3X03

Crystal structure of PIP4KIIBETA complex with AMPPNP

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)
A	d3x03a_	Alpha and beta proteins (a+b)	SAICAR synthase-like	SAICAR synthase-like	Phosphatidylinositol phosphate kinase IIbeta, PIPK IIbeta	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)
A	SCOP2B Superfamily	SAICAR synthase-like	8036596	3000802	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	PIP5K	e3x03A1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: SAICAR synthase	F: PIP5K	ECOD (1.6)
B	PIP5K	e3x03B1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: SAICAR synthase	F: PIP5K	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.800.10	Alpha Beta	2-Layer Sandwich	Phosphatidylinositol Phosphate Kinase II Beta	Phosphatidylinositol Phosphate Kinase II Beta	CATH (4.3.0)
A	3.30.810.10	Alpha Beta	2-Layer Sandwich	Phosphatidylinositol Phosphate Kinase Iibeta	Chain: A, domain 2	CATH (4.3.0)
B	3.30.800.10	Alpha Beta	2-Layer Sandwich	Phosphatidylinositol Phosphate Kinase II Beta	Phosphatidylinositol Phosphate Kinase II Beta	CATH (4.3.0)
B	3.30.810.10	Alpha Beta	2-Layer Sandwich	Phosphatidylinositol Phosphate Kinase Iibeta	Chain: A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01504	Phosphatidylinositol-4-phosphate 5-Kinase (PIP5K)	Phosphatidylinositol-4-phosphate 5-Kinase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Phosphatidylinositol 5-phosphate 4-kinase type-2 beta	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 phosphatidylinositol kinase activity kinase activity lipid kinase activity 1-phosphatidylinositol-5-phosphate 4-kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups identical protein binding protein binding protein homodimerization activity protein dimerization activity 1-phosphatidylinositol-4-phosphate 5-kinase activity guanyl nucleotide binding GTP binding guanyl ribonucleotide binding	membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion cellular process metabolic process cellular component organization or biogenesis vesicle fusion process utilizing autophagic mechanism cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation signal transduction cell communication 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 glycerolipid metabolic process phosphorus metabolic process lipid metabolic process positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization positive regulation of vacuole organization positive regulation of biological process autophagosome organization regulation of autophagy cellular component biogenesis positive regulation of metabolic process cellular component assembly positive regulation of autophagosome assembly positive regulation of macroautophagy positive regulation of cellular process positive regulation of autophagy autophagosome assembly organelle assembly vacuole organization positive regulation of cellular component biogenesis regulation of autophagosome assembly regulation of catabolic process regulation of vacuole organization regulation of cellular component biogenesis regulation of organelle organization positive regulation of catabolic process regulation of macroautophagy regulation of organelle assembly regulation of metabolic process positive regulation of organelle assembly 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate metabolic process 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process cellular response to nitrogen compound negative regulation of signaling response to peptide hormone negative regulation of biological process regulation of signal transduction insulin receptor signaling pathway regulation of cellular response to insulin stimulus negative regulation of cell communication cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus response to hormone negative regulation of cellular process enzyme-linked receptor protein signaling pathway cellular response to hormone stimulus regulation of signaling negative regulation of response to stimulus 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 negative regulation of signal transduction cellular response to oxygen-containing compound cellular response to chemical stimulus negative regulation of cellular response to insulin stimulus regulation of response to stimulus negative regulation of insulin receptor signaling pathway response to chemical response to insulin regulation of cell communication cellular response to insulin stimulus	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle vacuole autophagosome cytoplasm intracellular membrane-bounded organelle cytosol cell periphery plasma membrane membrane nucleus membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle vacuole autophagosome cytoplasm intracellular membrane-bounded organelle cytosol cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR027483	Phosphatidylinositol-4-phosphate 4/5-kinase, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR002498	Phosphatidylinositol-4-phosphate 4/5-kinase, core	Domain
A, B	IPR023610	Phosphatidylinositol-4/5-phosphate 5/4-kinase	Family
A, B	IPR027484	Phosphatidylinositol-4-phosphate 5-kinase, N-terminal	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P78356	atypical teratoid rhabdoid tumor idiopathic pulmonary fibrosis malignant ependymoma non-small cell lung carcinoma chronic obstructive pulmonary disease Interstitial fibrosis malignant glioma ovarian cancer glioblastoma interstitial lung disease medulloblastoma

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.