3SLP | pdb_00003slp

Crystal Structure of Lambda Exonuclease in Complex with a 12 BP Symmetric DNA Duplex

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)
C	d3slpc_	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	lambda exonuclease	lambda exonuclease	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)
B	d3slpb_	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	lambda exonuclease	lambda exonuclease	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)
A	d3slpa_	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	lambda exonuclease	lambda exonuclease	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Restriction endonuclease-like	8044442	3000104	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Restriction endonuclease-like	8044442	3000104	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Restriction endonuclease-like	8044442	3000104	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)
C	Glyco_hydro_3	e3slpC1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Glyco_hydro_3	ECOD (develop294)
B	Glyco_hydro_3	e3slpB1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Glyco_hydro_3	ECOD (develop294)
A	Ras	e3slpA1	A: alpha bundles	X: EF-hand	H: Insect pheromone/odorant-binding proteins	T: Insect pheromone/odorant-binding proteins	F: Ras	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.90.320.10	Alpha Beta	Alpha-Beta Complex	Lambda Exonuclease	Chain A	CATH (4.3.0)
B	3.90.320.10	Alpha Beta	Alpha-Beta Complex	Lambda Exonuclease	Chain A	CATH (4.3.0)
A	3.90.320.10	Alpha Beta	Alpha-Beta Complex	Lambda Exonuclease	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF09588	YqaJ-like viral recombinase domain (YqaJ)	YqaJ-like viral recombinase domain	This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a ...	This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, E	5'-D(GPCPGPAPCPTPAPGPTPCPGPC)-3'	-	-	-
A, B, C	Exonuclease	DNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid double-stranded DNA 5'-3' DNA exonuclease activity double-stranded DNA exodeoxyribonuclease activity hydrolase activity 5'-3' DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity exonuclease activity DNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid double-stranded DNA 5'-3' DNA exonuclease activity double-stranded DNA exodeoxyribonuclease activity hydrolase activity 5'-3' DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity exonuclease 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	IPR019080	YqaJ viral recombinase	Domain
A, B, C	IPR011604	PD-(D/E)XK endonuclease-like domain superfamily	Homologous Superfamily
A, B, C	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
A, B, C	IPR051703	NF-kappa-B Signaling Regulator	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.