3BM4 | pdb_00003bm4

Crystal Structure of Human ADP-ribose Pyrophosphatase NUDT5 In complex with magnesium and AMPcpr

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)
B	Redoxin	e3bm4B1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Redoxin	ECOD (v294.1)
A	Redoxin	e3bm4A1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Redoxin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
A	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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, B	ADP-sugar pyrophosphatase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding pyrophosphatase activity ADP-sugar pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity RNA binding snoRNA binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding pyrophosphatase activity ADP-sugar pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity RNA binding snoRNA binding nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity nucleoside diphosphate phosphatase activity 8-oxo-dGDP phosphatase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups ADP-ribose diphosphatase activity	ribose phosphate metabolic process ATP metabolic process carbohydrate derivative metabolic process ATP generation from poly-ADP-D-ribose nucleobase-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process purine nucleoside triphosphate metabolic process ribose phosphate metabolic process ATP metabolic process carbohydrate derivative metabolic process ATP generation from poly-ADP-D-ribose nucleobase-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process purine nucleoside triphosphate metabolic process primary metabolic process nucleotide metabolic process purine-containing compound metabolic process organophosphate metabolic process metabolic process cellular process macromolecule metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process monosaccharide metabolic process carbohydrate metabolic process catabolic process carbohydrate catabolic process pentose metabolic process monosaccharide catabolic process small molecule catabolic process pentose catabolic process D-ribose metabolic process D-ribose catabolic process organophosphate catabolic process nucleoside phosphate catabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process nucleoside diphosphate catabolic process cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle nucleus extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000086	NUDIX hydrolase domain	Domain
A, B	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A, B	IPR020084	NUDIX hydrolase, conserved site	Conserved Site
A, B	IPR020476	NUDIX hydrolase	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9UKK9	atypical teratoid rhabdoid tumor glioblastoma malignant glioma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm breast cancer heart disease medulloblastoma pancreatic ductal adenocarcinoma Sjogren syndrome chronic obstructive pulmonary disease large cell medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma

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.