4NDF | pdb_00004ndf

Human Aprataxin (Aptx) bound to RNA-DNA, AMP, and Zn - product complex

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	HIT-like	8089893	3000223	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8089891	3001077	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HIT-like	8089893	3000223	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8089891	3001077	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)
B	Lipase_3	e4ndfB3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lipase_3	ECOD (develop294)
A	Lipase_3	e4ndfA3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lipase_3	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.428.10	Alpha Beta	2-Layer Sandwich	HIT family, subunit A	HIT-like	CATH (4.3.0)
A	3.30.428.10	Alpha Beta	2-Layer Sandwich	HIT family, subunit A	HIT-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF11969	Scavenger mRNA decapping enzyme C-term binding (DcpS_C)	Scavenger mRNA decapping enzyme C-term binding	-	Family
A, B	PF16278	C2HE / C2H2 / C2HC zinc-binding finger (zf-C2HE)	C2HE / C2H2 / C2HC zinc-binding finger	zf-C2HE is an unusual zinc-binding domain found in fungi, plants and metazoa. It is often found at the C-terminus of HIT-domain-containing proteins, Pfam:PF01230. In fungi the fourth ligand is a Glu, in plants it is Cys and in metazoans it is usually ...	zf-C2HE is an unusual zinc-binding domain found in fungi, plants and metazoa. It is often found at the C-terminus of HIT-domain-containing proteins, Pfam:PF01230. In fungi the fourth ligand is a Glu, in plants it is Cys and in metazoans it is usually a His. The fourth ligand is often mutated in neurogenerative disease-states [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth E], F [auth H]	5'-D(GPAPAPTPCPAPTPAPAPC)-3'	-	-	-
C [auth D], E [auth G]	5'-R(PG)-D(PTPTPAPTPGPAPTPTPC)-3'	-	-	-
A, B	Aprataxin	DNA binding binding damaged DNA binding single-strand break-containing DNA binding nucleic acid binding RNA binding double-stranded RNA binding phosphoprotein binding protein binding chromatin binding pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides DNA-3'-diphospho-5'-guanosine diphosphatase activity hydrolase activity DNA binding binding damaged DNA binding single-strand break-containing DNA binding nucleic acid binding RNA binding double-stranded RNA binding phosphoprotein binding protein binding chromatin binding pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides DNA-3'-diphospho-5'-guanosine diphosphatase activity hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity DNA 5'-adenosine monophosphate hydrolase activity double-stranded DNA binding phosphoglycolate phosphatase activity phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity polynucleotide 3'-phosphatase activity mismatched DNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding single-stranded DNA binding	regulation of protein stability biological regulation regulation of biological quality cellular response to stimulus response to stimulus single strand break repair primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process regulation of protein stability biological regulation regulation of biological quality cellular response to stimulus response to stimulus single strand break repair primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm nucleoplasm chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR013087	Zinc finger C2H2-type	Domain
A, B	IPR011146	HIT-like domain	Domain
A, B	IPR041388	PNK, FHA domain	Domain
A, B	IPR032566	Aprataxin, C2HE/C2H2/C2HC zinc finger	Domain
A, B	IPR019808	Histidine triad, conserved site	Conserved Site
A, B	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
A, B	IPR047289	Aprataxin, forkhead associated domain	Domain
A, B	IPR036265	HIT-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q7Z2E3	ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia apraxia Charcot-Marie-Tooth disease neurodegenerative disease spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 1 intellectual disability ovarian cancer tuberculosis Ataxias, Hereditary peripheral neuropathy

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.