3BY4	Cell Cycle, Hydrolase	date	Jan 15, 2008
title	Structure Of Ovarian Tumor (Otu) Domain In Complex With Ubiq
authors	T.E.Messick, R.Marmorstein
compound		source
Molecule: Ubiquitin Thioesterase Otu1 Chain: A Fragment: Otu Domain Synonym: Otu1; Otu Domain-Containing Protein 1 Ec: 3.4.19.12 Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Gene: Otu1 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Ptyb2
Molecule: Ubiquitin Chain: B Synonym: Ubiquitin B Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ubiquitin B Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Ptyb2 Other_details: Propylamine Added By Intein-Mediated Ligatio
symmetry	Space Group: P 21 21 21	R_factor 0.189 R_Free 0.211
crystal cell	length a length b length c angle alpha angle beta angle gamma 46.304 73.215 88.880 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.55 Å
ligand	3CN	enzyme	Hydrolase E.C.3.4.19.12 BRENDA
note	3BY4 is a representative structure
Gene Ontology	Chain Function Process Component A
Primary reference	Structural basis for ubiquitin recognition by the Otu1 ovarian tumor domain protein., Messick TE, Russell NS, Iwata AJ, Sarachan KL, Shiekhattar R, Shanks JR, Reyes-Turcu FE, Wilkinson KD, Marmorstein R, J Biol Chem. 2008 Apr 18;283(16):11038-49. Epub 2008 Feb 12. PMID:18270205

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (90 Kb) [Save to disk] Biological Unit Coordinates (3by4.pdb1.gz) 86 Kb LPC: Ligand-Protein Contacts for 3BY4 CSU: Contacts of Structural Units for 3BY4 Likely Quarternary Molecular Structure file(s) for 3BY4 Structure Factors (917 Kb) Retrieve 3BY4 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3BY4 from S2C, [Save to disk] Re-refined 3by4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3BY4 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 3BY4

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 3BY4, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3by4_A] [3by4] [3by4_B] SWISS-PROT database: [P43558] [P62988] Domain organization of [OTU1_YEAST] [UBIQ_HUMAN] by SWISSPFAM Domains found in 3BY4: [UBQ] [ZnF_C2H2 ] by SMART

Other resources with information on 3BY4

Community annotation for 3BY4 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---