4GYZ | pdb_00004gyz

Mus Musculus Tdp2 Bound to dAMP and Mg2+

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)
I	Ank_2, Ank_4, Ank_5	e4gyzI2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (v294.1)
H	Ank_2, Ank_4, Ank_5	e4gyzH2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (v294.1)
G	Ank_2, Ank_4, Ank_5	e4gyzG2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (v294.1)
F	Ank_2, Ank_4, Ank_5	e4gyzF2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (v294.1)
E	Ank_2, Ank_4, Ank_5	e4gyzE2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (v294.1)
D	Ank_2, Ank_4, Ank_5	e4gyzD2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (v294.1)
C	Ank_2, Ank_4, Ank_5	e4gyzC2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (v294.1)
B	Ank_2, Ank_4, Ank_5	e4gyzB2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (v294.1)
A	TetR_N	e4gyzA1	A: a/b three-layered sandwiches	X: Globin-like	H: Nucleoside diphosphate kinases	T: Nucleoside diphosphate kinases	F: TetR_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)
H	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)
G	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)
F	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)
E	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)
D	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)
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, D, E A, B, C, D, E, F, G, H, I	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, D, E A, B, C, D, E, F, G, H, I	Tyrosyl-DNA phosphodiesterase 2	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding manganese ion binding transition metal ion binding phosphoric ester hydrolase activity 5'-tyrosyl-DNA phosphodiesterase activity tyrosyl-DNA phosphodiesterase activity catalytic activity, acting on DNA hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding manganese ion binding transition metal ion binding phosphoric ester hydrolase activity 5'-tyrosyl-DNA phosphodiesterase activity tyrosyl-DNA phosphodiesterase activity catalytic activity, acting on DNA hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity endonuclease activity nuclease activity DNA binding single-stranded DNA binding nucleic acid binding tyrosyl-RNA phosphodiesterase activity catalytic activity, acting on RNA	cellular response to stimulus double-strand break repair response to stimulus 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 cellular process macromolecule metabolic process DNA repair cellular response to stimulus double-strand break repair response to stimulus 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 cellular process macromolecule metabolic process DNA repair developmental process multicellular organismal process cellular developmental process cell development nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation neuron development anatomical structure development system development	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm nuclear body nucleoplasm inclusion body aggresome PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR005135	Endonuclease/exonuclease/phosphatase	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR051547	Tyrosyl-DNA phosphodiesterase 2-like	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR036691	Endonuclease/exonuclease/phosphatase superfamily	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.