2HD5 Hydrolase date Jun 20, 2006
title Usp2 In Complex With Ubiquitin
authors M.Renatus, M.Kroemer
compound source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase 2
Chain: A
Fragment: Residues 258-605
Synonym: Ubiquitin Thioesterase 2, Ubiquitin-Specific-Proce Protease 2, Deubiquitinating Enzyme 2, 41 Kda Ubiquitin-Spe Protease;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Usp2, Ubp41
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta (De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24a

Molecule: Polyubiquitin
Chain: B
Fragment: Residues 1-76

Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
symmetry Space Group: C 1 2 1
R_factor 0.177 R_Free 0.229
length a length b length c angle alpha angle beta angle gamma
106.903 45.534 76.360 90.00 110.01 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand ZN enzyme Hydrolase E.C. BRENDA

Primary referenceStructural Basis of Ubiquitin Recognition by the Deubiquitinating Protease USP2., Renatus M, Parrado SG, D'Arcy A, Eidhoff U, Gerhartz B, Hassiepen U, Pierrat B, Riedl R, Vinzenz D, Worpenberg S, Kroemer M, Structure. 2006 Aug;14(8):1293-302. PMID:16905103
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (72 Kb) [Save to disk]
  • Biological Unit Coordinates (2hd5.pdb1.gz) 67 Kb
  • LPC: Ligand-Protein Contacts for 2HD5
  • CSU: Contacts of Structural Units for 2HD5
  • Likely Quarternary Molecular Structure file(s) for 2HD5
  • Structure Factors (268 Kb)
  • Retrieve 2HD5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2HD5 from S2C, [Save to disk]
  • Re-refined 2hd5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2HD5 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 2HD5
  • 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 2HD5, from MSDmotif at EBI
  • Fold representative 2hd5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2hd5_B] [2hd5] [2hd5_A]
  • SWISS-PROT database: [P62990] [O75604]
  • Domain organization of [UBIQ_BOVIN] [UBP2_HUMAN] by SWISSPFAM
  • Domain found in 2HD5: [UBQ ] by SMART
  • Other resources with information on 2HD5
  • Community annotation for 2HD5 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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