2IVK | pdb_00002ivk

Crystal structure of the periplasmic endonuclease Vvn complexed with a 16-bp DNA

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
D	d2ivkd_	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	Endonuclease I	automated matches	(Vibrio vulnificus ) [TaxId: 672 ],	SCOPe (2.08)
C	d2ivkc_	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	Endonuclease I	automated matches	(Vibrio vulnificus ) [TaxId: 672 ],	SCOPe (2.08)
B	d2ivkb_	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	Endonuclease I	automated matches	(Vibrio vulnificus ) [TaxId: 672 ],	SCOPe (2.08)
A	d2ivka_	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	Endonuclease I	automated matches	(Vibrio vulnificus ) [TaxId: 672 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	His-Me finger endonucleases	8037797	3001893	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	His-Me finger endonucleases	8037797	3001893	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	His-Me finger endonucleases	8037797	3001893	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	His-Me finger endonucleases	8037797	3001893	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	Endonuclease_1	e2ivkD1	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: Endonuclease_1	ECOD (1.6)
C	Endonuclease_1	e2ivkC1	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: Endonuclease_1	ECOD (1.6)
B	Endonuclease_1	e2ivkB1	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: Endonuclease_1	ECOD (1.6)
A	Endonuclease_1	e2ivkA1	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: Endonuclease_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF04231	Endonuclease I (Endonuclease_1)	Endonuclease I	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I, J	5'-D(GPAPAPTPTPCPGPAPTPCP GPAPAPTPTPC)-3'	-	-	-
F, H	5'-D(APAPTPTPCPGPAPTPCPGP APAPTPTP*C)-3'	-	-	-
E, G	5'-D(GPAPAPTPTPCPGPAPTPCP GPAPAPTP*T)-3'	-	-	-
A, B, C, D	ENDONUCLEASE I	endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid catalytic activity cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR007346	Endonuclease I	Family
A, B, C, D	IPR044925	His-Me finger 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.