5FDK | pdb_00005fdk

Crystal structure of RecU(D88N) in complex with palindromic DNA duplex

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)
D	SCOP2B Superfamily	Restriction endonuclease-like	8042338	3000104	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Restriction endonuclease-like	8042338	3000104	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Restriction endonuclease-like	8042338	3000104	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Restriction endonuclease-like	8042338	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)
D	Bact_surface_Ig-like	e5fdkD1	A: a/b three-layered sandwiches	X: jelly-roll	H: AOC barrel-like	T: AOC barrel-like	F: Bact_surface_Ig-like	ECOD (v294.1)
C	AA9	e5fdkC1	A: a/b three-layered sandwiches	X: Long alpha-hairpin	H: Ribosomal protein L29 (L29p)	T: Ribosomal protein L29 (L29p)	F: AA9	ECOD (v294.1)
B	AA9	e5fdkB1	A: a/b three-layered sandwiches	X: Long alpha-hairpin	H: Ribosomal protein L29 (L29p)	T: Ribosomal protein L29 (L29p)	F: AA9	ECOD (v294.1)
A	AA9	e5fdkA1	A: a/b three-layered sandwiches	X: Long alpha-hairpin	H: Ribosomal protein L29 (L29p)	T: Ribosomal protein L29 (L29p)	F: AA9	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
C	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
B	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
A	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF03838	Recombination protein U (RecU)	Recombination protein U		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F, G, H	palindromic DNA	-	-	-
A, B, C, D	Holliday junction resolvase RecU	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity crossover junction DNA endonuclease activity DNA nuclease activity DNA endonuclease activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity crossover junction DNA endonuclease activity DNA nuclease activity DNA endonuclease activity DNA endonuclease activity, producing 3'-phosphomonoesters hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity catalytic activity	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 DNA recombination 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 DNA recombination cell cycle chromosome segregation cell cycle process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR004612	Holliday junction resolvase RecU	Family
A, B, C, D	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
A, B, C, D	IPR011856	tRNA endonuclease-like domain superfamily	Homologous Superfamily

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.