1R79 | pdb_00001r79

Solution Structure of The C1 Domain of The Human Diacylglycerol Kinase Delta

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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
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)
A	d1r79a1	Small proteins	Cysteine-rich domain	Cysteine-rich domain	Protein kinase cysteine-rich domain (cys2, phorbol-binding domain)	Diacylglycerol kinase delta	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1r79a3	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1r79a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	C1 domain	8028038	4003764	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cysteine-rich domain	8040417	3001452	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	C1_1	e1r79A1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: Cysteine-rich domain	F: C1_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.60.20	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00130	Phorbol esters/diacylglycerol binding domain (C1 domain) (C1_1)	Phorbol esters/diacylglycerol binding domain (C1 domain)	This domain is also known as the Protein kinase C conserved region 1 (C1) domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Diacylglycerol kinase, delta	binding lipid binding diacylglycerol binding protein heterodimerization activity protein binding protein dimerization activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding binding lipid binding diacylglycerol binding protein heterodimerization activity protein binding protein dimerization activity 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 kinase binding enzyme binding identical protein binding protein homodimerization activity kinase activity lipid kinase activity transferase activity ATP-dependent diacylglycerol kinase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups cation binding transition metal ion binding zinc ion binding metal ion binding	phosphatidic acid biosynthetic process glycerophospholipid biosynthetic process phosphatidic acid metabolic process glycerophospholipid metabolic process lipid biosynthetic process primary metabolic process phospholipid biosynthetic process phospholipid metabolic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process glycerolipid metabolic process phosphatidic acid biosynthetic process glycerophospholipid biosynthetic process phosphatidic acid metabolic process glycerophospholipid metabolic process lipid biosynthetic process primary metabolic process phospholipid biosynthetic process phospholipid metabolic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process glycerolipid metabolic process metabolic process cellular process phosphorus metabolic process lipid metabolic process neutral lipid metabolic process lipid catabolic process catabolic process neutral lipid catabolic process glycerolipid catabolic process acylglycerol catabolic process diacylglycerol metabolic process acylglycerol metabolic process diacylglycerol catabolic process localization import into cell transport endocytosis establishment of localization vesicle-mediated transport establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization lipid phosphorylation phosphorylation lipid modification cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway cell communication positive regulation of response to stimulus positive regulation of ERBB signaling pathway regulation of epidermal growth factor receptor signaling pathway epidermal growth factor receptor signaling pathway signal transduction enzyme-linked receptor protein signaling pathway positive regulation of cellular process positive regulation of epidermal growth factor receptor signaling pathway regulation of biological process regulation of ERBB signaling pathway regulation of signaling cell surface receptor signaling pathway biological regulation regulation of response to stimulus ERBB signaling pathway regulation of cell communication positive regulation of signaling multicellular organismal process regulation of body fluid levels wound healing cell activation hemostasis blood coagulation response to stress coagulation regulation of biological quality response to wounding platelet activation negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process negative regulation of cell communication intracellular signal transduction regulation of intracellular signal transduction negative regulation of cellular process intracellular signaling cassette negative regulation of phospholipase C/protein kinase C signal transduction negative regulation of response to stimulus negative regulation of signal transduction phospholipase C/protein kinase C signal transduction phospholipase C-activating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway regulation of localization positive regulation of cellular component organization regulation of cellular component organization cellular component organization positive regulation of endocytosis clathrin-dependent endocytosis cellular component organization or biogenesis positive regulation of receptor-mediated endocytosis regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport positive regulation of transport positive regulation of clathrin-dependent endocytosis receptor-mediated endocytosis regulation of clathrin-dependent endocytosis	cellular anatomical structure clathrin-coated pit membrane endomembrane system intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle intracellular vesicle cellular anatomical structure clathrin-coated pit membrane endomembrane system intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle intracellular vesicle intracellular membrane-bounded organelle vesicle nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001849	Pleckstrin homology domain	Domain
A	IPR000756	Diacylglycerol kinase, accessory domain	Domain
A	IPR011993	PH-like domain superfamily	Homologous Superfamily
A	IPR016064	NAD kinase/diacylglycerol kinase-like domain superfamily	Homologous Superfamily
A	IPR037606	Diacylglycerol kinase delta, SAM domain	Domain
A	IPR002219	Protein kinase C-like, phorbol ester/diacylglycerol-binding domain	Domain
A	IPR013761	Sterile alpha motif/pointed domain superfamily	Homologous Superfamily
A	IPR017438	Inorganic polyphosphate/ATP-NAD kinase, N-terminal	Homologous Superfamily
A	IPR054474	Diacylglycerol kinase eta/delta/kappa, helical domain	Domain
A	IPR001206	Diacylglycerol kinase, catalytic domain	Domain
A	IPR037607	Diacylglycerol kinase	Family
A	IPR047478	Diacylglycerol kinase delta, first protein kinase C conserved region 1	Domain
A	IPR047477	Diacylglycerol kinase delta, second protein kinase C conserved region 1	Domain
A	IPR046349	C1-like domain superfamily	Homologous Superfamily
A	IPR001660	Sterile alpha motif domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q16760	congestive heart failure gastric carcinoma nephrolithiasis pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ulcerative colitis Crohn disease inflammatory bowel disease open-angle glaucoma rheumatoid arthritis diabetes mellitus lung carcinoma osteosarcoma type 2 diabetes mellitus

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	OPM	Monotopic/peripheral	All beta monotopic/peripheral	C1 domain	C1 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.