2BGW | pdb_00002bgw

XPF from Aeropyrum pernix, complex with DNA

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)
B	d2bgwb1	All alpha proteins	SAM domain-like	RuvA domain 2-like	Hef domain-like	DNA repair endonuclease XPF	(Aeropyrum pernix ) [TaxId: 56636 ],	SCOPe (2.08)
B	d2bgwb2	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	XPF/Rad1/Mus81 nuclease	XPF endonuclease	(Aeropyrum pernix ) [TaxId: 56636 ],	SCOPe (2.08)
A	d2bgwa1	All alpha proteins	SAM domain-like	RuvA domain 2-like	Hef domain-like	DNA repair endonuclease XPF	(Aeropyrum pernix ) [TaxId: 56636 ],	SCOPe (2.08)
A	d2bgwa2	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	XPF/Rad1/Mus81 nuclease	XPF endonuclease	(Aeropyrum pernix ) [TaxId: 56636 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Restriction endonuclease-like	8038043	3000104	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Helix-hairpin-helix tandem	8038042	3000163	SCOP2B (2022-06-29)
A	SCOP2 Family	Hef domain-like	8025663	4001374	SCOP2 (2022-06-29)
A	SCOP2 Family	XPF/Rad1/Mus81 nuclease	8025664	4000517	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Helix-hairpin-helix tandem	8038042	3000163	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Restriction endonuclease-like	8038043	3000104	SCOP2 (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	RecU	e2bgwB2	A: beta barrels	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (v294.2)
B	Piwi	e2bgwB3	A: beta barrels	X: PH domain-like	H: PH domain-like	T: PH domain-like	F: Piwi	ECOD (v294.2)
A	ERCC4	e2bgwA2	A: beta barrels	X: Restriction endonuclease-like	H: Restriction endonuclease-like	T: Restriction endonuclease-like	F: ERCC4	ECOD (v294.2)
A	IMS_HHH_1	e2bgwA1	A: beta barrels	X: ETN0001 domain-like	H: YozE-like	T: YozE-like	F: IMS_HHH_1	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.10130	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	3.40.50.10130	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00633	Helix-hairpin-helix motif (HHH)	Helix-hairpin-helix motif	-	Motif
A, B	PF02732	ERCC4 domain (ERCC4)	ERCC4 domain	This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase [2-3]. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	5'-D(TPCPAPGPCPAPTPCPTPGP TPGPAPTP*C)-3'	-	-	-
C	5'-D(GPAPTPCPAPCPAPGPAPTP GPCPTPGP*A)-3'	-	-	-
A, B	XPF ENDONUCLEASE	DNA endonuclease activity endonuclease activity single-stranded DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity DNA nuclease activity DNA binding binding damaged DNA binding nucleic acid binding DNA endonuclease activity endonuclease activity single-stranded DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity DNA nuclease activity DNA binding binding damaged DNA binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding single-stranded DNA binding	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleotide-excision repair involved in interstrand cross-link repair nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response nucleotide-excision repair response to stress metabolic process cellular process interstrand cross-link repair cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleotide-excision repair involved in interstrand cross-link repair nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response nucleotide-excision repair response to stress metabolic process cellular process interstrand cross-link repair macromolecule metabolic process DNA repair double-strand break repair DNA recombination recombinational repair double-strand break repair via homologous recombination	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR010994	RuvA domain 2-like	Homologous Superfamily
A, B	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
A, B	IPR006166	ERCC4 domain	Domain
A, B	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	Domain

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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.