3UGB	Ligase Protein Binding	date	Nov 02, 2011
title	Ubch5c~Ubiquitin Conjugate
authors	R.C.Page, J.N.Pruneda, R.E.Klevit, S.Misra
compound		source
Molecule: Ubiquitin-Conjugating Enzyme E2 D3 Chain: A Fragment: Unp Residues 1-147 Synonym: Ubiquitin Carrier Protein D3, Ubiquitin-Conjugatin E2(17)Kb 3, Ubiquitin-Conjugating Enzyme E2-17 Kda 3, Ubiqu Protein Ligase D3; Ec: 6.3.2.19 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ubc5c, Ubch5c, Ube2d2, Ube2d3 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28n
Molecule: Polyubiquitin-C Chain: B Fragment: Unp Residues 1-76 Synonym: Ubiquitin Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ubc Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet24
symmetry	Space Group: P 1 21 1	R_factor 0.211 R_Free 0.252
crystal cell	length a length b length c angle alpha angle beta angle gamma 42.027 52.510 53.114 90.00 101.07 90.00
method	X-Ray Diffraction	resolution	2.35 Å
ligand	GOL	enzyme	Ligase E.C.6.3.2.19 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Structural Insights into the Conformation and Oligomerization of E2 approximately Ubiquitin Conjugates., Page RC, Pruneda JN, Amick J, Klevit RE, Misra S, Biochemistry. 2012 May 14. PMID:22551455

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk] Biological Unit Coordinates (3ugb.pdb1.gz) 150 Kb LPC: Ligand-Protein Contacts for 3UGB CSU: Contacts of Structural Units for 3UGB Structure Factors (116 Kb) Retrieve 3UGB in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3UGB from S2C, [Save to disk] Re-refined 3ugb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3UGB 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 3UGB

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 3UGB, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ugb] [3ugb_B] [3ugb_A] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 3UGB: [UBCc] [UBQ ] by SMART

Other resources with information on 3UGB

Community annotation for 3UGB at PDBWiki (http://pdbwiki.org)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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