3NIL | pdb_00003nil

The structure of UBR box (RDAA)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth F]	SCOP2B Superfamily	B-box zinc-binding domain	8095823	3001359	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	B-box zinc-binding domain	8095823	3001359	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	B-box zinc-binding domain	8095823	3001359	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	B-box zinc-binding domain	8095823	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)
D [auth F]	zf-UBR	e3nilF1	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)
C [auth D]	zf-UBR	e3nilD1	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)
B	zf-UBR	e3nilB1	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	e3nilA1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth F]	2.10.110.30	Mainly Beta	Ribbon	Cysteine Rich Protein		CATH (4.3.0)
C [auth D]	2.10.110.30	Mainly Beta	Ribbon	Cysteine Rich Protein		CATH (4.3.0)
B	2.10.110.30	Mainly Beta	Ribbon	Cysteine Rich Protein		CATH (4.3.0)
A	2.10.110.30	Mainly Beta	Ribbon	Cysteine Rich Protein		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C [auth D], D [auth F]	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
E [auth X]	Peptide RDAA	-	-	-
A, B, C [auth D], D [auth F]	E3 ubiquitin-protein ligase UBR1	proteasome regulatory particle binding protein-containing complex binding binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding transition metal ion binding zinc ion binding ion binding proteasome regulatory particle binding protein-containing complex binding binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding ubiquitin-like protein ligase activity ubiquitin protein ligase activity	protein polyubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal ubiquitin-dependent protein catabolic process via the N-end rule pathway catabolic process protein polyubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal ubiquitin-dependent protein catabolic process via the N-end rule pathway catabolic process proteolysis involved in protein catabolic 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 mitochondria-associated ubiquitin-dependent protein catabolic process cellular response to stimulus response to stimulus response to nitrogen compound ERAD pathway cellular response to stress response to chemical response to stress response to endoplasmic reticulum stress cytoplasm protein quality control cellular response to misfolded protein response to misfolded protein cellular response to topologically incorrect protein cytoplasm protein quality control by the ubiquitin-proteasome system response to topologically incorrect protein protein quality control for misfolded or incompletely synthesized proteins regulation of localization regulation of biological process nitrogen compound transport regulation of dipeptide transport transport regulation of transport oligopeptide transport regulation of peptide transport biological regulation establishment of localization peptide transport localization dipeptide transport amide transport regulation of oligopeptide transport cellular response to unfolded protein response to unfolded protein protein monoubiquitination ribosome-associated ubiquitin-dependent protein catabolic process stress-induced homeostatically regulated protein degradation pathway	protein-containing complex intracellular anatomical structure catalytic complex peptidase complex proteasome regulatory particle proteasome accessory complex cellular anatomical structure proteasome regulatory particle, base subcomplex proteasome complex endopeptidase complex intracellular protein-containing complex cytoplasm ubiquitin ligase complex transferase complex protein-containing complex intracellular anatomical structure catalytic complex peptidase complex proteasome regulatory particle proteasome accessory complex cellular anatomical structure proteasome regulatory particle, base subcomplex proteasome complex endopeptidase complex intracellular protein-containing complex cytoplasm ubiquitin ligase complex transferase complex UBR1-RAD6 ubiquitin ligase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C [auth D], D [auth F]	IPR039164	E3 ubiquitin-protein ligase UBR1-like	Family
A, B, C [auth D], D [auth F]	IPR055194	E3 ubiquitin-protein ligase UBR1-like, winged-helix domain	Domain
A, B, C [auth D], D [auth F]	IPR003126	Zinc finger, UBR-type	Domain
A, B, C [auth D], D [auth F]	IPR044046	E3 ubiquitin-protein ligase UBR-like, C-terminal	Domain

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.