5TDB | pdb_00005tdb

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	zf-UBR	e5tdbA1	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	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	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 cation binding organic acid binding binding ion binding anion 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 cation binding organic acid binding binding ion binding anion binding L-leucine binding amino acid binding carboxylic acid binding small molecule binding histone H2A ubiquitin ligase activity histone ubiquitin ligase activity histone modifying activity transition metal ion binding zinc ion binding metal ion binding	regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process retrotransposition regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression transposition macromolecule biosynthetic process regulation of gene expression regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process retrotransposition regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression transposition macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process transposable element silencing regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process 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 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 nuclear division organelle organization meiosis I cell cycle process male meiotic nuclear division 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 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 cellular response to stimulus positive regulation of cell communication immune response-regulating cell surface receptor signaling pathway positive regulation of signal transduction positive regulation of T cell receptor signaling pathway response to stimulus signaling positive regulation of biological process regulation of antigen receptor-mediated signaling pathway regulation of signal transduction cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process positive regulation of cellular process regulation of signaling cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response regulation of T cell receptor signaling pathway T cell receptor signaling pathway regulation of response to stimulus immune system process regulation of immune response regulation of cell communication antigen receptor-mediated signaling pathway activation of immune response positive regulation of antigen receptor-mediated signaling pathway positive regulation of signaling ubiquitin-dependent protein catabolic process via the N-end rule pathway negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of cell communication intracellular signal transduction negative regulation of TOR signaling regulation of intracellular signal transduction TOR signaling regulation of TOR signaling negative regulation of response to stimulus negative regulation of signal transduction protein polyubiquitination protein K63-linked ubiquitination chromatin organization chromatin remodeling heterochromatin formation epigenetic regulation of gene expression negative regulation of gene expression, epigenetic male meiosis I 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome protein-containing complex ubiquitin ligase complex catalytic complex transferase complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome protein-containing complex 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	IPR055194	E3 ubiquitin-protein ligase UBR1-like, winged-helix domain	Domain
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 R01GM157729.