5ITU

Crystal Structure of Human NEIL1(242K) bound to duplex DNA containing THF

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)
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)
A	SCOP2B Superfamily	FPG N-terminal domain-like	8056357	3000074	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8044633	3000068	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FPG N-terminal domain-like	8056357	3000074	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	S13-like H2TH domain	8044632	3000053	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8044633	3000068	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	FPG N-terminal domain-like	8056357	3000074	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	e5ituA3	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	e5ituA2	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: H2TH	ECOD (1.6)
A	Neil1-DNA_bind	e5ituA1	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: Neil1-DNA_bind	ECOD (1.6)
B	Fapy_DNA_glyco	e5ituB2	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)
B	H2TH	e5ituB1	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: H2TH	ECOD (1.6)
B	Neil1-DNA_bind	e5ituB3	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: Neil1-DNA_bind	ECOD (1.6)
C	Fapy_DNA_glyco	e5ituC1	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)
C	H2TH	e5ituC2	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: H2TH	ECOD (1.6)
C	Neil1-DNA_bind	e5ituC3	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: Neil1-DNA_bind	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)
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)
B	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	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	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
A, B, C	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, B, C	PF01149	Formamidopyrimidine-DNA glycosylase N-terminal domain (Fapy_DNA_glyco)	Formamidopyrimidine-DNA glycosylase N-terminal domain	Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidised purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges [1 ...	Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidised purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Endonuclease 8-like 1	DNA-(apurinic or apyrimidinic site) endonuclease activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid 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 DNA-(apurinic or apyrimidinic site) endonuclease activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid 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 organic cyclic compound binding damaged DNA binding nucleic acid binding	negative regulation of hydrolase activity regulation of catalytic activity negative regulation of biological process negative regulation of catalytic activity regulation of primary metabolic process nucleobase-containing compound metabolic process organic substance metabolic process regulation of nuclease activity negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process negative regulation of metabolic process biological regulation negative regulation of molecular function negative regulation of hydrolase activity regulation of catalytic activity negative regulation of biological process negative regulation of catalytic activity regulation of primary metabolic process nucleobase-containing compound metabolic process organic substance metabolic process regulation of nuclease activity negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process negative regulation of metabolic process biological regulation negative regulation of molecular function primary metabolic process regulation of macromolecule metabolic process regulation of molecular function organic cyclic compound metabolic process regulation of hydrolase activity metabolic process macromolecule metabolic process regulation of metabolic process negative regulation of nuclease activity cellular response to stimulus response to stimulus DNA metabolic process nucleic acid metabolic process base-excision repair cellular response to stress DNA damage response response to stress cellular process DNA repair base-excision repair, gap-filling deoxyribonucleotide catabolic process pyrimidine deoxyribonucleotide metabolic process pyrimidine-containing compound catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process pyrimidine nucleotide metabolic process DNA modification phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process organonitrogen compound catabolic process pyrimidine-containing compound metabolic process cellular metabolic process nucleotide metabolic process nucleobase-containing compound catabolic process macromolecule modification base-excision repair, AP site formation pyrimidine deoxyribonucleotide catabolic process catabolic process deoxyribose phosphate catabolic process pyrimidine nucleotide catabolic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process depyrimidination nucleotide catabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process 2'-deoxyribonucleotide metabolic process deoxyribose phosphate metabolic process organic cyclic compound catabolic process organophosphate metabolic process organic substance catabolic process response to oxidative stress	intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromosome cellular anatomical entity non-membrane-bounded organelle centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromosome cellular anatomical entity non-membrane-bounded organelle 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
D, F, H	DNA (5'-D(CPGPTPCPCPAPCPGPTPCPTPAP*C)-3')	-	-	-
E, G, I	DNA (5'-D(TPAPGPAPCPCPTPGPGPAPCPGP*G)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	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 National Science Foundation (DBI-1832184), 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 R01GM133198.