5C46

Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta in complex with GTP gamma S loaded Rab11

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth F]	d5c46f_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	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)
B [auth F]	SCOP2B Superfamily	Ras-like P-loop GTPases	8057254	3002022	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 [auth E]	KOG0903	e5c46E2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: KOG0903	ECOD (1.6)
A [auth E]	PI3_PI4_kinase	e5c46E1	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 [auth F]	Ras	e5c46F1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth F]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth E]	PF21245	PI4KB/PIK1, accessory (PIK) domain (PI4KB-PIK1_PIK)	PI4KB/PIK1, accessory (PIK) domain	-	Repeat
A [auth E]	PF00454	Phosphatidylinositol 3- and 4-kinase (PI3_PI4_kinase)	Phosphatidylinositol 3- and 4-kinase	-	Family
B [auth F]	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motil ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E]	Phosphatidylinositol 4-kinase beta	1-phosphatidylinositol 4-kinase activity phosphatidylinositol kinase activity kinase activity lipid kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein binding binding 14-3-3 protein binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding 1-phosphatidylinositol 4-kinase activity phosphatidylinositol kinase activity kinase activity lipid kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein binding binding 14-3-3 protein 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	phosphatidylinositol metabolic process glycerophospholipid 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 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 developmental process ear development sensory organ development inner ear development animal organ development anatomical structure development cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation signal transduction cell communication cellular component organization lysosome organization organelle organization vacuole organization lytic vacuole organization cellular component organization or biogenesis intracellular signal transduction phosphatidylinositol-mediated signaling localization import into cell transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle Golgi apparatus organelle intracellular membrane-bounded organelle endomembrane system endosome intracellular vesicle cytoplasmic vesicle cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle Golgi apparatus organelle intracellular membrane-bounded organelle endomembrane system endosome intracellular vesicle cytoplasmic vesicle vesicle Golgi membrane bounding membrane of organelle organelle membrane perinuclear region of cytoplasm mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane organelle subcompartment rough endoplasmic reticulum endoplasmic reticulum subcompartment rough endoplasmic reticulum membrane nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
B [auth F]	Ras-related protein Rab-11A	protein binding binding SNARE binding syntaxin binding cytoskeletal protein binding microtubule binding tubulin binding dynein light intermediate chain binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides protein binding binding SNARE binding syntaxin binding cytoskeletal protein binding microtubule binding tubulin binding dynein light intermediate chain binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding myosin V binding myosin binding G protein activity molecular function regulator activity	protein localization Golgi to plasma membrane transport establishment of protein localization cellular localization nitrogen compound transport post-Golgi vesicle-mediated transport transport establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport vesicle-mediated transport localization cellular macromolecule localization protein localization to cell periphery establishment of protein localization to membrane protein localization Golgi to plasma membrane transport establishment of protein localization cellular localization nitrogen compound transport post-Golgi vesicle-mediated transport transport establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport vesicle-mediated transport localization cellular macromolecule localization protein localization to cell periphery establishment of protein localization to membrane protein localization to plasma membrane localization within membrane protein localization to membrane establishment of localization vesicle-mediated transport to the plasma membrane protein transport macromolecule localization cellular process Golgi vesicle transport regulation of localization regulation of biological process regulation of cellular process regulation of transport biological regulation intracellular transport regulation of vesicle-mediated transport endocytic recycling endosomal transport regulation of cellular localization establishment of localization in cell regulation of endocytic recycling regulation of intracellular transport plasma membrane to endosome transport establishment of organelle localization mitotic metaphase chromosome alignment mitotic cell cycle metaphase chromosome alignment cellular component organization chromosome localization organelle localization mitotic sister chromatid segregation cell cycle cellular component organization or biogenesis chromosome segregation cell cycle process mitotic nuclear division organelle fission chromosome organization sister chromatid segregation organelle organization nuclear division mitotic cell cycle process nuclear chromosome segregation establishment of chromosome localization regulation of cytokinesis regulation of cell cycle process cytokinesis regulation of cell division cell division regulation of cell cycle transmembrane transport protein transmembrane transport vesicle localization establishment of melanosome localization establishment of vesicle localization cellular pigmentation pigment granule transport establishment of pigment granule localization pigmentation pigment granule localization melanosome transport melanosome localization regulation of cellular component organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component