3B7Y | pdb_00003b7y

Crystal structure of the C2 Domain of the E3 Ubiquitin-Protein Ligase NEDD4

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3b7yb_	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3b7ya_	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Prenyltransf	e3b7yB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Prenyltransf	ECOD (v294.1)
A	ABC_tran	e3b7yA1	A: a/b three-layered sandwiches	X: Profilin-like	H: sensor domains	T: sensor domains	F: ABC_tran	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.150	Mainly Beta	Sandwich	Immunoglobulin-like	C2 domain	CATH (4.3.0)
A	2.60.40.150	Mainly Beta	Sandwich	Immunoglobulin-like	C2 domain	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	E3 ubiquitin-protein ligase NEDD4	molecular function inhibitor activity sodium channel inhibitor activity channel regulator activity transporter inhibitor activity ion channel regulator activity ion channel inhibitor activity molecular function regulator activity sodium channel regulator activity transporter regulator activity channel inhibitor activity beta-2 adrenergic receptor binding protein binding binding adrenergic receptor binding molecular function inhibitor activity sodium channel inhibitor activity channel regulator activity transporter inhibitor activity ion channel regulator activity ion channel inhibitor activity molecular function regulator activity sodium channel regulator activity transporter regulator activity channel inhibitor activity beta-2 adrenergic receptor binding protein binding binding adrenergic receptor binding signaling receptor binding G protein-coupled receptor binding potassium channel regulator activity potassium channel inhibitor activity 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 proline-rich region binding protein domain specific binding phosphoprotein binding phosphoserine residue binding protein phosphorylated amino acid binding RNA polymerase binding enzyme binding ubiquitin binding ubiquitin-like protein binding ionotropic glutamate receptor binding glutamate receptor binding phosphothreonine residue binding transmembrane transporter binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process immune response immune system process adaptive immune response localization import into cell receptor internalization transport receptor-mediated endocytosis cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process immune response immune system process adaptive immune response localization import into cell receptor internalization transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport response to metal ion response to chemical response to calcium ion regulation of biological process catabolic process regulation of cellular process macroautophagy autophagy biological regulation regulation of catabolic process regulation of autophagy regulation of macroautophagy metabolic process process utilizing autophagic mechanism regulation of metabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process protein metabolic process macromolecule metabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of localization regulation of transport regulation of monoatomic ion transport negative regulation of monoatomic ion transport negative regulation of biological process negative regulation of transport regulation of sodium ion transport metal ion transport monoatomic ion transport negative regulation of sodium ion transport monoatomic cation transport regulation of metal ion transport sodium ion transport cellular response to growth factor stimulus signaling negative regulation of signaling regulation of signal transduction negative regulation of cellular response to growth factor stimulus cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication cell communication regulation of vascular endothelial growth factor receptor signaling pathway cellular response to endogenous stimulus negative regulation of vascular endothelial growth factor receptor signaling pathway negative regulation of cellular process signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus negative regulation of signal transduction vascular endothelial growth factor receptor signaling pathway regulation of response to stimulus regulation of cell communication response to growth factor intracellular receptor signaling pathway response to lipid hormone-mediated signaling pathway intracellular signal transduction response to hormone response to steroid hormone nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to hormone stimulus nuclear receptor-mediated corticosteroid signaling pathway cellular response to chemical stimulus cellular response to lipid nuclear receptor-mediated signaling pathway nuclear receptor-mediated glucocorticoid signaling pathway biological process involved in interspecies interaction between organisms formation of structure involved in a symbiotic process regulation of biological quality regulation of membrane potential virion assembly viral process viral budding viral life cycle progesterone receptor signaling pathway regulation of potassium ion transport monoatomic ion transmembrane transport potassium ion transmembrane transport regulation of monoatomic ion transmembrane transport export across plasma membrane potassium ion export across plasma membrane negative regulation of transmembrane transport monoatomic cation transmembrane transport negative regulation of monoatomic ion transmembrane transport negative regulation