2YUU

Solution structure of the first Phorbol esters/diacylglycerol binding domain of human Protein kinase C, 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	d2yuua1	Small proteins	Cysteine-rich domain	Cysteine-rich domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2yuua3	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2yuua2	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	8018920	4003764	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cysteine-rich domain	8057950	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	e2yuuA1	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	Protein kinase C delta type	protein binding binding insulin receptor substrate binding protein serine/threonine kinase activity diacylglycerol-dependent serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity diacylglycerol-dependent, calcium-independent serine/threonine kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups adenyl ribonucleotide binding protein binding binding insulin receptor substrate binding protein serine/threonine kinase activity diacylglycerol-dependent serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity diacylglycerol-dependent, calcium-independent serine/threonine kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding non-membrane spanning protein tyrosine kinase activity protein tyrosine kinase activity cation binding metal ion binding protein serine kinase activity enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity kinase binding enzyme binding protein kinase binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process regulation of cellular process reactive oxygen species metabolic process biological regulation positive regulation of biological process regulation of superoxide metabolic process positive regulation of reactive oxygen species metabolic process superoxide metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process regulation of cellular process reactive oxygen species metabolic process biological regulation positive regulation of biological process regulation of superoxide metabolic process positive regulation of reactive oxygen species metabolic process superoxide metabolic process positive regulation of metabolic process superoxide anion generation metabolic process positive regulation of superoxide anion generation regulation of superoxide anion generation regulation of metabolic process regulation of reactive oxygen species metabolic process positive regulation of cellular process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process regulation of protein stability regulation of biological quality protein stabilization positive regulation of cell communication positive regulation of signal transduction signaling regulation of signal transduction regulation of programmed cell death positive regulation of apoptotic signaling pathway cell communication positive regulation of response to stimulus signal transduction regulation of signaling positive regulation of programmed cell death regulation of apoptotic process cell death positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication apoptotic process programmed cell death positive regulation of signaling regulation of apoptotic signaling pathway regulation of catalytic activity negative regulation of biological process negative regulation of catalytic activity regulation of transferase activity regulation of MAP kinase activity intracellular signal transduction regulation of primary metabolic process negative regulation of kinase activity negative regulation of transferase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process intracellular signaling cassette negative regulation of protein modification process phosphorus metabolic process protein modification process negative regulation of protein metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of MAPK cascade regulation of molecular function regulation of kinase activity negative regulation of protein phosphorylation regulation of protein serine/threonine kinase activity macromolecule modification regulation of phosphorus metabolic process macromolecule metabolic process regulation of protein modification process regulation of protein phosphorylation negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of phosphate metabolic process negative regulation of cell communication regulation of intracellular signal transduction negative regulation of protein serine/threonine kinase activity negative regulation of cellular process protein metabolic process negative regulation of macromolecule metabolic process negative regulation of response to stimulus negative regulation of molecular function negative regulation of MAP kinase activity regulation of protein kinase activity regulation of macromolecule metabolic process negative regulation of protein kinase activity negative regulation of signal transduction negative regulation of phosphorus metabolic process MAPK cascade regulation of phosphorylation negative regulation of phosphorylation negative regulation of MAPK cascade multicellular organismal process regulation of body fluid levels regulation of cell activation negative regulation of cell adhesion negative regulation of platelet activation regulation of coagulation response to wounding negative regulation of homotypic cell-cell adhesion negative regulation of wound healing negative regulation of blood coagulation response to external stimulus blood coagulation negative regulation of hemostasis regulation of platelet activation negative regulation of response to external stimulus negative regulation of cell-cell adhesion regulation of wound healing negative regulation of multicellular organismal process platelet activation regulation of response to external stimulus homotypic cell-cell adhesion regulation of response to wounding cell adhesion cell-cell adhesion regulation of response to stress coagulation regulation of cell-cell adhesion regulation of multicellular organismal process regulation of hemostasis wound healing regulation of homotypic cell-cell adhesion regulation of cell adhesion regulation of blood coagulation hemostasis cell activation negative regulation of platelet aggregation negative regulation of response to wounding platelet aggregation negative regulation of cell activation regulation of platelet aggregation negative regulation of coagulation peptidyl-amino acid modification peptidyl-threonine modification peptidyl-threonine phosphorylation biological process involved in interspecies interaction between organisms response to other organism defense response response to biotic stimulus defense response to bacterium defense response to other organism response to bacterium response to external biotic stimulus cellular senescence protein localization