Annotations: 6CA4

Crystal structure of humanized D. rerio TDP2 by 14 mutations

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	TBP	e6ca4C1	A: beta barrels	X: Phosphorylase/hydrolase-like	H: Ribosomal protein S5 domain 2-like	T: Ribosomal protein S5 domain 2-like	F: TBP	ECOD (v294.2)
B	TNF	e6ca4B1	A: beta barrels	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: TNF	ECOD (v294.2)
A	TBP	e6ca4A1	A: beta barrels	X: Phosphorylase/hydrolase-like	H: Ribosomal protein S5 domain 2-like	T: Ribosomal protein S5 domain 2-like	F: TBP	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)
B	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)
A	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF03372	Endonuclease/Exonuclease/phosphatase family (Exo_endo_phos)	Endonuclease/Exonuclease/phosphatase family	This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling [1]. This family includes: AP endonuclease proteins EC:4.2.99.18 e.g Swiss:P27695, DNase I proteins EC:3. ...	This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling [1]. This family includes: AP endonuclease proteins EC:4.2.99.18 e.g Swiss:P27695, DNase I proteins EC:3.1.21.1 e.g. Swiss:P24855, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56 Swiss:O43426, Sphingomyelinase EC:3.1.4.12 Swiss:P11889 and Nocturnin Swiss:O35710.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Tyrosyl-DNA phosphodiesterase 2	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding nuclease activity catalytic activity, acting on a nucleic acid catalytic activity phosphoric ester hydrolase activity tyrosyl-DNA phosphodiesterase activity catalytic activity, acting on DNA cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding nuclease activity catalytic activity, acting on a nucleic acid catalytic activity phosphoric ester hydrolase activity tyrosyl-DNA phosphodiesterase activity catalytic activity, acting on DNA hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity hydrolase activity manganese ion binding transition metal ion binding 5'-tyrosyl-DNA phosphodiesterase activity single-stranded DNA binding	developmental process multicellular organism development multicellular organismal process determination of bilateral symmetry anatomical structure development pattern specification process determination of left/right symmetry left/right pattern formation regionalization specification of symmetry cellular response to stimulus negative regulation of transforming growth factor beta receptor signaling pathway regulation of cellular process cell surface receptor protein serine/threonine kinase signaling pathway developmental process multicellular organism development multicellular organismal process determination of bilateral symmetry anatomical structure development pattern specification process determination of left/right symmetry left/right pattern formation regionalization specification of symmetry cellular response to stimulus negative regulation of transforming growth factor beta receptor signaling pathway regulation of cellular process cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus response to stimulus negative regulation of signaling signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication regulation of transforming growth factor beta receptor signaling pathway cellular response to endogenous stimulus negative regulation of cellular process signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling regulation of biological process cell surface receptor signaling pathway negative regulation of response to stimulus regulation of cellular response to transforming growth factor beta stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus biological regulation negative regulation of signal transduction response to transforming growth factor beta regulation of response to stimulus transforming growth factor beta receptor signaling pathway regulation of cell communication cellular process response to growth factor transforming growth factor beta receptor superfamily signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway convergent extension involved in gastrulation epithelium development embryonic morphogenesis morphogenesis of an epithelium embryo development tissue development gastrulation anatomical structure morphogenesis tissue morphogenesis convergent extension double-strand break repair 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 macromolecule metabolic process DNA repair	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear body intracellular organelle nucleoplasm organelle lumen organelle cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear body intracellular organelle nucleoplasm organelle lumen organelle membraneless organelle PML body nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR005135	Endonuclease/exonuclease/phosphatase	Domain
A, B, C	IPR051547	Tyrosyl-DNA phosphodiesterase 2-like	Family
A, B, C	IPR036691	Endonuclease/exonuclease/phosphatase superfamily	Homologous Superfamily
A, B, C	IPR009060	UBA-like superfamily	Homologous Superfamily

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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.