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; Ec: 3.1.2.15 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
crystal cell	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 Diffraction	resolution	1.85 Å
ligand	ZN	enzyme	Hydrolase E.C.3.1.2.15 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Structural 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] (71 Kb) [Save to disk] Biological Unit Coordinates (2hd5.pdb1.gz) 65 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

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 2HD5, from MSDmotif at EBI

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)

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Images from IMB Jena Image Library of Biological Macromolecules.

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