assembly cilium assembly cilium organization organelle assembly plasma membrane bounded cell projection organization regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of organelle organization regulation of plasma membrane bounded cell projection assembly regulation of cilium assembly regulation of organelle assembly cell projection assembly regulation of plasma membrane bounded cell projection organization protein localization to microtubule cytoskeleton regulation of protein localization regulation of protein localization to centrosome protein localization to microtubule organizing center protein localization to cytoskeleton protein localization to organelle protein localization to centrosome vesicle-mediated transport between endosomal compartments early endosome to recycling endosome transport developmental process multicellular organismal process cellular developmental process cell development neuron projection development nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation neuron development anatomical structure development system development protein localization to cilium multivesicular body assembly vesicle organization multivesicular body organization endosome organization endomembrane system organization protein localization to cell surface positive regulation of cell division cytoskeleton-dependent cytokinesis regulation of mitotic cytokinetic process positive regulation of mitotic cytokinesis positive regulation of biological process mitotic cytokinetic process mitotic cytokinesis regulation of mitotic cytokinesis positive regulation of cytokinesis positive regulation of mitotic cytokinetic process positive regulation of cell cycle process positive regulation of cellular process regulation of cytokinetic process positive regulation of cell cycle cytokinetic process microtubule cytoskeleton organization astral microtubule organization cytoplasmic microtubule organization microtubule-based process supramolecular fiber organization cytoskeleton organization spindle organization membraneless organelle assembly microtubule cytoskeleton organization involved in mitosis spindle assembly mitotic spindle organization mitotic spindle assembly establishment of protein localization to organelle amyloid-beta clearance amyloid-beta clearance by transcytosis transcytosis secretion by cell exocytosis secretion export from cell exosomal secretion extracellular exosome biogenesis extracellular vesicle biogenesis regulation of early endosome to recycling endosome transport protein localization to synapse neurotransmitter receptor transport to postsynaptic membrane establishment of protein localization to postsynaptic membrane neurotransmitter receptor transport to plasma membrane neurotransmitter receptor transport, endosome to plasma membrane regulation of biological quality neurotransmitter receptor transport, endosome to postsynaptic membrane protein localization to postsynaptic membrane neurotransmitter receptor transport protein-containing complex localization endosome to plasma membrane protein transport regulation of postsynaptic membrane neurotransmitter receptor levels protein localization to postsynapse protein localization to cell junction receptor localization to synapse intracellular protein transport regulation of cell cycle phase transition G2/M transition of mitotic cell cycle cell cycle phase transition regulation of mitotic cell cycle positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle cell cycle G2/M phase transition positive regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of cell cycle G2/M phase transition positive regulation of cell cycle G2/M phase transition regulation of mitotic cell cycle phase transition positive regulation of cell cycle phase transition mitotic cell cycle phase transition positive regulation of locomotion regulation of cell motility 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 cell migration regulation of multicellular organismal process epithelial cell migration cell motility regulation of epithelial cell migration locomotion epithelium migration regulation of locomotion	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytoplasm cytosol synapse cell junction glutamatergic synapse membrane intracellular vesicle intracellular membrane-bounded organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane organelle membrane endocytic vesicle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment endomembrane system trans-Golgi network Golgi membrane endosome recycling endosome centrosome microtubule organizing center centriolar satellite centriole phagocytic vesicle transport vesicle cell division site cell periphery cleavage furrow plasma membrane plasma membrane region late endosome multivesicular body protein-containing complex endosome membrane recycling endosome membrane postsynaptic recycling endosome postsynaptic endosome postsynapse trans-Golgi network membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth E]	IPR015433	Phosphatidylinositol kinase	Family
A [auth E]	IPR018936	Phosphatidylinositol 3/4-kinase, conserved site	Conserved Site
A [auth E]	IPR000403	Phosphatidylinositol 3-/4-kinase, catalytic domain	Domain
A [auth E]	IPR001263	Phosphoinositide 3-kinase, accessory (PIK) domain	Domain
A [auth E]	IPR036940	Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily	Homologous Superfamily
A [auth E]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A [auth E]	IPR049160	PI4KB/PIK1, accessory domain	Domain
B [auth F]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth F]	IPR005225	Small GTP-binding domain	Domain
B [auth F]	IPR001806	Small GTPase	Family
B [auth F]	IPR050209	Rab GTPases family involved in membrane trafficking	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth E]	Pharos: Q9UBF8	astrocytic tumor osteosarcoma malignant ependymoma ovarian cancer oligodendroglioma psoriasis
B [auth F]	Pharos: P62491	Chloracne interstitial cystitis malignant pancreatic neoplasm ovarian cancer Pick disease dermatomyositis large cell medulloblastoma myopathy pancreatic ductal adenocarcinoma plasma cell myeloma Hodgkins lymphoma lymphoplasmacytic lymphoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm psoriasis

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.