4MEM | pdb_00004mem

Crystal Structure of the rat USP11 DUSP-UBL domains

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Aldo_ket_red	e4memB2	A: a/b three-layered sandwiches	X: jelly-roll	H: Galactose-binding domain-like	T: Galactose-binding domain-like	F: Aldo_ket_red	ECOD (v294.1)
B	Rieske	e4memB3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: Rieske	ECOD (v294.1)
A	Aldo_ket_red	e4memA2	A: a/b three-layered sandwiches	X: jelly-roll	H: Galactose-binding domain-like	T: Galactose-binding domain-like	F: Aldo_ket_red	ECOD (v294.1)
A	Cas9_PI2	e4memA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: Cas9_PI2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.2230.10	Alpha Beta	2-Layer Sandwich	DUSP-like	DUSP-like	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A	3.30.2230.10	Alpha Beta	2-Layer Sandwich	DUSP-like	DUSP-like	CATH (4.3.0)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF14836	Ubiquitin-like domain (Ubiquitin_3)	Ubiquitin-like domain	This ubiquitin-like domain is found in several ubiquitin carboxyl-terminal hydrolases [1] and in gametogenetin-binding protein.	Domain
A, B	PF06337	DUSP domain (DUSP)	DUSP domain	The DUSP (domain present in ubiquitin-specific protease) domain is found at the N-terminus of Ubiquitin-specific proteases. The structure of this domain has been solved [1]. Its tripod-like structure consists of a 3-fold alpha-helical bundle supporti ...	The DUSP (domain present in ubiquitin-specific protease) domain is found at the N-terminus of Ubiquitin-specific proteases. The structure of this domain has been solved [1]. Its tripod-like structure consists of a 3-fold alpha-helical bundle supporting a triple-stranded anti-parallel beta-sheet [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Ubiquitin carboxyl-terminal hydrolase 11	cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity transcription factor binding transcription coregulator binding transcription corepressor binding protein binding binding cysteine-type endopeptidase activity cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity transcription factor binding transcription coregulator binding transcription corepressor binding protein binding binding cysteine-type endopeptidase activity endopeptidase activity	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein deubiquitination protein modification by small protein removal macromolecule modification catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein deubiquitination protein modification by small protein removal macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation or removal	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR028135	Ubiquitin-like domain, USP-type	Domain
A, B	IPR035927	DUSP-like superfamily	Homologous Superfamily
A, B	IPR028889	Ubiquitin specific protease UPS, catalytic domain	Domain
A, B	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A, B	IPR006615	Peptidase C19, ubiquitin-specific peptidase, DUSP domain	Domain
A, B	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
A, B	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B	IPR050185	Ubiquitin carboxyl-terminal hydrolase	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.