1VP7 | pdb_00001vp7

Crystal structure of Exodeoxyribonuclease VII small subunit (NP_881400.1) from Bordetella pertussis at 2.40 A resolution

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1vp7a_	All alpha proteins	Spectrin repeat-like	XseB-like	XseB-like	Exonuclease VII small subunit XseB	(Bordetella pertussis Tohama I ) [TaxId: 257313 ],	SCOPe (2.08)
B	d1vp7b_	All alpha proteins	Spectrin repeat-like	XseB-like	XseB-like	Exonuclease VII small subunit XseB	(Bordetella pertussis Tohama I ) [TaxId: 257313 ],	SCOPe (2.08)
C	d1vp7c_	All alpha proteins	Spectrin repeat-like	XseB-like	XseB-like	Exonuclease VII small subunit XseB	(Bordetella pertussis Tohama I ) [TaxId: 257313 ],	SCOPe (2.08)
F	d1vp7f_	All alpha proteins	Spectrin repeat-like	XseB-like	XseB-like	Exonuclease VII small subunit XseB	(Bordetella pertussis Tohama I ) [TaxId: 257313 ],	SCOPe (2.08)
E	d1vp7e_	All alpha proteins	Spectrin repeat-like	XseB-like	XseB-like	Exonuclease VII small subunit XseB	(Bordetella pertussis Tohama I ) [TaxId: 257313 ],	SCOPe (2.08)
D	d1vp7d_	All alpha proteins	Spectrin repeat-like	XseB-like	XseB-like	Exonuclease VII small subunit XseB	(Bordetella pertussis Tohama I ) [TaxId: 257313 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	XseB-like	8030812	4002913	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	XseB-like	8043191	3001891	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	XseB-like	8043191	3001891	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	XseB-like	8043191	3001891	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	XseB-like	8043191	3001891	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	XseB-like	8043191	3001891	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	XseB-like	8043191	3001891	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	Exonuc_VII_S	e1vp7A1	A: alpha bundles	X: Spectrin repeat-like	H: XseB-like (From Topology)	T: XseB-like	F: Exonuc_VII_S	ECOD (1.6)
B	Exonuc_VII_S	e1vp7B1	A: alpha bundles	X: Spectrin repeat-like	H: XseB-like (From Topology)	T: XseB-like	F: Exonuc_VII_S	ECOD (1.6)
C	Exonuc_VII_S	e1vp7C1	A: alpha bundles	X: Spectrin repeat-like	H: XseB-like (From Topology)	T: XseB-like	F: Exonuc_VII_S	ECOD (1.6)
F	Exonuc_VII_S	e1vp7F1	A: alpha bundles	X: Spectrin repeat-like	H: XseB-like (From Topology)	T: XseB-like	F: Exonuc_VII_S	ECOD (1.6)
E	Exonuc_VII_S	e1vp7E1	A: alpha bundles	X: Spectrin repeat-like	H: XseB-like (From Topology)	T: XseB-like	F: Exonuc_VII_S	ECOD (1.6)
D	Exonuc_VII_S	e1vp7D1	A: alpha bundles	X: Spectrin repeat-like	H: XseB-like (From Topology)	T: XseB-like	F: Exonuc_VII_S	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.287.1040	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Exonuclease VII, small subunit	CATH (4.3.0)
B	1.10.287.1040	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Exonuclease VII, small subunit	CATH (4.3.0)
C	1.10.287.1040	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Exonuclease VII, small subunit	CATH (4.3.0)
F	1.10.287.1040	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Exonuclease VII, small subunit	CATH (4.3.0)
E	1.10.287.1040	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Exonuclease VII, small subunit	CATH (4.3.0)
D	1.10.287.1040	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Exonuclease VII, small subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF02609	Exonuclease VII small subunit (Exonuc_VII_S)	Exonuclease VII small subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	exodeoxyribonuclease VII small subunit	DNA exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds exodeoxyribonuclease VII activity catalytic activity exonuclease activity	catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex intracellular protein-containing complex exodeoxyribonuclease VII complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR037004	Exonuclease VII, small subunit superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR003761	Exonuclease VII, small subunit	Family

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.