3U53 | pdb_00003u53

Crystal structure of human Ap4A hydrolase

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)
D	d3u53d_	Alpha and beta proteins (a+b)	Nudix	Nudix	MutT-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3u53c_	Alpha and beta proteins (a+b)	Nudix	Nudix	MutT-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3u53b_	Alpha and beta proteins (a+b)	Nudix	Nudix	MutT-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3u53a_	Alpha and beta proteins (a+b)	Nudix	Nudix	MutT-like	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)
D	SCOP2B Superfamily	Nudix	8044160	3000098	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nudix	8044160	3000098	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nudix	8044160	3000098	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nudix	8044160	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)
D	NUDIX_1	e3u53D2	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
C	NUDIX_1	e3u53C2	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
B	NUDIX_1	e3u53B2	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
A	NUDIX_1	e3u53A2	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
C	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
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, C, D	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, C, D	Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]	pyrophosphatase activity bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity bis(5'-nucleosyl)-tetraphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding pyrophosphatase activity bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity bis(5'-nucleosyl)-tetraphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	ribose phosphate metabolic process purine ribonucleoside monophosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process AMP metabolic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleoside monophosphate biosynthetic process purine ribonucleoside monophosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine nucleoside monophosphate metabolic process ribose phosphate metabolic process purine ribonucleoside monophosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process AMP metabolic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleoside monophosphate biosynthetic process purine ribonucleoside monophosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine nucleoside monophosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside monophosphate metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process nucleoside monophosphate biosynthetic process purine-containing compound metabolic process biosynthetic process organophosphate metabolic process AMP biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process purine ribonucleotide metabolic process ribonucleoside monophosphate biosynthetic process purine nucleotide biosynthetic process apoptotic process cell death programmed cell death ATP metabolic process ATP biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process ribonucleoside triphosphate biosynthetic process nucleoside triphosphate metabolic process cellular response to stimulus response to oxidative stress cellular response to chemical stimulus response to stimulus cellular response to stress response to stress response to chemical cellular response to oxidative stress cellular response to chemical stress	membrane-bounded organelle intracellular anatomical structure mitochondrion membrane-enclosed lumen intracellular membrane-bounded organelle mitochondrial matrix intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR051325	Nudix hydrolase domain-containing protein	Family
A, B, C, D	IPR003565	Bis(5'-nucleosyl)-tetraphosphatase	Family
A, B, C, D	IPR000086	NUDIX hydrolase domain	Domain
A, B, C, D	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR020084	NUDIX hydrolase, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P50583	breast cancer breast carcinoma lung cancer Mammary Neoplasms, Human osteosarcoma idiopathic scoliosis 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.