5TDB

Crystal structure of the human UBR-box domain from UBR2 in complex with asymmetrically double methylated 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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	B-box zinc-binding domain	8095824	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)
A	F_UNCLASSIFIED	e5tdbA1	A: few secondary structure elements	X: Carboxypeptidase inhibitor (From Topology)	H: Carboxypeptidase inhibitor (From Topology)	T: Carboxypeptidase inhibitor	F: F_UNCLASSIFIED	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
A	E3 ubiquitin-protein ligase UBR2	cation binding organic acid binding binding ion binding anion binding L-leucine binding amino acid binding carboxylic acid binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity cation binding organic acid binding binding ion binding anion binding L-leucine binding amino acid binding carboxylic acid 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 histone ubiquitin ligase activity histone modifying activity transition metal ion binding zinc ion binding metal ion binding	cellular response to acid chemical cellular response to stimulus cellular response to nitrogen compound cellular response to amino acid stimulus response to organic substance response to stimulus response to organonitrogen compound response to endogenous 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 cellular response to endogenous stimulus response to acid chemical cellular response to acid chemical cellular response to stimulus cellular response to nitrogen compound cellular response to amino acid stimulus response to organic substance response to stimulus response to organonitrogen compound response to endogenous 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 cellular response to endogenous stimulus response to acid chemical cellular response to chemical stimulus cellular response to organonitrogen compound response to chemical cellular process cellular response to organic substance response to L-leucine developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation homologous recombination meiotic cell cycle process nucleobase-containing compound metabolic process cellular component organization organic substance metabolic process meiosis I meiotic nuclear division cell cycle cellular component organization or biogenesis reciprocal homologous recombination cell cycle process DNA recombination meiotic cell cycle organelle fission primary metabolic process DNA metabolic process nucleic acid metabolic process reciprocal meiotic recombination organic cyclic compound metabolic process nuclear division organelle organization meiosis I cell cycle process metabolic process macromolecule metabolic process regulation of biological process regulation of cellular process negative regulation of cellular process biological regulation negative regulation of biological process retrotransposon silencing transposition retrotransposition male meiotic nuclear division organonitrogen compound metabolic process protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal organonitrogen compound catabolic process 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 organic substance catabolic process signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication negative regulation of TOR signaling regulation of intracellular signal transduction signal transduction TOR signaling regulation of signaling regulation of TOR signaling negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus regulation of cell communication cellular biosynthetic process negative regulation of cellular metabolic process protein-DNA complex organization chromatin organization organic substance biosynthetic process chromatin remodeling negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process regulation of metabolic process male meiosis I	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol intracellular organelle protein-containing complex protein-DNA complex organelle intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle ubiquitin ligase complex catalytic complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol intracellular organelle protein-containing complex protein-DNA complex organelle intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B	DA2-ILE-PHE-SER peptide	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR044046	E3 ubiquitin-protein ligase UBR-like, C-terminal	Domain
A	IPR003769	Adaptor protein ClpS, core	Domain
A	IPR042065	E3 ubiquitin-protein ligase ELL-like	Homologous Superfamily
A	IPR039164	E3 ubiquitin-protein ligase UBR1-like	Family
A	IPR003126	Zinc finger, UBR-type	Domain
A	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A	IPR047508	E3 ubiquitin-protein ligase UBR2, UBR-box	Domain
A	IPR014719	Ribosomal protein bL12, C-terminal/adaptor protein ClpS-like	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q8IWV8	osteosarcoma Sjogren syndrome ovarian cancer psoriasis

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	DA2	Parent Component: ARG RESID: AA0068 PSI-MOD : asymmetric dimethyl-L-arginine MOD:00077

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 R01GM133198.