3N3K	Hydrolase	date	May 20, 2010
title	The Catalytic Domain Of Usp8 In Complex With A Usp8 Specific
authors	J.R.Walker, G.V.Avvakumov, S.Xue, Y.Li, A.Allali-Hassani, R.Lam, A S.Sidhu, J.Weigelt, C.Bountra, C.H.Arrowsmith, A.M.Edwards, A.Bo S.Dhe-Paganon, Structural Genomics Consortium, Structural Gen Consortium (Sgc)
compound		source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase 8 Chain: A Fragment: Catalytic Domain Synonym: Ubiquitin Thioesterase 8, Ubiquitin-Specific-Proce Protease 8, Deubiquitinating Enzyme 8, Ubiquitin Isopeptida Hubpy; Ec: 3.1.2.15 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Kiaa0055, Ubpy, Usp8 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 (De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28-Lic
Molecule: Ubiquitin Chain: B Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Rps27a, Uba52, Uba80, Ubb, Ubc, Ubcep1, Ubcep2, Ubq Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 (De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28alic
symmetry	Space Group: P 61	R_factor 0.178 R_Free 0.242
crystal cell	length a length b length c angle alpha angle beta angle gamma 69.983 69.983 181.549 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.60 Å
ligand	ZN	enzyme	Hydrolase E.C.3.1.2.15 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	A strategy for modulation of enzymes in the ubiquitin system., Ernst A, Avvakumov G, Tong J, Fan Y, Zhao Y, Alberts P, Persaud A, Walker JR, Neculai AM, Neculai D, Vorobyov A, Garg P, Beatty L, Chan PK, Juang YC, Landry MC, Yeh C, Zeqiraj E, Karamboulas K, Allali-Hassani A, Vedadi M, Tyers M, Moffat J, Sicheri F, Pelletier L, Durocher D, Raught B, Rotin D, Yang J, Moran MF, Dhe-Paganon S, Sidhu SS, Science. 2013 Feb 1;339(6119):590-5. doi: 10.1126/science.1230161. Epub 2013 Jan , 3. PMID:23287719

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (154 Kb) [Save to disk] Biological Unit Coordinates (3n3k.pdb1.gz) 145 Kb LPC: Ligand-Protein Contacts for 3N3K CSU: Contacts of Structural Units for 3N3K Structure Factors (215 Kb) Retrieve 3N3K in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3N3K from S2C, [Save to disk] Re-refined 3n3k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3N3K 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 3N3K

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 3N3K, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3n3k_B] [3n3k_A] [3n3k] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3N3K: [UBQ ] by SMART

Other resources with information on 3N3K

Community annotation for 3N3K at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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