4GAO | pdb_00004gao

DCNL complex with N-terminally acetylated NEDD8 E2 peptide

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)
G	SCOP2B Superfamily	EF-hand	8055671	3001983	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	EF-hand	8055672	3001983	SCOP2B (2022-06-29)
D	SCOP2 Family	DCNL PONY Domain-like	8051686	4007471	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	EF-hand	8055672	3001983	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	EF-hand	8055671	3001983	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	EF-hand	8055672	3001983	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EF-hand	8055671	3001983	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-hand	8055672	3001983	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-hand	8055671	3001983	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)
G	SmpA_OmlA	e4gaoG2	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
G	Cobalamin_bind	e4gaoG3	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (v294.1)
D	SmpA_OmlA	e4gaoD2	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
D	Cobalamin_bind	e4gaoD3	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (v294.1)
B	SmpA_OmlA	e4gaoB2	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
B	Cobalamin_bind	e4gaoB3	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (v294.1)
A		e4gaoA2	A: a/b three-layered sandwiches	X: Globin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: (Phosphotyrosine protein) phosphatases II	F:	ECOD (v294.1)
A	Cobalamin_bind	e4gaoA3	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
G	1.10.238.200	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
D	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
D	1.10.238.200	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
B	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
B	1.10.238.200	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, D, G	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
C, E, F, H	NEDD8-conjugating enzyme Ubc12	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity NEDD8 transferase activity catalytic activity, acting on a protein acyltransferase activity NEDD8 conjugating enzyme activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process multicellular organismal process regulation of cellular component organization regulation of cellular process cellular component organization cellular component biogenesis multicellular organism development macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process multicellular organismal process regulation of cellular component organization regulation of cellular process cellular component organization cellular component biogenesis multicellular organism development cellular component assembly regulation of postsynapse assembly cell junction assembly anatomical structure development regulation of synapse structure or activity synapse organization cellular component organization or biogenesis regulation of synapse assembly regulation of biological quality system development developmental process regulation of biological process postsynapse organization postsynapse assembly biological regulation regulation of postsynapse organization nervous system development regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol presynapse synapse cell junction postsynapse membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol presynapse synapse cell junction postsynapse membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen glutamatergic synapse
A, B, D, G	DCN1-like protein 2	protein binding binding ubiquitin-like protein binding ubiquitin-like protein conjugating enzyme binding enzyme binding ubiquitin conjugating enzyme binding cullin family protein binding	primary metabolic process macromolecule modification metabolic process cellular 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 biological process regulation of cellular process regulation of protein modification process primary metabolic process macromolecule modification metabolic process cellular 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 biological process regulation of cellular process regulation of protein modification process regulation of post-translational protein modification regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process regulation of primary metabolic process regulation of protein neddylation regulation of protein modification by small protein conjugation or removal regulation of metabolic process positive regulation of protein metabolic process positive regulation of biological process positive regulation of post-translational protein modification positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein neddylation	cellular anatomical structure intracellular anatomical structure cytoplasm protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, E, F, H	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
C, E, F, H	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
C, E, F, H	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
C, E, F, H	IPR050113	Ubiquitin-conjugating enzyme E2-like	Family
A, B, D, G	IPR042460	DCN1-like, PONY binding domain	Homologous Superfamily
A, B, D, G	IPR009060	UBA-like superfamily	Homologous Superfamily
A, B, D, G	IPR005176	Potentiating neddylation domain	Domain
A, B, D, G	IPR014764	Defective-in-cullin neddylation protein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, E, F, H	Pharos: P61081	astrocytic tumor dermatomyositis oligodendroglioma psoriasis colorectal adenoma glioblastoma osteosarcoma colorectal cancer lung cancer plasma cell myeloma
A, B, D, G	Pharos: Q6PH85	glioblastoma osteosarcoma malignant glioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia malignant mesothelioma subependymal giant cell astrocytoma

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.