6PCL | pdb_00006pcl

Crystal structure of human diphosphoinositol polyphosphate phosphohydrolase 1 in complex with 5-IP7

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	d6pcla_	Alpha and beta proteins (a+b)	Nudix	Nudix	MutT-like	Diphosphoinositol polyphosphate phosphohydrolase	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	Nudix	8041411	3000098	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	Metallophos,Metallophos_C	e6pclA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Metallophos,Metallophos_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00293	NUDIX domain (NUDIX)	NUDIX domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Diphosphoinositol polyphosphate phosphohydrolase 1	pyrophosphatase activity inositol diphosphate tetrakisphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity diphosphoinositol-polyphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides catalytic activity bis(5'-adenosyl)-hexaphosphatase activity inositol bisdiphosphate tetrakisphosphate diphosphatase activity inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity inositol diphosphate pentakisphosphate diphosphatase activity cation binding manganese ion binding pyrophosphatase activity inositol diphosphate tetrakisphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity diphosphoinositol-polyphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides catalytic activity bis(5'-adenosyl)-hexaphosphatase activity inositol bisdiphosphate tetrakisphosphate diphosphatase activity inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity inositol diphosphate pentakisphosphate diphosphatase activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding bis(5'-adenosyl)-pentaphosphatase activity magnesium ion binding endopolyphosphatase activity zinc ion binding 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity	nucleoside phosphate metabolic process catabolic process organophosphate catabolic process primary metabolic process diadenosine polyphosphate metabolic process nucleoside phosphate catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organophosphate metabolic process diadenosine polyphosphate catabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process nucleoside phosphate metabolic process catabolic process organophosphate catabolic process primary metabolic process diadenosine polyphosphate metabolic process nucleoside phosphate catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organophosphate metabolic process diadenosine polyphosphate catabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process nucleotide catabolic process diadenosine hexaphosphate catabolic process regulation of biological process signaling biological regulation cell-cell signaling cell communication polyol metabolic process alcohol catabolic process polyol catabolic process alcohol metabolic process inositol phosphate metabolic process diphosphoinositol polyphosphate metabolic process diphosphoinositol polyphosphate catabolic process inositol phosphate catabolic process small molecule catabolic process diadenosine pentaphosphate catabolic process RNA metabolic process macromolecule metabolic process nucleic acid metabolic process RNA decapping ribose phosphate metabolic process ribonucleotide catabolic process carbohydrate derivative metabolic process purine nucleotide metabolic process ribonucleotide metabolic process purine ribonucleotide catabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process adenosine 5'-(hexahydrogen pentaphosphate) catabolic process purine-containing compound catabolic process purine-containing compound metabolic process purine ribonucleotide metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A	IPR047198	Diphosphoinositol polyphosphate phosphohydrolase-like, NUDIX domain	Domain
A	IPR000086	NUDIX hydrolase domain	Domain
A	IPR020084	NUDIX hydrolase, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O95989	atrial fibrillation glioblastoma lung cancer metabolic syndrome X osteosarcoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor invasive ductal breast carcinoma malignant glioma neoplasm ovarian cancer rheumatoid arthritis breast cancer large cell medulloblastoma medulloblastoma atrial fibrillation glioblastoma lung cancer metabolic syndrome X osteosarcoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor invasive ductal breast carcinoma malignant glioma neoplasm ovarian cancer rheumatoid arthritis breast cancer large cell medulloblastoma medulloblastoma non-alcoholic fatty liver disease pancreatic ductal adenocarcinoma subependymal giant cell astrocytoma

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.