5T2W | pdb_00005t2w

Structure of thymine DNA glycosylase bound to substrate analog 2'-F-5-formyl-dC

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	Uracil-DNA glycosylase-like	8032454	3001106	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	PK_Tyr_Ser-Thr	e5t2wA1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: PK_Tyr_Ser-Thr	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03167	Uracil DNA glycosylase superfamily (UDG)	Uracil DNA glycosylase superfamily		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D]	DNA (27-MER)	-	-	-
B [auth C]	DNA (28-MER)	-	-	-
A	G/T mismatch-specific thymine DNA glycosylase	binding nucleic acid binding protein binding protein domain specific binding transcription regulator activity transcription coregulator activity uracil DNA N-glycosylase activity hydrolase activity, acting on glycosyl bonds deaminated base DNA N-glycosylase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds binding nucleic acid binding protein binding protein domain specific binding transcription regulator activity transcription coregulator activity uracil DNA N-glycosylase activity hydrolase activity, acting on glycosyl bonds deaminated base DNA N-glycosylase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity DNA binding damaged DNA binding mismatch base pair DNA N-glycosylase activity pyrimidine-specific mismatch base pair DNA N-glycosylase activity ion binding anion binding chloride ion binding small molecule binding cation binding magnesium ion binding metal ion binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding double-stranded DNA binding G/T mismatch-specific thymine-DNA glycosylase activity G/U mismatch-specific uracil-DNA glycosylase activity transcription factor binding DNA-binding transcription factor binding mismatched DNA binding SUMO binding ubiquitin-like protein binding kinase binding protein kinase C binding enzyme binding protein kinase binding alkali metal ion binding sodium ion binding	regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling cellular process regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling cellular process regulation of macromolecule biosynthetic process metabolic process cellular component organization or biogenesis macromolecule metabolic process regulation of metabolic process cellular response to stimulus pyrimidine deoxyribonucleotide catabolic process catabolic process response to stimulus pyrimidine deoxyribonucleotide metabolic process pyrimidine-containing compound catabolic process carbohydrate derivative metabolic process organophosphate catabolic process deoxyribose phosphate catabolic process nucleoside phosphate catabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process pyrimidine nucleotide catabolic process base-excision repair DNA modification cellular response to stress response to stress nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process depyrimidination nucleotide catabolic process DNA repair nucleoside phosphate metabolic process carbohydrate derivative catabolic process pyrimidine-containing compound metabolic process 2'-deoxyribonucleotide metabolic process primary metabolic process DNA metabolic process nucleotide metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process DNA damage response organophosphate metabolic process macromolecule modification base-excision repair, AP site formation developmental process multicellular organismal process regulation of embryonic development regulation of multicellular organismal development regulation of developmental process embryo development multicellular organism development anatomical structure development regulation of multicellular organismal process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process chromosomal 5-methylcytosine DNA demethylation, oxidation pathway positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process chromosomal 5-methylcytosine DNA demethylation pathway positive regulation of gene expression	cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular membraneless organelle nuclear body membraneless organelle PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036895	Uracil-DNA glycosylase-like domain superfamily	Homologous Superfamily
A	IPR003310	G/T mismatch-specific thymine DNA glycosylasee TDG-like, eukaryotes	Family
A	IPR005122	Uracil-DNA glycosylase-like	Domain
A	IPR015637	Uracil DNA glycosylase family 2	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q13569	atypical teratoid rhabdoid tumor invasive ductal breast carcinoma lymphoplasmacytic lymphoma Pick disease progressive supranuclear palsy dermatomyositis large cell medulloblastoma medulloblastoma plasma cell myeloma glioblastoma lung cancer osteosarcoma primitive neuroectodermal tumor

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.