4PDI | pdb_00004pdi

Crystal structure of a complex between an inhibited LlFpg and a N7-Benzyl-Fapy-dG containing DNA

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)
A	SCOP2B Superfamily	FPG N-terminal domain-like	8056367	3000074	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S13-like H2TH domain	8056368	3000053	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8056369	3000068	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)
A	Fapy_DNA_glyco	e4pdiA1	A: beta barrels	X: MutM N-terminal domain-like	H: N-terminal domain of MutM-like DNA repair proteins (From Topology)	T: N-terminal domain of MutM-like DNA repair proteins	F: Fapy_DNA_glyco	ECOD (1.6)
A	H2TH	e4pdiA3	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: H2TH	ECOD (1.6)
A	zf-FPG_IleRS	e4pdiA2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: C-terminal, Zn-finger domain of MutM-like DNA repair proteins (From Topology)	T: C-terminal, Zn-finger domain of MutM-like DNA repair proteins	F: zf-FPG_IleRS	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.190.10	Alpha Beta	Alpha-Beta Barrel	N-terminal domain of MutM-like DNA repair proteins	MutM-like, N-terminal	CATH (4.3.0)
A	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	DNA (5'-D(GPCPGPAPGPAPAPAPCPAPAPAPGPA)-3')	-	-	-
B	DNA (5'-D(CPTPCPTPTPTP(SOS)PTPTPTPCPTPCPG)-3')	-	-	-
A	Formamidopyrimidine-DNA glycosylase	hydrolase activity, acting on glycosyl bonds oxidized base lesion DNA N-glycosylase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid oxidized purine nucleobase lesion DNA N-glycosylase activity hydrolase activity 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity DNA binding double-stranded DNA binding binding nucleic acid binding hydrolase activity, acting on glycosyl bonds oxidized base lesion DNA N-glycosylase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid oxidized purine nucleobase lesion DNA N-glycosylase activity hydrolase activity 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity DNA binding double-stranded DNA binding binding nucleic acid binding DNA-(apurinic or apyrimidinic site) endonuclease activity endonuclease activity DNA nuclease activity DNA endonuclease activity nuclease activity class I DNA-(apurinic or apyrimidinic site) endonuclease activity lyase activity carbon-oxygen lyase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding damaged DNA binding	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process base-excision repair cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000214	Zinc finger, DNA glycosylase/AP lyase-type	Domain
A	IPR015887	DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site	Binding Site
A	IPR012319	Formamidopyrimidine-DNA glycosylase, catalytic domain	Domain
A	IPR015886	Formamidopyrimidine-DNA glycosylase, H2TH DNA-binding	Domain
A	IPR020629	Formamidopyrimidine-DNA glycosylase	Family
A	IPR035937	Formamidopyrimidine-DNA glycosylase, N-terminal	Homologous Superfamily
A	IPR010663	Zinc finger, FPG/IleRS-type	Domain
A	IPR010979	Small ribosomal subunit protein uS13-like, H2TH	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.