3M62	Ligase Protein Binding	date	Mar 15, 2010
title	Crystal Structure Of Ufd2 In Complex With The Ubiquitin-Like Domain Of Rad23
authors	P.Haenzelmann, H.Schindelin
compound		source
Molecule: Ubiquitin Conjugation Factor E4 Chain: A Synonym: Ubiquitin Fusion Degradation Protein 2, Ub Fusion Engineered: Yes Mutation: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932 Gene: D1255, Ufd2, Ydl190c Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21-Ril (De3)
Molecule: Uv Excision Repair Protein Rad23 Chain: B Fragment: Unp Residues 1-84, Ubiquitin-Like Domain Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932 Gene: Rad23, Sygp-Orf29, Yel037c Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21-Ril (De3)
symmetry	Space Group: P 21 21 21	R_factor 0.200 R_Free 0.257
crystal cell	length a length b length c angle alpha angle beta angle gamma 65.040 126.550 180.870 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.40 Å
ligand	1PE, K	enzyme
Gene Ontology	Chain Function Process Component A
Primary reference	The yeast E4 ubiquitin ligase Ufd2 interacts with the ubiquitin-like domains of Rad23 and Dsk2 via a novel and distinct ubiquitin-like binding domain., Hanzelmann P, Stingele J, Hofmann K, Schindelin H, Raasi S, J Biol Chem. 2010 Jun 25;285(26):20390-8. Epub 2010 Apr 28. PMID:20427284

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (176 Kb) [Save to disk] Biological Unit Coordinates (3m62.pdb1.gz) 169 Kb LPC: Ligand-Protein Contacts for 3M62 CSU: Contacts of Structural Units for 3M62 Structure Factors (3097 Kb) Retrieve 3M62 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3M62 from S2C, [Save to disk] Re-refined 3m62 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3M62 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 3M62

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 3M62, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3m62_A] [3m62] [3m62_B] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 3M62: [UBQ] [Ubox ] by SMART

Other resources with information on 3M62

Community annotation for 3M62 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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