2WDT	Hydrolase Protein Binding	date	Mar 26, 2009
title	Crystal Structure Of Plasmodium Falciparum Uchl3 In Complex Suicide Inhibitor Ubvme
authors	W.A.Weihofen, K.Artavanis-Tsakonas, R.Gaudet, H.L.Ploegh
compound		source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase L3 Chain: A, C Synonym: Uchl3, Uch-L3, Ubiquitin Thiolesterase Ec: 3.4.19.12 Engineered: Yes		Organism_scientific: Plasmodium Falciparum Organism_common: Malaria Parasite Organism_taxid: 5833 Strain: Clone 3d7 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28a
Molecule: Ubiquitin Chain: B, D Fragment: Residues 1-75 Engineered: Yes Other_details: C-Terminal Gly76 Of Wildtype Ubiquitin Is Re A Vinyl Methylester Moiety (Ubvme)		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Ptyb
symmetry	Space Group: P 21 21 2	R_factor 0.187 R_Free 0.235
crystal cell	length a length b length c angle alpha angle beta angle gamma 134.400 75.300 85.700 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	CL, GVE	enzyme	Hydrolase E.C.3.4.19.12 BRENDA
Gene Ontology	Chain Function Process Component A, C
Primary reference	Characterization and Structural Studies of the Plasmodium falciparum Ubiquitin and Nedd8 Hydrolase UCHL3., Artavanis-Tsakonas K, Weihofen WA, Antos JM, Coleman BI, Comeaux CA, Duraisingh MT, Gaudet R, Ploegh HL, J Biol Chem. 2010 Feb 26;285(9):6857-66. Epub 2009 Dec 30. PMID:20042598

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (105 Kb) [Save to disk] Biological Unit Coordinates (2wdt.pdb1.gz) 47 Kb Biological Unit Coordinates (2wdt.pdb2.gz) 49 Kb LPC: Ligand-Protein Contacts for 2WDT CSU: Contacts of Structural Units for 2WDT Structure Factors (526 Kb) Retrieve 2WDT in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2WDT from S2C, [Save to disk] Re-refined 2wdt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2WDT 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 2WDT

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 2WDT, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2wdt_B] [2wdt_A] [2wdt_D] [2wdt] [2wdt_C] SWISS-PROT database: [Q8IKM8] [P62988] Domain organization of [Q8IKM8_PLAF7] [UBIQ_HUMAN] by SWISSPFAM Domain found in 2WDT: [UBQ ] by SMART

Other resources with information on 2WDT

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

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