regulation of localization cellular localization establishment of protein localization nitrogen compound transport regulation of protein localization nucleocytoplasmic transport transport positive regulation of nucleocytoplasmic transport nuclear transport positive regulation of establishment of protein localization regulation of protein localization to nucleus positive regulation of protein transport localization import into nucleus regulation of protein import into nucleus cellular macromolecule localization establishment of localization in cell protein import into nucleus positive regulation of intracellular transport regulation of intracellular transport regulation of transport positive regulation of protein localization to nucleus regulation of establishment of protein localization positive regulation of protein import into nucleus intracellular transport regulation of nucleocytoplasmic transport protein localization to nucleus regulation of protein transport establishment of localization positive regulation of transport establishment of protein localization to organelle regulation of cellular localization protein transport macromolecule localization protein localization to organelle positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport intracellular protein transport positive regulation of phosphorylation positive regulation of protein metabolic process positive regulation of phosphate metabolic process positive regulation of molecular function positive regulation of protein modification process positive regulation of macromolecule metabolic process positive regulation of protein kinase activity positive regulation of protein phosphorylation positive regulation of transferase activity positive regulation of phosphorus metabolic process positive regulation of catalytic activity positive regulation of kinase activity activation of protein kinase activity sphingolipid catabolic process regulation of amide metabolic process catabolic process sphingomyelin catabolic process phospholipid catabolic process regulation of lipid metabolic process organophosphate catabolic process regulation of sphingomyelin catabolic process positive regulation of phospholipid catabolic process phospholipid metabolic process positive regulation of lipid catabolic process positive regulation of lipid metabolic process amide metabolic process sphingomyelin metabolic process membrane lipid metabolic process regulation of phospholipid catabolic process regulation of membrane lipid metabolic process lipid catabolic process positive regulation of sphingomyelin catabolic process regulation of phospholipid metabolic process sphingolipid metabolic process regulation of catabolic process regulation of lipid catabolic process membrane lipid catabolic process positive regulation of phospholipid metabolic process positive regulation of catabolic process organophosphate metabolic process positive regulation of amide metabolic process lipid metabolic process cellular response to nitrogen compound response to peptide hormone insulin receptor signaling pathway regulation of cellular response to insulin stimulus cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus response to hormone enzyme-linked receptor protein signaling pathway cellular response to hormone stimulus cell surface receptor signaling pathway response to endogenous stimulus regulation of insulin receptor signaling pathway response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus negative regulation of cellular response to insulin stimulus negative regulation of insulin receptor signaling pathway response to chemical response to insulin cellular response to insulin stimulus filopodium assembly regulation of cellular component organization cell projection organization negative regulation of filopodium assembly regulation of filopodium assembly plasma membrane bounded cell projection assembly cellular component organization cellular component biogenesis negative regulation of plasma membrane bounded cell projection assembly cellular component assembly cellular component organization or biogenesis negative regulation of cell projection organization plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of plasma membrane bounded cell projection assembly cell projection assembly regulation of plasma membrane bounded cell projection organization post-translational protein modification cell chemotaxis chemotaxis taxis cell migration cell motility locomotion peptidyl-serine modification peptidyl-serine phosphorylation regulation of glial cell apoptotic process negative regulation of programmed cell death negative regulation of glial cell apoptotic process glial cell apoptotic process negative regulation of apoptotic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process regulation of mRNA catabolic process regulation of nucleobase-containing compound metabolic process RNA catabolic process regulation of biosynthetic process mRNA catabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of mRNA stability regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of RNA stability nucleic acid catabolic process regulation of macromolecule biosynthetic process regulation of mRNA metabolic process regulation of phospholipid transport phospholipid translocation phospholipid transport regulation of lipid transporter activity regulation of lipid transport regulation of transporter activity positive regulation of lipid transporter activity plasma membrane organization endomembrane system organization membrane organization lipid localization regulation of phospholipid translocation positive regulation of phospholipid scramblase activity lipid transport positive regulation of lipid localization regulation of membrane lipid distribution lipid translocation regulation of phospholipid scramblase activity regulation of plasma membrane organization positive regulation of lipid transport regulation of lipid localization positive regulation of transporter activity organophosphate ester transport cellular response to oxidative stress cellular response to chemical stress response to oxidative stress response to hydroperoxide cellular response to hydroperoxide regulation of cytoskeleton organization regulation of actin filament-based process actin cytoskeleton organization regulation of organelle organization organelle organization regulation of actin cytoskeleton organization actin filament-based process cytoskeleton organization neutrophil activation myeloid leukocyte activation granulocyte activation leukocyte activation sphingolipid biosynthetic process lipid biosynthetic process regulation of sphingolipid biosynthetic process regulation of ceramide biosynthetic process ceramide metabolic process amide biosynthetic process ceramide