3HD0 | pdb_00003hd0

Crystal structure of Tm1865, an Endonuclease V from Thermotoga Maritima

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth D]	SCOP2B Superfamily	Ribonuclease H-like	8092724	3000143	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8092724	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8092724	3000143	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 D]	Ribosomal_L36	e3hd0D1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (v294.1)
B	Ribosomal_L36	e3hd0B1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (v294.1)
A	V-set	e3hd0A1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: HMA-related	T: HMA, heavy metal-associated domain	F: V-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth D]	3.30.2170.10	Alpha Beta	2-Layer Sandwich	archaeoglobus fulgidus dsm 4304 fold	archaeoglobus fulgidus dsm 4304 superfamily	CATH (4.3.0)
B	3.30.2170.10	Alpha Beta	2-Layer Sandwich	archaeoglobus fulgidus dsm 4304 fold	archaeoglobus fulgidus dsm 4304 superfamily	CATH (4.3.0)
A	3.30.2170.10	Alpha Beta	2-Layer Sandwich	archaeoglobus fulgidus dsm 4304 fold	archaeoglobus fulgidus dsm 4304 superfamily	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C [auth D]	PF04493	Endonuclease V (Endonuclease_5)	Endonuclease V	Endonuclease V is specific for single-stranded DNA or for duplex DNA that contains uracil or that is damaged by a variety of agents [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C [auth D]	Endonuclease V	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding RNA binding nucleic acid binding single-stranded RNA binding endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on RNA cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding RNA binding nucleic acid binding single-stranded RNA binding endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity DNA nuclease activity deoxyribonuclease V activity DNA endonuclease activity catalytic activity, acting on DNA DNA endonuclease activity, producing 5'-phosphomonoesters	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C [auth D]	IPR007581	Endonuclease V	Family
A, B, C [auth D]	IPR053396	Endonuclease V-like	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.