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 Diffractionresolution 2.8 Å
ligand ZN enzyme Hydrolase E.C.3.1.2.15 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceThe 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.
  • 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_B] [2vhf] [2vhf_A]
  • 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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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