4PH4 | pdb_00004ph4

The crystal structure of Human VPS34 in complex with PIK-III

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth B]	Fic	e4ph4B1	A: alpha bundles	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Fic	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	1.25.40.70	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Phosphatidylinositol 3-kinase, accessory domain (PIK)	CATH (4.3.0)
A [auth B]	3.30.1010.10	Alpha Beta	2-Layer Sandwich	Phosphatidylinositol 3-kinase Catalytic Subunit	Chain A, domain 4	CATH (4.3.0)
A [auth B]	1.10.1070.11	Mainly Alpha	Orthogonal Bundle	Phosphatidylinositol 3-kinase Catalytic Subunit	Chain A, Domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	PF00613	Phosphoinositide 3-kinase family, accessory domain (PIK domain) (PI3Ka)	Phosphoinositide 3-kinase family, accessory domain (PIK domain)	-	Repeat
A [auth B]	PF00454	Phosphatidylinositol 3- and 4-kinase (PI3_PI4_kinase)	Phosphatidylinositol 3- and 4-kinase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	Phosphatidylinositol 3-kinase catalytic subunit type 3	phosphatidylinositol kinase activity kinase activity lipid kinase activity transferase activity catalytic activity 1-phosphatidylinositol-3-kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding phosphatidylinositol kinase activity kinase activity lipid kinase activity transferase activity catalytic activity 1-phosphatidylinositol-3-kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups 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 catalytic activity, acting on a protein protein kinase activity	phosphatidylinositol metabolic process glycerophospholipid biosynthetic process phosphatidylinositol-3-phosphate biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process primary metabolic process phosphatidylinositol phosphate biosynthetic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process phospholipid metabolic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process phosphatidylinositol metabolic process glycerophospholipid biosynthetic process phosphatidylinositol-3-phosphate biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process primary metabolic process phosphatidylinositol phosphate biosynthetic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process phospholipid metabolic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process glycerolipid metabolic process phosphorus metabolic process lipid metabolic process cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation cellular component organization or biogenesis process utilizing autophagic mechanism regulation of biological process regulation of cellular process biological regulation regulation of catabolic process regulation of autophagy regulation of macroautophagy regulation of metabolic process cell division cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress response to starvation cellular response to glucose starvation cellular response to starvation signaling intracellular signal transduction cell communication phosphatidylinositol-mediated signaling signal transduction regulation of cytokinesis regulation of cell cycle process cytokinesis regulation of cell division cell cycle regulation of cell cycle cell cycle process autophagosome assembly organelle assembly vacuole organization autophagosome organization cellular component biogenesis localization organelle organization cellular component assembly macromolecule localization protein localization to phagophore assembly site intracellular protein localization vesicle organization endosome organization endomembrane system organization regulation of immune effector process lymphocyte mediated immunity positive regulation of leukocyte mediated immunity positive regulation of response to biotic stimulus response to biotic stimulus positive regulation of leukocyte mediated cytotoxicity positive regulation of immune response positive regulation of natural killer cell mediated immunity leukocyte mediated immunity regulation of immune system process natural killer cell mediated immunity positive regulation of immune system process regulation of natural killer cell mediated immunity immune response response to other organism regulation of innate immune response response to external stimulus leukocyte mediated cytotoxicity immune effector process regulation of leukocyte mediated immunity regulation of response to stimulus defense response to other organism positive regulation of defense response natural killer cell mediated cytotoxicity regulation of immune response positive regulation of natural killer cell mediated cytotoxicity regulation of cell killing positive regulation of cell killing regulation of defense response regulation of response to biotic stimulus regulation of natural killer cell mediated cytotoxicity biological process involved in interspecies interaction between organisms regulation of response to external stimulus positive regulation of lymphocyte mediated immunity positive regulation of biological process positive regulation of response to stimulus positive regulation of response to external stimulus regulation of response to stress innate immune response positive regulation of immune effector process response to external biotic stimulus positive regulation of