2GFO	Hydrolase	date	Mar 22, 2006
title	Structure Of The Catalytic Domain Of Human Ubiquitin Carboxy Hydrolase 8
authors	J.R.Walker, G.V.Avvakumov, S.Xue, E.M.Newman, P.J.Finerty Jr., C. Cole, J.Weigelt, M.Sundstrom, C.Arrowsmith, A.Edwards, A.Bochkar Paganon, Structural Genomics Consortium (Sgc)
compound		source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase 8 Chain: A Fragment: Catalytic Domain Synonym: Ubiquitin Thiolesterase 8, Ubiquitin-Specific Proc Protease 8, Deubiquitinating Enzyme 8, Hubpy; Ec: 3.1.2.15 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Usp8, Kiaa0055, Ubpy Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28-Lic
symmetry	Space Group: P 61	R_factor 0.168 R_Free 0.210
crystal cell	length a length b length c angle alpha angle beta angle gamma 67.173 67.173 194.458 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.00 Å
ligand	MSE, ZN	enzyme	Hydrolase E.C.3.1.2.15 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Amino-terminal Dimerization, NRDP1-Rhodanese Interaction, and Inhibited Catalytic Domain Conformation of the Ubiquitin-specific Protease 8 (USP8)., Avvakumov GV, Walker JR, Xue S, Finerty PJ Jr, Mackenzie F, Newman EM, Dhe-Paganon S, J Biol Chem. 2006 Dec 8;281(49):38061-70. Epub 2006 Oct 11. PMID:17035239

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (69 Kb) [Save to disk] Biological Unit Coordinates (2gfo.pdb1.gz) 60 Kb LPC: Ligand-Protein Contacts for 2GFO CSU: Contacts of Structural Units for 2GFO Likely Quarternary Molecular Structure file(s) for 2GFO Structure Factors (480 Kb) Retrieve 2GFO in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2GFO from S2C, [Save to disk] Re-refined 2gfo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2GFO 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 2GFO

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 2GFO, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2gfo_A] [2gfo] SWISS-PROT database: [P40818] Domain organization of [UBP8_HUMAN] by SWISSPFAM

Other resources with information on 2GFO

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

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