1W1D

Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain bound to Inositol (1,3,4,5)-tetrakisphosphate

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

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1w1da1	All beta proteins	PH domain-like barrel	PH domain-like	Pleckstrin-homology domain (PH domain)	3-phosphoinositide dependent protein kinase-1	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1w1da2	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	SCOP2B Superfamily	PH domain-like	8043213	3000134	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)
A	PH_3	e1w1dA1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: PH_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF14593	PH domain (PH_3)	PH domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1	binding 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 binding 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 phospholipase binding protein binding enzyme binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein serine/threonine kinase activity enzyme regulator activity enzyme activator activity molecular function activator activity phospholipase activator activity molecular function regulator activity lipase activator activity 3-phosphoinositide-dependent protein kinase activity	regulation of cellular process positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process phosphorus metabolic process protein modification process positive regulation of protein phosphorylation regulation of biological process regulation of cellular process positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process phosphorus metabolic process protein modification process positive regulation of protein phosphorylation regulation of biological process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process primary metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity activation of protein kinase activity macromolecule modification regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of molecular function positive regulation of protein modification process organic substance metabolic process protein metabolic process activation of protein kinase B activity positive regulation of protein kinase activity positive regulation of cellular process organonitrogen compound metabolic process positive regulation of transferase activity biological regulation positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process regulation of phosphorylation cellular process positive regulation of protein localization to plasma membrane protein localization regulation of localization cellular localization regulation of protein localization localization cellular macromolecule localization regulation of protein localization to membrane positive regulation of protein localization to cell periphery protein localization to cell periphery protein localization to plasma membrane positive regulation of protein localization to membrane localization within membrane regulation of protein localization to cell periphery protein localization to membrane regulation of cellular localization macromolecule localization positive regulation of protein localization regulation of protein localization to plasma membrane cellular response to stimulus response to stimulus cell surface receptor signaling pathway signaling cell death extrinsic apoptotic signaling pathway cell communication apoptotic signaling pathway signal transduction apoptotic process programmed cell death peptidyl-amino acid modification peptidyl-threonine modification peptidyl-threonine phosphorylation cellular component organization organelle organization actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization insulin-like growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway cell migration cell motility protein autophosphorylation response to osmotic stress hyperosmotic response response to stress response to abiotic stimulus regulation of phospholipase activity positive regulation of phospholipase activity positive regulation of lipase activity positive regulation of hydrolase activity regulation of hydrolase activity regulation of lipase activity negative regulation of biological process negative regulation of catalytic activity negative regulation of cellular metabolic process negative regulation of kinase activity negative regulation of transferase activity negative regulation of protein modification process negative regulation of protein metabolic process negative regulation of metabolic process negative regulation of protein phosphorylation negative regulation of phosphate metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of molecular function negative regulation of protein kinase activity negative regulation of phosphorus metabolic process negative regulation of phosphorylation negative regulation of transforming growth factor beta receptor signaling pathway cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus negative regulation of signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of signal transduction negative regulation of cell communication regulation of transforming growth factor beta receptor signaling pathway cellular response to endogenous stimulus regulation of signaling negative regulation of response to stimulus regulation of cellular response to transforming growth factor beta stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus negative regulation of signal transduction response to transforming growth factor beta regulation of response to stimulus transforming growth factor beta receptor signaling pathway regulation of cell communication response to growth factor transforming growth factor beta receptor superfamily signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway ERBB signaling pathway epidermal growth factor receptor signaling pathway cell population proliferation positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of vascular endothelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation positive regulation of endothelial cell proliferation vascular endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation positive regulation of vascular endothelial cell proliferation negative regulation of cardiac muscle cell apoptotic process muscle cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of cardiac muscle cell apoptotic process regulation of muscle cell apoptotic process regulation of programmed cell death cardiac muscle cell apoptotic process negative regulation of apoptotic process regulation of striated muscle cell apoptotic process striated muscle cell apoptotic process negative regulation of muscle cell apoptotic process negative regulation of striated muscle cell apoptotic process multicellular organismal process regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation positive regulation of leukocyte activation regulation of multicellular organismal process regulation of immune system process regulation of cell-cell adhesion positive regulation of immune system process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation immune system process lymphocyte costimulation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process T cell costimulation regulation of lymphocyte activation cellular developmental process cell development epithelial cell differentiation multicellular organism development pancreas development columnar/cuboidal epithelial cell development cell differentiation anatomical structure development endocrine pancreas development type B pancreatic cell differentiation system development developmental process epithelium development glandular epithelial cell development endocrine system development animal organ development type B pancreatic cell development tissue development glandular epithelial cell differentiation epithelial cell development enteroendocrine cell differentiation columnar/cuboidal epithelial