Q8WUI4]
  • Domain organization of [HDAC7_HUMAN] by SWISSPFAM
  • Other resources with information on 3C0Z
  • Community annotation for 3C0Z 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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