5ITX | pdb_00005itx

Crystal Structure of Human NEIL1(P2G R242K) bound to duplex DNA containing Thymine Glycol

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	FPG N-terminal domain-like	8056357	3000074	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	S13-like H2TH domain	8044632	3000053	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8044633	3000068	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	FPG N-terminal domain-like	8056357	3000074	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	S13-like H2TH domain	8044632	3000053	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8044633	3000068	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	FPG N-terminal domain-like	8056357	3000074	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8044633	3000068	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S13-like H2TH domain	8044632	3000053	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)
E		e5itxE1	A: MocoBD/DmpA-related	X: MocoBD/DmpA-related	H: Retrovirus capsid protein-C	T: TIG	F:	ECOD (20:10:01)
C [auth B]		e5itxB1	A: MocoBD/DmpA-related	X: MocoBD/DmpA-related	H: Retrovirus capsid protein-C	T: TIG	F:	ECOD (20:10:01)
A		e5itxA1	A: MocoBD/DmpA-related	X: MocoBD/DmpA-related	H: Retrovirus capsid protein-C	T: TIG	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	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)
E	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C [auth B]	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)
C [auth B]	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E	PF09292	Endonuclease VIII-like 1, DNA bind (Neil1-DNA_bind)	Endonuclease VIII-like 1, DNA bind	Members of this family are predominantly found in Endonuclease VIII-like 1 and adopt a glucocorticoid receptor-like fold. They allow for DNA binding [1].	Domain
A, C [auth B]	PF09292	Endonuclease VIII-like 1, DNA bind (Neil1-DNA_bind)	Endonuclease VIII-like 1, DNA bind	Members of this family are predominantly found in Endonuclease VIII-like 1 and adopt a glucocorticoid receptor-like fold. They allow for DNA binding [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E	Endonuclease 8-like 1	DNA-(apurinic or apyrimidinic site) endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid DNA nuclease activity DNA endonuclease activity catalytic activity, acting on DNA nuclease activity class I DNA-(apurinic or apyrimidinic site) endonuclease activity lyase activity catalytic activity carbon-oxygen lyase activity hydrolase activity, acting on glycosyl bonds hydrolase activity DNA N-glycosylase activity DNA-(apurinic or apyrimidinic site) endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid DNA nuclease activity DNA endonuclease activity catalytic activity, acting on DNA nuclease activity class I DNA-(apurinic or apyrimidinic site) endonuclease activity lyase activity catalytic activity carbon-oxygen lyase activity hydrolase activity, acting on glycosyl bonds hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding DNA binding damaged DNA binding nucleic acid 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 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 base-excision repair, gap-filling pyrimidine deoxyribonucleotide catabolic process deoxyribonucleotide catabolic process catabolic process pyrimidine deoxyribonucleotide metabolic process pyrimidine-containing compound catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process deoxyribose phosphate catabolic process pyrimidine nucleotide metabolic process pyrimidine nucleotide catabolic process DNA modification deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process depyrimidination nucleotide catabolic process nucleoside phosphate metabolic process carbohydrate derivative catabolic process pyrimidine-containing compound metabolic process 2'-deoxyribonucleotide metabolic process nucleotide metabolic process nucleobase-containing compound catabolic process organophosphate metabolic process macromolecule modification base-excision repair, AP site formation response to oxidative stress	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B [auth D], D [auth C], F	DNA (26-MER)	-	-	-
A, C [auth B]	Endonuclease 8-like 1	DNA-(apurinic or apyrimidinic site) endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid DNA nuclease activity DNA endonuclease activity catalytic activity, acting on DNA nuclease activity class I DNA-(apurinic or apyrimidinic site) endonuclease activity lyase activity catalytic activity carbon-oxygen lyase activity hydrolase activity, acting on glycosyl bonds hydrolase activity DNA N-glycosylase activity DNA-(apurinic or apyrimidinic site) endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid DNA nuclease activity DNA endonuclease activity catalytic activity, acting on DNA nuclease activity class I DNA-(apurinic or apyrimidinic site) endonuclease activity lyase activity catalytic activity carbon-oxygen lyase activity hydrolase activity, acting on glycosyl bonds hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding DNA binding damaged DNA binding nucleic acid 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 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 base-excision repair, gap-filling pyrimidine deoxyribonucleotide catabolic process deoxyribonucleotide catabolic process catabolic process pyrimidine deoxyribonucleotide metabolic process pyrimidine-containing compound catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process deoxyribose phosphate catabolic process pyrimidine nucleotide metabolic process pyrimidine nucleotide catabolic process DNA modification deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process depyrimidination nucleotide catabolic process nucleoside phosphate metabolic process carbohydrate derivative catabolic process pyrimidine-containing compound metabolic process 2'-deoxyribonucleotide metabolic process nucleotide metabolic process nucleobase-containing compound catabolic process organophosphate metabolic process macromolecule modification base-excision repair, AP site formation response to oxidative stress	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E	IPR012319	Formamidopyrimidine-DNA glycosylase, catalytic domain	Domain
E	IPR015886	Formamidopyrimidine-DNA glycosylase, H2TH DNA-binding	Domain
E	IPR015371	Endonuclease VIII-like 1, DNA binding	Domain
E	IPR035937	Formamidopyrimidine-DNA glycosylase, N-terminal	Homologous Superfamily
E	IPR010979	Small ribosomal subunit protein uS13-like, H2TH	Homologous Superfamily
A, C [auth B]	IPR012319	Formamidopyrimidine-DNA glycosylase, catalytic domain	Domain
A, C [auth B]	IPR015886	Formamidopyrimidine-DNA glycosylase, H2TH DNA-binding	Domain
A, C [auth B]	IPR015371	Endonuclease VIII-like 1, DNA binding	Domain
A, C [auth B]	IPR035937	Formamidopyrimidine-DNA glycosylase, N-terminal	Homologous Superfamily
A, C [auth B]	IPR010979	Small ribosomal subunit protein uS13-like, H2TH	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E	Pharos: Q96FI4	metabolic syndrome X Dyslipidemias glucose intolerance hyperinsulinism obesity disorder medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor fatty liver disease psoriasis breast cancer familial hyperlipidemia gastric carcinoma malignant glioma glioblastoma metabolic syndrome X Dyslipidemias glucose intolerance hyperinsulinism obesity disorder medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor fatty liver disease psoriasis breast cancer familial hyperlipidemia gastric carcinoma malignant glioma glioblastoma hyperlipidemia large cell medulloblastoma
A, C [auth B]	Pharos: Q96FI4	metabolic syndrome X Dyslipidemias glucose intolerance hyperinsulinism obesity disorder medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor fatty liver disease psoriasis breast cancer familial hyperlipidemia gastric carcinoma malignant glioma glioblastoma metabolic syndrome X Dyslipidemias glucose intolerance hyperinsulinism obesity disorder medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor fatty liver disease psoriasis breast cancer familial hyperlipidemia gastric carcinoma malignant glioma glioblastoma hyperlipidemia large cell medulloblastoma

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.