2V5W	Hydrolase Hydrolase Substrate	date	Jul 10, 2007
title	Crystal Structure Of Hdac8-Substrate Complex
authors	S.Di Marco, A.Vannini, C.Volpari
compound		source
Molecule: Histone Deacetylase 8 Chain: A, B Synonym: Hdac8, Hd8 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_plasmid: Pet21b
Molecule: Glycyl-Glycyl-Glycine Chain: G Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: Peptidic Substrate Chain: I, L Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
symmetry	Space Group: P 1 21 1	R_factor 0.176 R_Free 0.230
crystal cell	length a length b length c angle alpha angle beta angle gamma 52.304 151.801 57.552 90.00 117.02 90.00
method	X-Ray Diffraction	resolution	2.00 Å
ligand	ACE, ALY, K, MCM, ZN	enzyme
Gene Ontology	Chain Function Process Component A, B
Primary reference	Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8-substrate complex., Vannini A, Volpari C, Gallinari P, Jones P, Mattu M, Carfi A, De Francesco R, Steinkuhler C, Di Marco S, EMBO Rep. 2007 Sep;8(9):879-84. Epub 2007 Aug 10. PMID:17721440

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (136 Kb) [Save to disk] Biological Unit Coordinates (2v5w.pdb1.gz) 65 Kb Biological Unit Coordinates (2v5w.pdb2.gz) 67 Kb LPC: Ligand-Protein Contacts for 2V5W CSU: Contacts of Structural Units for 2V5W Likely Quarternary Molecular Structure file(s) for 2V5W Structure Factors (907 Kb) Retrieve 2V5W in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2V5W from S2C, [Save to disk] Re-refined 2v5w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2V5W 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 2V5W

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 2V5W, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2v5w] [2v5w_L] [2v5w_I] [2v5w_G] [2v5w_A] [2v5w_B] SWISS-PROT database: [Q9BY41] Domain organization of [HDAC8_HUMAN] by SWISSPFAM

Other resources with information on 2V5W

Community annotation for 2V5W at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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