3PHD	Protein Binding	date	Nov 03, 2010
title	Crystal Structure Of Human Hdac6 In Complex With Ubiquitin
authors	A.Dong, W.Qui, M.Ravichandran, A.Schuetz, P.Loppnau, F.Li, F.Macke I.Kozieradzki, H.Ouyang, Structural Genomics Consortium (Sgc)
compound		source
Molecule: Histone Deacetylase 6 Chain: A, B, C, D Synonym: Hd6 Ec: 3.5.1.98 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Hdac6, Kiaa0901, Jm21 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Rosetta-R3 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet15-Mhl
Molecule: Polyubiquitin Chain: E, F, G, H Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ubb, Uba52, Ubcep2, Ubc, Rps27a, Uba80, Ubcep1 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 43 21 2	R_factor 0.235 R_Free 0.265
crystal cell	length a length b length c angle alpha angle beta angle gamma 133.748 133.748 118.768 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.00 Å
ligand	ZN	enzyme	Hydrolase E.C.3.5.1.98 BRENDA
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Protein aggregates are recruited to the aggresome by histone deacetylase 6 via unanchored ubiquitin C-termini., Ouyang H, Ali YO, Ravichandran M, Dong A, Qiu W, Mackenzie F, Dhe-Paganon S, Arrowsmith CH, Zhai RG, J Biol Chem. 2011 Nov 8. PMID:22069321

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk] Biological Unit Coordinates (3phd.pdb1.gz) 67 Kb LPC: Ligand-Protein Contacts for 3PHD CSU: Contacts of Structural Units for 3PHD Structure Factors (255 Kb) Retrieve 3PHD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3PHD from S2C, [Save to disk] Re-refined 3phd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3PHD 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 3PHD

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 3PHD, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3phd_E] [3phd_C] [3phd_G] [3phd_D] [3phd_F] [3phd] [3phd_H] [3phd_A] [3phd_B] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 3PHD: [UBQ] [ZnF_UBP ] by SMART

Other resources with information on 3PHD

Community annotation for 3PHD at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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