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	Hexokinase_2	e2bgwB2	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: Hexokinase_2	ECOD (v295.2)
B		e2bgwB3	A: alpha arrays	X: DEATH domain	H: PH domain-like	T: PH domain-like	F:	ECOD (v295.2)
A	ERCC4	e2bgwA2	A: alpha arrays	X: Restriction endonuclease-like	H: Restriction endonuclease-like	T: Restriction endonuclease-like	F: ERCC4	ECOD (v295.2)
A	IMS_HHH_1	e2bgwA1	A: alpha arrays	X: Urease, gamma-subunit	H: p53 tetramerization domain	T: p53 tetramerization domain	F: IMS_HHH_1	ECOD (v295.2)

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 binding binding damaged DNA binding nucleic acid binding single-stranded DNA 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 binding binding damaged DNA binding nucleic acid binding single-stranded DNA 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	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	IPR060101	SAM-like helix-hairpin-helix tandem	Domain
A, B	IPR006166	ERCC4 domain	Domain
A, B	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	Domain