cell differentiation positive regulation of response to biotic stimulus pattern recognition receptor signaling pathway toll-like receptor signaling pathway response to biotic stimulus immune response-activating signaling pathway positive regulation of immune response innate immune response-activating signaling pathway immune response response to other organism regulation of innate immune response response to external stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway positive regulation of defense response activation of innate immune response regulation of immune response regulation of toll-like receptor signaling pathway activation of immune response regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus positive regulation of response to stimulus positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress innate immune response response to external biotic stimulus positive regulation of innate immune response defense response defense response to symbiont negative regulation of toll-like receptor signaling pathway negative regulation of immune system process positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction intracellular signal transduction 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 calcium-mediated signaling positive regulation of locomotion regulation of cell motility regulation of blood vessel endothelial cell migration endothelial cell migration positive regulation of cell migration positive regulation of epithelial cell migration tissue migration ameboidal-type cell migration positive regulation of cell motility regulation of cell migration blood vessel endothelial cell migration regulation of endothelial cell migration epithelial cell migration regulation of epithelial cell migration locomotion positive regulation of blood vessel endothelial cell migration epithelium migration regulation of locomotion positive regulation of endothelial cell migration cellular response to nitrogen compound response to organic substance response to peptide hormone insulin receptor signaling pathway response to hormone cellular response to organic substance cellular response to hormone stimulus response to organonitrogen compound 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 cellular response to organonitrogen compound response to chemical response to insulin cellular response to insulin stimulus regulation of developmental process angiogenesis regulation of vasculature development positive regulation of developmental process tube morphogenesis regulation of anatomical structure morphogenesis blood vessel development regulation of multicellular organismal development blood vessel morphogenesis tube development positive regulation of angiogenesis vasculature development circulatory system development anatomical structure morphogenesis positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis regulation of sprouting angiogenesis positive regulation of sprouting angiogenesis sprouting angiogenesis regulation of calcium ion transport positive regulation of cation transmembrane transport positive regulation of calcium ion transport intracellular calcium ion homeostasis calcium ion transport positive regulation of monoatomic ion transport positive regulation of monoatomic ion transmembrane transport monoatomic cation homeostasis monoatomic cation transport intracellular monoatomic ion homeostasis regulation of release of sequestered calcium ion into cytosol regulation of monoatomic ion transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport maintenance of location transmembrane transport release of sequestered calcium ion into cytosol regulation of transmembrane transport chemical homeostasis inorganic ion homeostasis transport homeostatic process monoatomic ion transmembrane transport calcium ion homeostasis regulation of monoatomic ion transmembrane transport negative regulation of sequestering of calcium ion metal ion transport maintenance of location in cell regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport intracellular monoatomic cation homeostasis monoatomic ion homeostasis positive regulation of calcium ion transmembrane transport positive regulation of transmembrane transport monoatomic ion transport intracellular chemical homeostasis positive regulation of release of sequestered calcium ion into cytosol regulation of metal ion transport regulation of sequestering of calcium ion calcium ion transmembrane import into cytosol regulation of transport sequestering of calcium ion cellular homeostasis positive regulation of transport regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport negative regulation of endothelial cell apoptotic process regulation of epithelial cell apoptotic process epithelial cell apoptotic process negative regulation of epithelial cell apoptotic process endothelial cell apoptotic process regulation of endothelial cell apoptotic process cellular response to epidermal growth factor stimulus response to epidermal growth factor canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction establishment of organelle localization regulation of immune effector process regulation of myeloid leukocyte mediated immunity regulated exocytosis cell activation involved in immune response leukocyte degranulation myeloid leukocyte mediated immunity vesicle-mediated transport myeloid leukocyte activation establishment of localization in cell leukocyte mediated immunity vacuolar localization mast cell degranulation immune effector process regulation of secretion regulation of leukocyte mediated immunity exocytosis lysosome localization regulation of mast cell degranulation regulation of regulated secretory pathway secretion by cell regulation of secretion by cell organelle localization leukocyte activation involved in immune response mast cell activation regulation of leukocyte degranulation mast cell mediated immunity secretion export from cell regulation of vesicle-mediated transport myeloid cell activation involved in immune response mast cell activation involved in immune response regulation of exocytosis	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol anchoring junction cell junction focal adhesion cell-substrate junction cell periphery plasma membrane membrane membrane-bounded organelle intracellular organelle cytoplasmic vesicle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol anchoring junction cell junction focal adhesion cell-substrate junction cell periphery plasma membrane membrane membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle intracellular vesicle intracellular membrane-bounded organelle vesicle postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization synapse asymmetric synapse cell projection nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR039046	PDPK1 family	Family
A	IPR000719	Protein kinase domain	Domain
A	IPR033931	PDK1-type, PH domain	Domain
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR011993	PH-like domain superfamily	Homologous Superfamily
A	IPR011009	Protein kinase-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: O15530	diffuse large B-cell lymphoma breast carcinoma congestive heart failure Neoplasm of uncertain or unknown behavior of breast pilocytic astrocytoma astrocytic tumor breast cancer heart failure medulloblastoma osteosarcoma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor glioblastoma malignant ependymoma ovarian cancer diffuse large B-cell lymphoma breast carcinoma congestive heart failure Neoplasm of uncertain or unknown behavior of breast pilocytic astrocytoma astrocytic tumor breast cancer heart failure medulloblastoma osteosarcoma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor glioblastoma malignant ependymoma ovarian cancer subependymal giant cell astrocytoma breast adenocarcinoma large cell medulloblastoma malignant glioma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.