biosynthetic process regulation of lipid biosynthetic process membrane lipid biosynthetic process regulation of defense response negative regulation of inflammatory response regulation of inflammatory response negative regulation of defense response inflammatory response termination of signal transduction peptidyl-tyrosine modification negative regulation of peptidyl-tyrosine phosphorylation regulation of peptidyl-tyrosine phosphorylation peptidyl-tyrosine phosphorylation glycolipid metabolic process carbohydrate derivative metabolic process regulation of glucosylceramide catabolic process ceramide catabolic process glycosylceramide metabolic process carbohydrate derivative catabolic process positive regulation of glucosylceramide catabolic process glycosphingolipid catabolic process glycosphingolipid metabolic process liposaccharide metabolic process glucosylceramide metabolic process glycosylceramide catabolic process glycolipid catabolic process glucosylceramide catabolic process regulation of cellular component size regulation of protein-containing complex assembly protein-containing complex assembly negative regulation of protein polymerization regulation of actin filament polymerization negative regulation of supramolecular fiber organization negative regulation of actin filament polymerization protein polymerization actin polymerization or depolymerization regulation of actin filament organization actin filament polymerization protein-containing complex organization negative regulation of cytoskeleton organization actin filament organization regulation of actin polymerization or depolymerization negative regulation of protein-containing complex assembly negative regulation of organelle organization regulation of protein polymerization regulation of actin filament length regulation of supramolecular fiber organization supramolecular fiber organization regulation of anatomical structure size regulation of endodeoxyribonuclease activity regulation of deoxyribonuclease activity regulation of nuclease activity positive regulation of endodeoxyribonuclease activity positive regulation of deoxyribonuclease activity positive regulation of nucleobase-containing compound metabolic process positive regulation of nuclease activity DNA metabolic process positive regulation of hydrolase activity positive regulation of DNA metabolic process regulation of hydrolase activity regulation of DNA metabolic process cell population proliferation B cell activation B cell proliferation lymphocyte activation leukocyte proliferation mononuclear cell proliferation lymphocyte proliferation cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide cellular response to reactive oxygen species 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 response to lipid response to fatty acid cellular response to fatty acid cellular response to lipid intrinsic apoptotic signaling pathway in response to oxidative stress intrinsic apoptotic signaling pathway response to angiotensin cellular response to angiotensin immune response-regulating cell surface receptor signaling pathway involved in phagocytosis import into cell immune response-regulating cell surface receptor signaling pathway Fc-gamma receptor signaling pathway involved in phagocytosis vesicle-mediated transport immune response-activating signaling pathway Fc receptor signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process phagocytosis Fc-gamma receptor signaling pathway positive regulation of immune system process immune response-activating cell surface receptor signaling pathway Fc receptor mediated stimulatory signaling pathway regulation of immune response endocytosis activation of immune response positive regulation of ceramide biosynthetic process positive regulation of sphingolipid biosynthetic process positive regulation of biosynthetic process positive regulation of lipid biosynthetic process	cell-cell junction cellular anatomical structure anchoring junction cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cell-cell junction cellular anatomical structure anchoring junction cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm intracellular organelle mitochondrion intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen organelle lumen nuclear periphery nuclear lumen nuclear matrix endosome intracellular vesicle lytic vacuole vacuole endomembrane system endolysosome cytoplasmic vesicle lysosome cell periphery plasma membrane membrane cytoplasmic vesicle lumen vacuolar lumen vesicle lumen azurophil granule secretory granule lumen azurophil granule lumen secretory granule primary lysosome secretory vesicle nucleoplasm endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR034667	Novel protein kinase C delta, catalytic domain	Domain
A	IPR020454	Diacylglycerol/phorbol-ester binding	Domain
A	IPR014376	Protein kinase C, delta/epsilon/eta/theta types	Family
A	IPR000719	Protein kinase domain	Domain
A	IPR017892	Protein kinase, C-terminal	Domain
A	IPR050236	Serine/threonine-protein kinases, AGC	Family
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR000008	C2 domain	Domain
A	IPR000961	AGC-kinase, C-terminal	Domain
A	IPR002219	Protein kinase C-like, phorbol ester/diacylglycerol-binding domain	Domain
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR035892	C2 domain superfamily	Homologous Superfamily
A	IPR027436	Protein kinase C, delta	Family
A	IPR046349	C1-like domain superfamily	Homologous Superfamily
A	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q05655	autoimmune lymphoproliferative syndrome type 3 common variable immunodeficiency autoimmune lymphoproliferative syndrome visual epilepsy Liver Cirrhosis, Experimental hypertensive disorder intestinal cancer autosomal systemic lupus erythematosus type 16 non-alcoholic fatty liver disease parkinsonian disorder drug-induced liver injury agammaglobulinemia intestinal neoplasm atypical teratoid rhabdoid tumor large cell medulloblastoma autoimmune lymphoproliferative syndrome type 3 common variable immunodeficiency autoimmune lymphoproliferative syndrome visual epilepsy Liver Cirrhosis, Experimental hypertensive disorder intestinal cancer autosomal systemic lupus erythematosus type 16 non-alcoholic fatty liver disease parkinsonian disorder drug-induced liver injury agammaglobulinemia intestinal neoplasm atypical teratoid rhabdoid tumor large cell medulloblastoma lung carcinoma autosomal recessive juvenile Parkinson disease 2 B cell deficiency oligodendroglioma Crohn disease actinic keratosis interstitial cystitis toxic encephalopathy autism spectrum disorder malignant ependymoma cancer osteosarcoma acute myeloid leukemia lung cancer medulloblastoma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	OPM				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.