5VMD | pdb_00005vmd

Crystal structure of UBR-box from UBR6 in a domain-swapping conformation

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)
D	SCOP2B Superfamily	B-box zinc-binding domain	8095826	3001359	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	B-box zinc-binding domain	8095826	3001359	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	B-box zinc-binding domain	8095826	3001359	SCOP2B (2022-06-29)
A	SCOP2 Family	UBR-box zinc-binding domain	8095822	4006721	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	B-box zinc-binding domain	8095826	3001359	SCOP2 (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	zf-UBR	e5vmdD1	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	zf-UBR	e5vmdC1	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	e5vmdB1	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	e5vmdA1	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, C, D	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, B, C, D	F-box only protein 11	catalytic activity, acting on a protein transferase activity, transferring one-carbon groups arginine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity protein-arginine N-methyltransferase activity ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups arginine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity protein-arginine N-methyltransferase activity ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity aminoacyltransferase activity ubiquitin-like protein transferase activity acyltransferase activity ubiquitin-protein transferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process regulation of biological process regulation of cellular process regulation of apoptotic process biological regulation apoptotic process regulation of programmed cell death cell death macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process regulation of biological process regulation of cellular process regulation of apoptotic process biological regulation apoptotic process regulation of programmed cell death cell death programmed cell death protein ubiquitination post-translational protein modification 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 multicellular organismal process system process sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus regulation of epithelial to mesenchymal transition regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation mesenchyme development cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation regulation of multicellular organismal process developmental process negative regulation of developmental process animal organ development tissue development negative regulation of epithelial to mesenchymal transition epithelial to mesenchymal transition mesenchymal cell differentiation negative regulation of multicellular organismal process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm cytosol nucleoplasm chromosome protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR051550	SCF Complex Subunits and Alginate Epimerases	Family
A, B, C, D	IPR039448	Right handed beta helix domain	Domain
A, B, C, D	IPR001810	F-box domain	Domain
A, B, C, D	IPR047504	F-box only protein 11, UBR-box	Domain
A, B, C, D	IPR007742	Periplasmic copper-binding protein NosD, beta helix domain	Domain
A, B, C, D	IPR036047	F-box-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR012334	Pectin lyase fold	Homologous Superfamily
A, B, C, D	IPR003126	Zinc finger, UBR-type	Domain
A, B, C, D	IPR006633	Carbohydrate-binding/sugar hydrolysis domain	Domain
A, B, C, D	IPR006626	Parallel beta-helix repeat	Repeat
A, B, C, D	IPR047505	F-box only protein 11, F-box domain	Domain
A, B, C, D	IPR022441	Parallel beta-helix repeat-2	Repeat
A, B, C, D	IPR011050	Pectin lyase fold/virulence factor	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q86XK2	astrocytic tumor diffuse large B-cell lymphoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma tuberculosis attention deficit hyperactivity disorder, inattentive type lung cancer osteosarcoma psoriasis breast cancer medulloblastoma ovarian cancer Sjogren syndrome

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.