5V89

Structure of DCN4 PONY domain bound to CUL1 WHB

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	DCNL PONY Domain-like	8055675	4007471	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	EF-hand	8055676	3001983	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	EF-hand	8055677	3001983	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)
A	F_UNCLASSIFIED	e5v89A2	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF03556	e5v89A1	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: PF03556	ECOD (1.6)
B [auth C]	PF10557	e5v89C1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF10557	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
A	1.10.238.200	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
B [auth C]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03556	Cullin binding (Cullin_binding)	Cullin binding	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DCN1-like protein 4	protein binding binding ubiquitin-like protein binding ubiquitin-like protein conjugating enzyme binding enzyme binding ubiquitin conjugating enzyme binding cullin family protein binding	organonitrogen compound metabolic process primary metabolic process organic substance metabolic process macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of protein modification process positive regulation of protein metabolic process organonitrogen compound metabolic process primary metabolic process organic substance metabolic process macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process positive regulation of protein neddylation regulation of protein neddylation regulation of metabolic process	protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity
B [auth C]	Cullin-1	ubiquitin ligase complex scaffold activity protein-macromolecule adaptor activity molecular adaptor activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction cellular process positive regulation of signaling developmental process anatomical structure morphogenesis animal organ development anatomical structure development animal organ morphogenesis cell death apoptotic signaling pathway apoptotic process intrinsic apoptotic signaling pathway programmed cell death cell population proliferation organonitrogen compound metabolic process primary metabolic process organic substance metabolic process protein ubiquitination macromolecule modification metabolic 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 organonitrogen compound catabolic process 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 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process organic substance catabolic process protein polyubiquitination protein K48-linked ubiquitination mitotic cell cycle process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition cell cycle process protein monoubiquitination	cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane Parkin-FBXW7-Cul1 ubiquitin ligase complex cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane Parkin-FBXW7-Cul1 ubiquitin ligase complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen SCF ubiquitin ligase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR042460	DCN1-like, PONY binding domain	Homologous Superfamily
A	IPR005176	Potentiating neddylation domain	Domain
A	IPR014764	Defective-in-cullin neddylation protein	Family
B [auth C]	IPR045093	Cullin	Family
B [auth C]	IPR019559	Cullin protein, neddylation domain	Domain
B [auth C]	IPR016158	Cullin homology domain	Domain
B [auth C]	IPR016157	Cullin, conserved site	Conserved Site
B [auth C]	IPR001373	Cullin, N-terminal	Domain
B [auth C]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B [auth C]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
B [auth C]	IPR036317	Cullin homology domain superfamily	Homologous Superfamily
B [auth C]	IPR016159	Cullin repeat-like-containing domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q92564	Alzheimer disease osteosarcoma Pick disease large cell medulloblastoma ovarian cancer progressive supranuclear palsy lung cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis
B [auth C]	Pharos: Q13616	Stevens-Johnson syndrome Drug-Induced Stevens Johnson Syndrome ovarian cancer toxic epidermal necrolysis inflammatory bowel disease

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.