5DC8	Hydrolase	date	Aug 23, 2015
title	Crystal Structure Of H142a-Y306f Hdac8 In Complex With A Tet Substrate
authors	C.Decroos, M.S.Lee, D.W.Christianson
compound		source
Molecule: Histone Deacetylase 8 Chain: A, B Synonym: Hd8 Ec: 3.5.1.98 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Hdac8, Hdacl1, Cda07 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Phd2-Xa-His
Molecule: Fluor-De-Lys Tetrapeptide Assay Substrate Chain: C, D Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
symmetry	Space Group: P 21 21 21	R_factor 0.128 R_Free 0.149
crystal cell	length a length b length c angle alpha angle beta angle gamma 82.800 97.887 104.612 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.30 Å
ligand	ACE, ALY, GOL, K, MCM, ZN	enzyme	Hydrolase E.C.3.5.1.98 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	General Base-General Acid Catalysis in Human Histone Deacetylase 8., Gantt SM Fsgm, Decroos C, Lee MS, Gullett LE, Bowman CM, Christianson DW, Fierke CA, Biochemistry. 2016 Jan 25. PMID:26806311

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (282 Kb) [Save to disk] Biological Unit Coordinates (5dc8.pdb1.gz) 139 Kb Biological Unit Coordinates (5dc8.pdb2.gz) 138 Kb LPC: Ligand-Protein Contacts for 5DC8 CSU: Contacts of Structural Units for 5DC8 Structure Factors (3152 Kb) Retrieve 5DC8 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5DC8 from S2C, [Save to disk] Re-refined 5dc8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5DC8 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 5DC8

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5dc8_D] [5dc8_C] [5dc8_B] [5dc8] [5dc8_A] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 5DC8

Community annotation for 5DC8 at PDBWiki (http://pdbwiki.org)

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---