5CVN	Hydrolase Protein Binding	date	Jul 27, 2015
title	Wdr48 (2-580):Usp46~Ubiquitin Ternary Complex
authors	S.F.Harris, J.Yin
compound		source
Molecule: Wd Repeat-Containing Protein 48 Chain: A Fragment: Unp Residues 2-580 Synonym: Usp1-Associated Factor 1,Wd Repeat Endosomal Prote Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Wdr48, Kiaa1449, Uaf1 Expression_system: Trichoplusia Ni Expression_system_common: Cabbage Looper Expression_system_taxid: 7111 Expression_system_vector_type: Baculovirus
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase 46 Chain: B Fragment: Unp Residues 25-366 Synonym: Deubiquitinating Enzyme 46,Ubiquitin Thioesterase Ubiquitin-Specific-Processing Protease 46; Ec: 3.4.19.12 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Usp46 Expression_system: Trichoplusia Ni Expression_system_common: Cabbage Looper Expression_system_taxid: 7111 Expression_system_vector_type: Baculovirus
Molecule: Polyubiquitin-B Chain: D Fragment: Unp Residues 1-76 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ubb Expression_system: Trichoplusia Ni Expression_system_common: Cabbage Looper Expression_system_taxid: 7111 Expression_system_vector_type: Baculovirus
symmetry	Space Group: I 2 2 2	R_factor 0.175 R_Free 0.222
crystal cell	length a length b length c angle alpha angle beta angle gamma 103.437 154.189 182.854 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.36 Å
ligand	ZN	enzyme	Hydrolase E.C.3.4.19.12 BRENDA
Gene Ontology	Chain Function Process Component B
Primary reference	Structural Insights into WD-Repeat 48 Activation of Ubiquitin-Specific Protease 46., Yin J, Schoeffler AJ, Wickliffe K, Newton K, Starovasnik MA, Dueber EC, Harris SF, Structure. 2015 Sep 12. pii: S0969-2126(15)00359-7. doi:, 10.1016/j.str.2015.08.010. PMID:26388029

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (317 Kb) [Save to disk] Biological Unit Coordinates (5cvn.pdb1.gz) 310 Kb LPC: Ligand-Protein Contacts for 5CVN CSU: Contacts of Structural Units for 5CVN Structure Factors (233 Kb) Retrieve 5CVN in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5CVN from S2C, [Save to disk] Re-refined 5cvn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5CVN 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 5CVN

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5cvn] [5cvn_A] [5cvn_B] [5cvn_D] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 5CVN: [UBQ] [WD40 ] by SMART

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Community annotation for 5CVN at PDBWiki (http://pdbwiki.org)

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