6W4R | pdb_00006w4r

Structure of Tdp1 catalytic domain in complex with inhibitor XZ633p

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6w4ra1	Alpha and beta proteins (a+b)	Phospholipase D/nuclease	Phospholipase D/nuclease	Tyrosyl-DNA phosphodiesterase TDP1	Tyrosyl-DNA phosphodiesterase TDP1	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6w4rb1	Alpha and beta proteins (a+b)	Phospholipase D/nuclease	Phospholipase D/nuclease	Tyrosyl-DNA phosphodiesterase TDP1	Tyrosyl-DNA phosphodiesterase TDP1	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Phospholipase D/nuclease-like	8037449	3000664	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Phospholipase D/nuclease-like	8037447	3000664	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phospholipase D/nuclease-like	8037449	3000664	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phospholipase D/nuclease-like	8037447	3000664	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	Tyr-DNA_phospho_1st	e6w4rA2	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: Tyr-DNA_phospho_1st	ECOD (1.6)
A	Tyr-DNA_phospho_2nd	e6w4rA1	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: Tyr-DNA_phospho_2nd	ECOD (1.6)
B	Tyr-DNA_phospho_1st	e6w4rB2	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: Tyr-DNA_phospho_1st	ECOD (1.6)
B	Tyr-DNA_phospho_2nd	e6w4rB1	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: Tyr-DNA_phospho_2nd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF06087	Tyrosyl-DNA phosphodiesterase (Tyr-DNA_phospho)	Tyrosyl-DNA phosphodiesterase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Tyrosyl-DNA phosphodiesterase 1	hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exonuclease activity catalytic activity phosphoric ester hydrolase activity tyrosyl-DNA phosphodiesterase activity 3'-tyrosyl-DNA phosphodiesterase activity catalytic activity, acting on DNA phosphoric diester hydrolase activity DNA binding double-stranded DNA binding binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exonuclease activity catalytic activity phosphoric ester hydrolase activity tyrosyl-DNA phosphodiesterase activity 3'-tyrosyl-DNA phosphodiesterase activity catalytic activity, acting on DNA phosphoric diester hydrolase activity DNA binding double-stranded DNA binding binding nucleic acid binding single-stranded DNA binding	cellular response to stimulus response to stimulus single 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 cellular process macromolecule metabolic process DNA repair cellular response to stimulus response to stimulus single 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 cellular process macromolecule metabolic process DNA repair double-strand break repair	cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle cytoplasm nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle cytoplasm nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR010347	Tyrosyl-DNA phosphodiesterase I	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9NUW8	spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 1 Ataxias, Hereditary breast cancer epithelioid cell uveal melanoma medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor Charcot-Marie-Tooth disease large cell medulloblastoma neurodegenerative disease psoriasis tuberculosis autosomal recessive cerebellar ataxia cutaneous lupus erythematosus lung cancer spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 1 Ataxias, Hereditary breast cancer epithelioid cell uveal melanoma medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor Charcot-Marie-Tooth disease large cell medulloblastoma neurodegenerative disease psoriasis tuberculosis autosomal recessive cerebellar ataxia cutaneous lupus erythematosus lung cancer non-small cell lung carcinoma spinocerebellar ataxia, autosomal recessive, with axonal neuropathy uveal melanoma

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.