6NFT | pdb_00006nft

Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (4-oxoquinazolin-3(4H)-yl)acetic acid

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d6nftb_	Small proteins	RING/U-box	RING/U-box	Zf-UBP	Ubiquitin carboxyl-terminal hydrolase 5, UBP5	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6nfta_	Small proteins	RING/U-box	RING/U-box	Zf-UBP	Ubiquitin carboxyl-terminal hydrolase 5, UBP5	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	RING/U-box like	8032890	3000160	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RING/U-box like	8032890	3000160	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	zf-UBP	e6nftB1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-UBP	ECOD (1.6)
A	zf-UBP	e6nftA1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-UBP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02148	Zn-finger in ubiquitin-hydrolases and other protein (zf-UBP)	Zn-finger in ubiquitin-hydrolases and other protein		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Ubiquitin carboxyl-terminal hydrolase 5	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity ubiquitin-like protein peptidase activity deubiquitinase activity protein binding binding ubiquitin binding ubiquitin-like protein binding cysteine-type deubiquitinase activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity ubiquitin-like protein peptidase activity deubiquitinase activity protein binding binding ubiquitin binding ubiquitin-like protein binding cysteine-type deubiquitinase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation protein catabolic process at synapse regulation of biological process catabolic process regulation of cellular process biological regulation metabolic process cellular process regulation of catabolic process regulation of metabolic process regulation protein catabolic process at presynapse negative regulation of proteolysis negative regulation of proteolysis involved in protein catabolic process proteolysis involved in protein catabolic process negative regulation of biological process regulation protein catabolic process at synapse regulation of biological process catabolic process regulation of cellular process biological regulation metabolic process cellular process regulation of catabolic process regulation of metabolic process regulation protein catabolic process at presynapse negative regulation of proteolysis negative regulation of proteolysis involved in protein catabolic process proteolysis involved in protein catabolic process negative regulation of biological process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of primary metabolic process regulation of proteolysis involved in protein catabolic process regulation of proteolysis modification-dependent macromolecule catabolic process proteolysis negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of ubiquitin-dependent protein catabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process protein catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process macromolecule metabolic process positive regulation of proteasomal protein catabolic process positive regulation of protein metabolic process positive regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process positive regulation of macromolecule metabolic process positive regulation of cellular process proteasomal protein catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process positive regulation of proteolysis regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of protein catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal negative regulation of protein catabolic process negative regulation of proteasomal ubiquitin-dependent protein catabolic process negative regulation of proteasomal protein catabolic process regulation of protein stability regulation of biological quality protein deubiquitination protein modification by small protein removal protein K48-linked deubiquitination adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of immune effector process T cell mediated immunity regulation of response to biotic stimulus response to stimulus negative regulation of response to biotic stimulus immune response to tumor cell negative regulation of immune response to tumor cell negative regulation of response to tumor cell negative regulation of lymphocyte mediated immunity regulation of response to tumor cell response to biotic stimulus T cell mediated immune response to tumor cell negative regulation of T cell mediated immune response to tumor cell regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of T cell mediated immune response to tumor cell leukocyte mediated immunity regulation of immune system process regulation of T cell mediated immunity response to tumor cell immune response regulation of adaptive immune response negative regulation of response to stimulus negative regulation of immune response negative regulation of immune effector process regulation of immune response to tumor cell negative regulation of adaptive immune response adaptive immune response immune effector process negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of leukocyte mediated immunity regulation of lymphocyte mediated immunity regulation of response to stimulus negative regulation of immune system process immune system process regulation of immune response negative regulation of leukocyte mediated immunity negative regulation of T cell mediated immunity	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol presynapse synapse cell junction membrane-bounded organelle intracellular organelle organelle lytic vacuole vacuole intracellular membrane-bounded organelle lysosome cellular anatomical structure intracellular anatomical structure cytoplasm cytosol presynapse synapse cell junction membrane-bounded organelle intracellular organelle organelle lytic vacuole vacuole intracellular membrane-bounded organelle lysosome nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR016652	Ubiquitinyl hydrolase	Family
A, B	IPR041432	Ubiquitinyl hydrolase, variant UBP zinc finger	Domain
A, B	IPR001607	Zinc finger, UBP-type	Domain
A, B	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A, B	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B	IPR050185	Ubiquitin carboxyl-terminal hydrolase	Family
A, B	IPR015940	Ubiquitin-associated domain	Domain
A, B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B	IPR028889	Ubiquitin specific protease UPS, catalytic domain	Domain
A, B	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
A, B	IPR009060	UBA-like superfamily	Homologous Superfamily
A, B	IPR041812	Ubiquitin carboxyl-terminal hydrolase 5, UBA1 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P45974	colorectal cancer large cell medulloblastoma diabetes mellitus drug-induced liver injury

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.