3T9C | pdb_00003t9c

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP and inositol hexakisphosphate (IP6)

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	RimK	e3t9cA5	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: RimK	ECOD (1.6)
A	KOG1057	e3t9cA6	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: KOG1057	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.11950	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18086	Diphosphoinositol pentakisphosphate kinase 2 N-terminal domain (PPIP5K2_N)	Diphosphoinositol pentakisphosphate kinase 2 N-terminal domain	This is the N-terminal domain found in the Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 (PPIP5K2), EC:2.7.4.24. Structure analysis of human PPIP5K2 indicate that this region forms alpha-beta-alpha domain [1].PPIP5K2 is o ...	This is the N-terminal domain found in the Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 (PPIP5K2), EC:2.7.4.24. Structure analysis of human PPIP5K2 indicate that this region forms alpha-beta-alpha domain [1].PPIP5K2 is one of the mammalian PPIP5K isoforms responsible for synthesis of diphosphoinositol polyphosphates (inositol pyrophosphates; PP-InsPs), regulatory molecules that function at the interface of cell signaling and organismic homeostasis [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Inositol Pyrophosphate Kinase	inositol-1,3,4,5,6-pentakisphosphate kinase activity kinase activity transferase activity inositol phosphate kinase activity catalytic activity phosphotransferase activity, phosphate 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 inositol-1,3,4,5,6-pentakisphosphate kinase activity kinase activity transferase activity inositol phosphate kinase activity catalytic activity phosphotransferase activity, phosphate 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 inositol hexakisphosphate 5-kinase activity inositol hexakisphosphate kinase activity inositol hexakisphosphate 1-kinase activity diphosphoinositol pentakisphosphate kinase activity 5-diphosphoinositol pentakisphosphate 1-kinase activity	polyol metabolic process inositol metabolic process alcohol metabolic process small molecule metabolic process metabolic process cellular process small molecule biosynthetic process inositol phosphate metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process inositol phosphate biosynthetic process phosphate-containing compound metabolic process polyol biosynthetic process polyol metabolic process inositol metabolic process alcohol metabolic process small molecule metabolic process metabolic process cellular process small molecule biosynthetic process inositol phosphate metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process inositol phosphate biosynthetic process phosphate-containing compound metabolic process polyol biosynthetic process alcohol biosynthetic process phosphorus metabolic process multicellular organismal process system process sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000560	Histidine phosphatase superfamily, clade-2	Family
A	IPR029033	Histidine phosphatase superfamily	Homologous Superfamily
A	IPR037446	Histidine acid phosphatase, VIP1 family	Family
A	IPR033379	Histidine acid phosphatase active site	Active Site
A	IPR040557	VIP1, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O43314	rheumatoid arthritis diabetes mellitus malignant colon neoplasm ovarian cancer Hashimoto thyroiditis medulloblastoma primitive neuroectodermal tumor hypothyroidism nonsyndromic genetic deafness

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.