3SPD | pdb_00003spd

Crystal structure of aprataxin ortholog Hnt3 in complex with DNA

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8089894	3001077	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HIT-like	8089896	3000223	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8089894	3001077	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HIT-like	8089896	3000223	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8089894	3001077	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HIT-like	8089896	3000223	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	HIT-like	8089896	3000223	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8089894	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)
A	DcpS_C	e3spdA1	A: a+b three layers	X: HIT-like	H: HIT-related (From Topology)	T: HIT-related	F: DcpS_C	ECOD (1.6)
A	zf-C2HE	e3spdA2	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: zf-C2HE	ECOD (1.6)
B	DcpS_C	e3spdB1	A: a+b three layers	X: HIT-like	H: HIT-related (From Topology)	T: HIT-related	F: DcpS_C	ECOD (1.6)
B	zf-C2HE	e3spdB2	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: zf-C2HE	ECOD (1.6)
C	DcpS_C	e3spdC1	A: a+b three layers	X: HIT-like	H: HIT-related (From Topology)	T: HIT-related	F: DcpS_C	ECOD (1.6)
C	zf-C2HE	e3spdC2	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: zf-C2HE	ECOD (1.6)
D	DcpS_C	e3spdD1	A: a+b three layers	X: HIT-like	H: HIT-related (From Topology)	T: HIT-related	F: DcpS_C	ECOD (1.6)
D	zf-C2HE	e3spdD2	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: zf-C2HE	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)
C	3.30.428.10	Alpha Beta	2-Layer Sandwich	HIT family, subunit A	HIT-like	CATH (4.3.0)
D	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, C, D	PF01230	HIT domain (HIT)	HIT domain		Domain
A, B, C, D	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
A, B, C, D	Aprataxin-like protein	DNA binding binding damaged DNA binding single-strand break-containing DNA binding nucleic acid 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 DNA binding binding damaged DNA binding single-strand break-containing DNA binding nucleic acid 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 RNA binding double-stranded RNA binding mismatched DNA binding ribonucleoside binding nucleoside binding guanosine binding purine ribonucleoside binding heterocyclic compound binding carbohydrate derivative binding purine nucleoside binding small molecule binding guanyl nucleotide binding nucleotide binding GMP binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding ribonucleotide binding cation binding transition metal ion binding zinc ion binding metal ion 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 single-stranded DNA binding	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 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 mismatch repair	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
E, G	DNA (5'-D(TPAPTPTPCPCPGPAPTPAPGPTPGPAP*C)-3')	-	-	-
F, H	DNA (5'-D(GPTPCPAPCPTPAPTPCPGPGPAPAPTPGPAP*G)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR011146	HIT-like domain	Domain
A, B, C, D	IPR032566	Aprataxin, C2HE/C2H2/C2HC zinc finger	Domain
A, B, C, D	IPR036265	HIT-like superfamily	Homologous Superfamily

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.