of cation transmembrane transport negative regulation of potassium ion transport export from cell negative regulation of potassium ion transmembrane transport regulation of potassium ion transmembrane transport transmembrane transport regulation of transmembrane transport negative regulation of potassium ion export across plasma membrane regulation of potassium ion export across plasma membrane potassium ion transport regulation of monoatomic cation transmembrane transport RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process protein monoubiquitination developmental process multicellular organismal process blood vessel morphogenesis tube development vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis anatomical structure development blood vessel development system development plasma membrane bounded cell projection organization cellular developmental process cell projection organization cell development neuron projection development nervous system development cellular component organization generation of neurons neurogenesis neuron differentiation cell differentiation neuron development cellular component organization or biogenesis heart development animal organ development mesenchyme development tissue development endocardial cushion development receptor catabolic process receptor metabolic process cellular localization nucleocytoplasmic transport positive regulation of nucleocytoplasmic transport nuclear transport positive regulation of biological process intracellular transport regulation of nucleocytoplasmic transport positive regulation of transport regulation of cellular localization establishment of localization in cell positive regulation of intracellular transport positive regulation of cellular process regulation of intracellular transport cell junction organization neuromuscular junction development synapse organization positive regulation of protein metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of protein metabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of protein catabolic process regulation of cellular component organization regulation of synapse organization regulation of synapse structure or activity positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling T cell activation cell activation lymphocyte activation leukocyte activation protein polyubiquitination protein K63-linked ubiquitination response to light stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to light stimulus response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV vacuolar transport lysosomal transport regulation of neuron projection development regulation of developmental process plasma membrane bounded cell projection morphogenesis cell morphogenesis cell projection morphogenesis dendrite development neuron projection morphogenesis regulation of dendrite morphogenesis regulation of anatomical structure morphogenesis regulation of cell projection organization dendrite morphogenesis cell morphogenesis involved in neuron differentiation regulation of dendrite development regulation of plasma membrane bounded cell projection organization establishment of protein localization protein targeting establishment of protein localization to vacuole protein localization to vacuole protein localization to lysosome establishment of protein localization to organelle protein transport protein targeting to lysosome protein localization to organelle macromolecule localization intracellular protein localization protein targeting to vacuole intracellular protein transport heart morphogenesis outflow tract morphogenesis animal organ morphogenesis	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle membraneless organelle extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle membraneless organelle intracellular membraneless organelle chromatin chromosome synapse cell junction glutamatergic synapse Golgi apparatus intracellular membrane-bounded organelle endomembrane system perinuclear region of cytoplasm protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex cell periphery cell cortex plasma membrane membrane apicolateral plasma membrane plasma membrane region nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen postsynapse postsynaptic cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR035983	HECT, E3 ligase catalytic domain	Homologous Superfamily
A, B	IPR036020	WW domain superfamily	Homologous Superfamily
A, B	IPR050409	E3 ubiquitin-protein ligase	Family
A, B	IPR000569	HECT domain	Domain
A, B	IPR035892	C2 domain superfamily	Homologous Superfamily
A, B	IPR001202	WW domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P46934	Stevens-Johnson syndrome keloid acute myeloid leukemia Drug-Induced Stevens Johnson Syndrome lung cancer pilocytic astrocytoma toxic epidermal necrolysis bipolar disorder glioblastoma lung carcinoma plantar fibromatosis coronary artery disease malignant glioma myocardial ischemia reactive cutaneous fibrous lesion Stevens-Johnson syndrome keloid acute myeloid leukemia Drug-Induced Stevens Johnson Syndrome lung cancer pilocytic astrocytoma toxic epidermal necrolysis bipolar disorder glioblastoma lung carcinoma plantar fibromatosis coronary artery disease malignant glioma myocardial ischemia reactive cutaneous fibrous lesion testicular germ cell tumor

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Monotopic/peripheral	All beta monotopic/peripheral	C2 domain	C2 domain

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.