3A33	Ligase	date	Jun 08, 2009
title	Ubch5b~Ubiquitin Conjugate
authors	E.Sakata, T.Satoh, S.Yamamoto, Y.Yamaguchi, M.Yagi-Utsumi, E.Kuri S.Wakatsuki, K.Kato
compound		source
Molecule: Ubiquitin-Conjugating Enzyme E2 D2 Chain: A Synonym: Ubiquitin-Protein Ligase D2, Ubiquitin Carrier Pro Ubiquitin-Conjugating Enzyme E2-17 Kda 2, E2(17)Kb 2; Ec: 6.3.2.19 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ubch5b Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3)Codon-Plus Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28a
Molecule: Ubiquitin Chain: B Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3)Codon-Plus Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgex6p-1 (Modified)
symmetry	Space Group: P 61 2 2	R_factor 0.228 R_Free 0.280
crystal cell	length a length b length c angle alpha angle beta angle gamma 72.500 72.500 176.600 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	GOL	enzyme	Ligase E.C.6.3.2.19 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Crystal structure of UbcH5b approximately ubiquitin intermediate: insight into the formation of the self-assembled E2 approximately Ub conjugates., Sakata E, Satoh T, Yamamoto S, Yamaguchi Y, Yagi-Utsumi M, Kurimoto E, Tanaka K, Wakatsuki S, Kato K, Structure. 2010 Jan 13;18(1):138-47. PMID:20152160

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (43 Kb) [Save to disk] Biological Unit Coordinates (3a33.pdb1.gz) 74 Kb LPC: Ligand-Protein Contacts for 3A33 CSU: Contacts of Structural Units for 3A33 Structure Factors (107 Kb) Retrieve 3A33 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3A33 from S2C, [Save to disk] Re-refined 3a33 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3A33 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 3A33

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 3A33, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3a33] [3a33_B] [3a33_A] SWISS-PROT database: [P62837] [P62988] Belongs to the peroxisomal protein importer (ppi) family according to TCDB. Domain organization of [UB2D2_HUMAN] [UBIQ_HUMAN] by SWISSPFAM Domains found in 3A33: [UBCc] [UBQ ] by SMART

Other resources with information on 3A33

Community annotation for 3A33 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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