5TDC | pdb_00005tdc

Crystal structure of the human UBR-box domain from UBR1 in complex with monomethylated arginine peptide.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth C]	SCOP2B Superfamily	B-box zinc-binding domain	8095825	3001359	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	B-box zinc-binding domain	8095825	3001359	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 [auth C]	zf-UBR	e5tdcC1	A: few secondary structure elements	X: B-box zinc-binding domain-like	H: UBR box (From Topology)	T: UBR box	F: zf-UBR	ECOD (1.6)
A	zf-UBR	e5tdcA1	A: few secondary structure elements	X: B-box zinc-binding domain-like	H: UBR box (From Topology)	T: UBR box	F: zf-UBR	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C]	PF02207	Putative zinc finger in N-recognin (UBR box) (zf-UBR)	Putative zinc finger in N-recognin (UBR box)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth B], D	NMM-ILE-PHE-SER peptide	-	-	-
A, B [auth C]	E3 ubiquitin-protein ligase UBR1	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity organic acid binding anion binding L-leucine binding amino acid binding carboxylic acid binding	ubiquitin-dependent protein catabolic process via the N-end rule pathway catabolic process proteolysis involved in protein catabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process ubiquitin-dependent protein catabolic process via the N-end rule pathway catabolic process proteolysis involved in protein catabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process cellular response to stimulus regulation of cellular process response to stimulus negative regulation of signaling signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction negative regulation of cell communication intracellular signal transduction cell communication negative regulation of TOR signaling regulation of intracellular signal transduction negative regulation of cellular process signal transduction TOR signaling regulation of signaling regulation of biological process regulation of TOR signaling negative regulation of response to stimulus biological regulation negative regulation of signal transduction regulation of response to stimulus regulation of cell communication 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 cellular response to acid chemical cellular response to nitrogen compound cellular response to amino acid stimulus response to oxygen-containing compound response to nitrogen compound response to amino acid cellular response to L-leucine cellular response to oxygen-containing compound response to acid chemical cellular response to chemical stimulus response to chemical response to L-leucine	protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol ubiquitin ligase complex transferase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C]	IPR039164	E3 ubiquitin-protein ligase UBR1-like	Family
A, B [auth C]	IPR055194	E3 ubiquitin-protein ligase UBR1-like, winged-helix domain	Domain
A, B [auth C]	IPR003126	Zinc finger, UBR-type	Domain
A, B [auth C]	IPR044046	E3 ubiquitin-protein ligase UBR-like, C-terminal	Domain
A, B [auth C]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B [auth C]	IPR003769	Adaptor protein ClpS, core	Domain
A, B [auth C]	IPR042065	E3 ubiquitin-protein ligase ELL-like	Homologous Superfamily
A, B [auth C]	IPR047507	E3 ubiquitin-protein ligase UBR1, UBR-box	Domain
A, B [auth C]	IPR014719	Ribosomal protein bL12, C-terminal/adaptor protein ClpS-like	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B [auth C]	Pharos: Q8IWV7	Johanson-Blizzard syndrome atypical teratoid rhabdoid tumor ovarian cancer glioblastoma juvenile dermatomyositis intellectual disability large cell medulloblastoma

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.