5F8A | pdb_00005f8a

Crystal structure of the ternary EcoRV-DNA-Lu complex with uncleaved DNA substrate. Lanthanide binding to EcoRV-DNA complex inhibits cleavage.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2B Superfamily	Restriction endonuclease-like	8041617	3000104	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Restriction endonuclease-like	8041617	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 [auth A]	Asp	e5f8aA1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: Asp	ECOD (v294.1)
D [auth B]	Asp	e5f8aB1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: Asp	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	3.40.600.10	Alpha Beta	3-Layer(aba) Sandwich	ECO RV Endonuclease	Chain A	CATH (4.3.0)
D [auth B]	3.40.600.10	Alpha Beta	3-Layer(aba) Sandwich	ECO RV Endonuclease	Chain A	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth A], D [auth B]	Type-2 restriction enzyme EcoRV	DNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity type II site-specific deoxyribonuclease activity restriction endodeoxyribonuclease activity DNA endonuclease activity DNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity type II site-specific deoxyribonuclease activity restriction endodeoxyribonuclease activity DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response DNA restriction-modification system defense response to symbiont response to external stimulus primary metabolic process clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids DNA metabolic process response to biotic stimulus nucleic acid metabolic process nucleobase-containing compound metabolic process DNA modification biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response DNA restriction-modification system defense response to symbiont response to external stimulus primary metabolic process clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids DNA metabolic process response to biotic stimulus nucleic acid metabolic process nucleobase-containing compound metabolic process DNA modification defense response to other organism response to stress macromolecule modification metabolic process cellular process response to external biotic stimulus macromolecule metabolic process	-
A [auth C], B [auth D]	DNA (5'-D(APAPAPGPAPTPAPTPCPTPTPT)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
C [auth A], D [auth B]	IPR037057	DNA mismatch repair MutH/Type II restriction endonuclease superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR019755	Restriction endonuclease, type II, EcoRV, Proteobacteria	Family
C [auth A], D [auth B]	IPR015314	Restriction endonuclease, type II, EcoRV	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.