1VKG	Hydrolase	date	May 13, 2004
title	Crystal Structure Of Human Hdac8 Complexed With Cra-19156
authors	J.R.Somoza, R.J.Skene, B.A.Katz, C.Mol, J.D.Ho, A.J.Jennings, C.Lu A.Arvai, J.J.Buggy, E.Chi, J.Tang, B.C.Sang, E.Verner, R.Wynands E.M.Leahy, D.R.Dougan, G.Snell, M.Navre, M.W.Knuth, R.V.Swanson, D.E.Mcree, L.W.Tari
compound		source
Molecule: Histone Deacetylase 8 Chain: A, B Synonym: Hdac8 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Hdac8, Hdacl1 Expression_system: Spodoptera Frugiperda Expression_system_common: Fall Armyworm Expression_system_taxid: 7108 Expression_system_strain: Sf9 Expression_system_vector_type: Baculovirus Expression_system_vector: Psxb2 Expression_system_plasmid: Pfastbachta
symmetry	Space Group: P 21 21 21	R_factor 0.237 R_Free 0.304
crystal cell	length a length b length c angle alpha angle beta angle gamma 82.630 92.710 98.760 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	CRI, NA, ZN	enzyme
related structures	by homologous chain: 1T64, 1T67
Gene Ontology	Chain Function Process Component A, B
Primary reference	Structural Snapshots of Human HDAC8 Provide Insights into the Class I Histone Deacetylases., Somoza JR, Skene RJ, Katz BA, Mol C, Ho JD, Jennings AJ, Luong C, Arvai A, Buggy JJ, Chi E, Tang J, Sang BC, Verner E, Wynands R, Leahy EM, Dougan DR, Snell G, Navre M, Knuth MW, Swanson RV, McRee DE, Tari LW, Structure (Camb) 2004 Jul;12(7):1325-34. PMID:15242608

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (235 Kb) [Save to disk] Biological Unit Coordinates (1vkg.pdb1.gz) 227 Kb LPC: Ligand-Protein Contacts for 1VKG CSU: Contacts of Structural Units for 1VKG Likely Quarternary Molecular Structure file(s) for 1VKG Structure Factors (173 Kb) Retrieve 1VKG in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1VKG from S2C, [Save to disk] Re-refined 1vkg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1VKG 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 1VKG

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 1VKG, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1vkga_, region A [Jmol] [rasmolscript] [script source]     - Domain d1vkgb_, region B [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1vkg] [1vkg_A] [1vkg_B] SWISS-PROT database: [Q9BY41] Domain organization of [HDAC8_HUMAN] by SWISSPFAM

Other resources with information on 1VKG

Community annotation for 1VKG at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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