5HNK | pdb_00005hnk

Crystal structure of T5Fen in complex intact substrate and metal ions.

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 A]	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8037738	3000537	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	PIN domain-like	8044460	3001041	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	PIN domain-like	8044460	3001041	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8037738	3000537	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]	5_3_exonuc	e5hnkA1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: 5_3_exonuc	ECOD (1.6)
C [auth A]	5_3_exonuc_N	e5hnkA2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: 5_3_exonuc_N	ECOD (1.6)
D [auth B]	5_3_exonuc	e5hnkB2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: 5_3_exonuc	ECOD (1.6)
D [auth B]	5_3_exonuc_N	e5hnkB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: 5_3_exonuc_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
C [auth A]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
D [auth B]	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
D [auth B]	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
C [auth A], D [auth B]	PF02739	5'-3' exonuclease, N-terminal resolvase-like domain (5_3_exonuc_N)	5'-3' exonuclease, N-terminal resolvase-like domain		Domain
C [auth A], D [auth B]	PF01367	5'-3' exonuclease, C-terminal SAM fold (5_3_exonuc)	5'-3' exonuclease, C-terminal SAM fold		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth X], B [auth Y]	DNA (5'-D(APAPAPAPGPCPGPTPAPCPGPC)-3')	-	-	-
C [auth A], D [auth B]	Exodeoxyribonuclease	DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity double-stranded DNA endonuclease activity catalytic activity DNA nuclease activity DNA binding binding nucleic acid binding DNA exonuclease activity DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity double-stranded DNA endonuclease activity catalytic activity DNA nuclease activity DNA binding binding nucleic acid binding DNA exonuclease activity exonuclease activity 5'-flap endonuclease activity flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters 5'-3' exonuclease activity 5'-3' DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters double-stranded DNA 5'-3' DNA exonuclease activity double-stranded DNA exodeoxyribonuclease activity cation binding ion binding metal ion binding small molecule binding	viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process metabolic process cellular process viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process DNA-templated DNA replication lagging strand elongation DNA strand elongation DNA replication DNA replication, Okazaki fragment processing DNA strand elongation involved in DNA replication viral gene expression late viral transcription viral transcription	viral replication complex host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus host cell nuclear part host intracellular organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR002421	5'-3' exonuclease	Domain
C [auth A], D [auth B]	IPR020045	DNA polymerase I-like, H3TH domain	Domain
C [auth A], D [auth B]	IPR043666	Flap endonuclease D15-like	Family
C [auth A], D [auth B]	IPR038969	Flap endonuclease	Family
C [auth A], D [auth B]	IPR029060	PIN-like domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR036279	5'-3' exonuclease, C-terminal domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR008918	Helix-hairpin-helix motif, class 2	Conserved Site
C [auth A], D [auth B]	IPR020046	5'-3' exonuclease, alpha-helical arch, N-terminal	Domain

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.