2VHF	Hydrolase	date	Nov 21, 2007
title	Structure Of The Cyld Usp Domain
authors	D.Komander, C.J.Lord, H.Scheel, S.Swift, K.Hofmann, A.Ashworth, D.Barford
compound		source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase Cyld Chain: A, B Fragment: Usp Deubiquitinase Domain, Residues 583-956 Synonym: Ubiquitin Thioesterase Cyld, Ubiquitin-Specific -Processing Protease Cyld, Deubiquitinating Enzyme Cyld, Cyld; Ec: 3.1.2.15 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Spodoptera Frugiperda Expression_system_taxid: 7108 Expression_system_cell_line: Sf9 Expression_system_vector_type: Baculovirus Expression_system_plasmid: Pfastbac
symmetry	Space Group: P 21 21 21	R_factor 0.233 R_Free 0.281
crystal cell	length a length b length c angle alpha angle beta angle gamma 60.494 89.083 171.806 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.8 Å
ligand	ZN	enzyme	Hydrolase E.C.3.1.2.15 BRENDA
Primary reference	The Structure of the CYLD USP Domain Explains Its Specificity for Lys63-Linked Polyubiquitin and Reveals a B Box Module., Komander D, Lord CJ, Scheel H, Swift S, Hofmann K, Ashworth A, Barford D, Mol Cell. 2008 Feb 29;29(4):451-64. PMID:18313383

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (228 Kb) [Save to disk] Biological Unit Coordinates (2vhf.pdb1.gz) 113 Kb Biological Unit Coordinates (2vhf.pdb2.gz) 111 Kb LPC: Ligand-Protein Contacts for 2VHF CSU: Contacts of Structural Units for 2VHF Likely Quarternary Molecular Structure file(s) for 2VHF Structure Factors (173 Kb) Retrieve 2VHF in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2VHF from S2C, [Save to disk] Re-refined 2vhf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2VHF 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2VHF

Cartoon representation from PDB Cartoon 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 Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 2VHF, from MSDmotif at EBI Fold representative 2vhf from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2vhf_A] [2vhf_B] SWISS-PROT database: [Q9NQC7] Domain organization of [CYLD_HUMAN] by SWISSPFAM Alignments of the sequence of 2VHF with the sequences similar proteins can be viewed for 2VHF's classification [CYLD_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [CYLD_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2VHF

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

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