2X6F

THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 IN COMPLEX WITH 3-METHYLADENINE

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PI3Ka	e2x6fA2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PI3Ka	ECOD (1.6)
A	PI3_PI4_kinase	e2x6fA1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: PI3_PI4_kinase	ECOD (1.6)
B	PI3Ka	e2x6fB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PI3Ka	ECOD (1.6)
B	PI3_PI4_kinase	e2x6fB2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: PI3_PI4_kinase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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	3.30.1010.10	Alpha Beta	2-Layer Sandwich	Phosphatidylinositol 3-kinase Catalytic Subunit	Chain A, domain 4	CATH (4.3.0)
A	1.10.1070.11	Mainly Alpha	Orthogonal Bundle	Phosphatidylinositol 3-kinase Catalytic Subunit	Chain A, Domain 5	CATH (4.3.0)
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)
B	3.30.1010.10	Alpha Beta	2-Layer Sandwich	Phosphatidylinositol 3-kinase Catalytic Subunit	Chain A, domain 4	CATH (4.3.0)
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, 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, B	PHOSPHOTIDYLINOSITOL 3 KINASE 59F	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 organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	cellular biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process phospholipid metabolic process phosphate-containing compound metabolic process phosphorus metabolic process phosphatidylinositol metabolic process glycerophospholipid biosynthetic process phosphatidylinositol-3-phosphate biosynthetic process cellular metabolic process primary metabolic process phosphatidylinositol phosphate biosynthetic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process cellular biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process phospholipid metabolic process phosphate-containing compound metabolic process phosphorus metabolic process phosphatidylinositol metabolic process glycerophospholipid biosynthetic process phosphatidylinositol-3-phosphate biosynthetic process cellular metabolic process primary metabolic process phosphatidylinositol phosphate biosynthetic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process cellular lipid metabolic process metabolic process cellular process glycerolipid metabolic process lipid metabolic process developmental process multicellular organismal process cellular developmental process cell development developmental maturation nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation neuron remodeling anatomical structure maturation cell differentiation neuron development anatomical structure development neuron maturation cell maturation system development autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization cellular catabolic process organelle organization cellular component assembly cellular component organization or biogenesis process utilizing autophagic mechanism localization import into cell transport endocytosis establishment of localization vesicle-mediated transport RNA transport nitrogen compound transport nucleic acid transport dsRNA transport establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport regulation of localization cellular localization regulation of biological process regulation of cellular process regulation of transport biological regulation intracellular transport regulation of vesicle-mediated transport endosomal transport vesicle-mediated transport between endosomal compartments regulation of early endosome to late endosome transport early endosome to late endosome transport regulation of cellular localization establishment of localization in cell regulation of intracellular transport 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 starvation signaling intracellular signal transduction cell communication phosphatidylinositol-mediated signaling signal transduction establishment or maintenance of cell polarity autophagy of peroxisome protein localization establishment of protein localization protein targeting establishment of protein localization to vacuole lysosomal transport protein targeting to lysosome cellular macromolecule localization protein targeting to vacuole protein localization to vacuole protein localization to lysosome establishment of protein localization to organelle protein transport protein localization to organelle vacuolar transport intracellular protein transport multicellular organismal-level homeostasis epithelial structure maintenance homeostatic process anatomical structure homeostasis tissue homeostasis sexual reproduction regulation of developmental process regulation of reproductive process reproductive process positive regulation of biological process cellular process involved in reproduction in multicellular organism regulation of programmed cell death developmental process involved in reproduction female gamete generation gamete generation apoptotic process involved in development positive regulation of developmental process nurse cell apoptotic process positive regulation of cellular process positive regulation of reproductive process positive regulation of programmed cell death positive regulation of apoptotic process involved in development regulation of apoptotic process oogenesis multicellular organismal reproductive process regulation of apoptotic process involved in development cell death positive regulation of apoptotic process positive regulation of nurse cell apoptotic process regulation of nurse cell apoptotic process programmed cell death involved in cell development germ cell development apoptotic process programmed cell death larval midgut histolysis larval midgut cell programmed cell death instar larval or pupal development metamorphosis anatomical structure regression anatomical structure morphogenesis instar larval or pupal morphogenesis post-embryonic animal morphogenesis post-embryonic development	membrane cellular anatomical entity membrane-bounded organelle omegasome intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle endomembrane system phosphatidylinositol 3-kinase complex, class III, type II protein-containing complex catalytic complex membrane protein complex transferase complex membrane cellular anatomical entity membrane-bounded organelle omegasome intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle endomembrane system 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 cytoplasm early endosome endosome intracellular vesicle cytoplasmic vesicle vesicle vacuolar membrane autophagosome membrane vacuole autophagosome bounding membrane of organelle organelle membrane phosphatidylinositol 3-kinase complex, class III, type I peroxisome microbody phagophore assembly site

InterPro: Protein Family Classification InterPro Database Homepage

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

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.