4NDH

Human Aprataxin (Aptx) bound to 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)
A	SCOP2 Family	DcpS C-terminal domain-like	8089892	4001251	SCOP2 (2022-06-29)
A	SCOP2 Family	C2HE zinc finger-like	8045257	4004379	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HIT-like	8089893	3000223	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	beta-beta-alpha zinc fingers	8089891	3001077	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8089891	3001077	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HIT-like	8089893	3000223	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	DcpS_C	e4ndhA3	A: a+b three layers	X: HIT-like	H: HIT-related (From Topology)	T: HIT-related	F: DcpS_C	ECOD (1.6)
A	UNK_F_TYPE	e4ndhA4	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: UNK_F_TYPE	ECOD (1.6)
B	DcpS_C	e4ndhB3	A: a+b three layers	X: HIT-like	H: HIT-related (From Topology)	T: HIT-related	F: DcpS_C	ECOD (1.6)
B	UNK_F_TYPE	e4ndhB4	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.428.10	Alpha Beta	2-Layer Sandwich	HIT family, subunit A	HIT-like	CATH (4.3.0)
B	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	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
A, B	PF11969	Scavenger mRNA decapping enzyme C-term binding (DcpS_C)	Scavenger mRNA decapping enzyme C-term binding	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Aprataxin	DNA binding binding organic cyclic compound binding damaged DNA binding single-strand break-containing DNA binding nucleic acid binding RNA binding double-stranded RNA binding phosphoprotein binding protein binding protein-containing complex binding chromatin binding DNA exonuclease activity 5'-3' exonuclease activity DNA binding binding organic cyclic compound binding damaged DNA binding single-strand break-containing DNA binding nucleic acid binding RNA binding double-stranded RNA binding phosphoprotein binding protein binding protein-containing complex binding chromatin binding DNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity 5'-3' DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA DNA 5'-adenosine monophosphate hydrolase activity exonuclease activity catalytic activity double-stranded DNA binding phosphoglycolate phosphatase activity phosphoric ester hydrolase activity phosphatase activity polynucleotide 3'-phosphatase activity mismatched DNA binding pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides DNA-3'-diphospho-5'-guanosine diphosphatase hydrolase activity, acting on acid anhydrides cation 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 cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process regulation of protein stability biological regulation regulation of biological quality cellular response to stimulus response to stimulus single strand break repair cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process heterocycle metabolic process cellular response to stress DNA damage response response to stress nitrogen compound metabolic process metabolic process cellular process macromolecule metabolic process cellular aromatic compound metabolic process DNA repair DNA ligation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle cytoplasm nucleoplasm protein-containing complex protein-DNA complex chromatin chromosome
C [auth D], D [auth E], E [auth G], F [auth H]	5'-D(PGPTPTPCPTPAPGPAPAPC)-3'	-	-	-

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 National Science Foundation (DBI-1832184), 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 R01GM133198.