6DIE | pdb_00006die

Crystal structure of Tdp1 catalytic domain in complex with Zenobia fragment benzene-1,2,4-tricarboxylic acid from single soak

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d6dieb1	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)
A	d6diea1	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)
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)
A	SCOP2B Superfamily	Phospholipase D/nuclease-like	8037447	3000664	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Phospholipase D/nuclease-like	8037449	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)
B	NUDIX	e6dieB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F: NUDIX	ECOD (v294.1)
A	NUDIX	e6dieA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F: NUDIX	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.870.10	Alpha Beta	2-Layer Sandwich	Endonuclease	Chain A	CATH (utative)
A	3.30.870.10	Alpha Beta	2-Layer Sandwich	Endonuclease	Chain A	CATH (utative)

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	Tdp1 catalytic domain (residues 149-609)	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 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 single strand break repair	cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.