cellular process positive regulation of innate immune response defense response regulation of leukocyte mediated cytotoxicity defense response to symbiont regulation of lymphocyte mediated immunity immune system process cell killing synaptic vesicle endocytosis import into cell cellular localization transport synaptic vesicle cycle establishment of localization vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling establishment of localization in cell endocytosis intracellular signaling cassette phosphatidylinositol 3-kinase/protein kinase B signal transduction gene expression macromolecule biosynthetic process protein maturation proteolysis protein processing protein metabolic process macromolecule metabolic process autophagy of peroxisome pexophagy host-mediated activation of viral genome replication host-mediated perturbation of viral genome replication host-mediated perturbation of viral process modulation of process of another organism host-mediated perturbation of symbiont process host-mediated activation of viral process establishment of protein localization protein targeting establishment of protein localization to vacuole intracellular transport protein localization to vacuole lysosomal transport protein localization to lysosome establishment of protein localization to organelle protein transport protein targeting to lysosome protein localization to organelle vacuolar transport protein targeting to vacuole intracellular protein transport regulation of protein modification process positive regulation of protein metabolic process lipoprotein biosynthetic process lipoprotein metabolic process regulation of primary metabolic process protein lipidation positive regulation of metabolic process positive regulation of protein modification process positive regulation of lipoprotein metabolic process positive regulation of biosynthetic process positive regulation of protein lipidation regulation of lipoprotein metabolic process positive regulation of macromolecule metabolic process protein modification process regulation of biosynthetic process regulation of protein lipidation regulation of protein metabolic process regulation of macromolecule metabolic process macromolecule modification regulation of macromolecule biosynthetic process endosomal transport vesicle-mediated transport between endosomal compartments early endosome to late endosome transport response to acid chemical response to chemical response to oxygen-containing compound response to nitrogen compound response to amino acid response to L-leucine	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton organelle membraneless organelle cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton organelle membraneless organelle cytoplasm cytosol phosphatidylinositol 3-kinase complex, class III, type II protein-containing complex catalytic complex membrane protein complex transferase complex phosphatidylinositol 3-kinase complex transferase complex, transferring phosphorus-containing groups phosphatidylinositol 3-kinase complex, class III extrinsic component of membrane synapse cell junction glutamatergic synapse vacuole autophagosome intracellular membrane-bounded organelle intracellular vesicle phagocytic vesicle phagocytic vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane vesicle organelle membrane endocytic vesicle endosome postsynaptic endosome endomembrane system postsynapse peroxisome microbody autolysosome lytic vacuole secondary lysosome lysosome presynapse presynaptic endosome phagophore assembly site midbody cell periphery plasma membrane GABA-ergic synapse phosphatidylinositol 3-kinase complex, class III, type I late endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR016024	Armadillo-type fold	Homologous Superfamily
A [auth B]	IPR057756	Phosphatidylinositol 3-kinase type3/VPS34-like	Domain
A [auth B]	IPR008290	Phosphatidylinositol 3-kinase, Vps34 type	Family
A [auth B]	IPR015433	Phosphatidylinositol 3-/4-kinase	Family
A [auth B]	IPR002420	C2 phosphatidylinositol 3-kinase-type domain	Domain
A [auth B]	IPR000403	Phosphatidylinositol 3-/4-kinase, catalytic domain	Domain
A [auth B]	IPR001263	Phosphoinositide 3-kinase, accessory (PIK) domain	Domain
A [auth B]	IPR018936	Phosphatidylinositol 3-/4-kinase, conserved site	Conserved Site
A [auth B]	IPR042236	Phosphoinositide 3-kinase, accessory (PIK) domain superfamily	Homologous Superfamily
A [auth B]	IPR036940	Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily	Homologous Superfamily
A [auth B]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A [auth B]	IPR035892	C2 domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B]	Pharos: Q8NEB9	atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma malignant colon neoplasm medulloblastoma schizophrenia bipolar disorder intellectual disability lung adenocarcinoma malignant ependymoma osteosarcoma breast cancer invasive ductal breast carcinoma lung cancer malignant glioma atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma malignant colon neoplasm medulloblastoma schizophrenia bipolar disorder intellectual disability lung adenocarcinoma malignant ependymoma osteosarcoma breast cancer invasive ductal breast carcinoma lung cancer malignant glioma ovarian cancer

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.