6Q01 | pdb_00006q01

TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2

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	d6q01b_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
A	d6q01a_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Ubiquitin-like	8098884	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8098884	3000157	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)
D	UBA_4	e6q01D1	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: UBA_4	ECOD (1.6)
C	UBA_4	e6q01C1	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: UBA_4	ECOD (1.6)
B	ubiquitin_1	e6q01B1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
A	ubiquitin_1	e6q01A1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF14555	UBA-like domain (UBA_4)	UBA-like domain		Domain
A, B	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Tyrosyl-DNA phosphodiesterase 2	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity nuclease activity catalytic activity, acting on a nucleic acid catalytic activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity nuclease activity catalytic activity, acting on a nucleic acid catalytic activity 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 hydrolase activity DNA binding single-stranded DNA binding nucleic acid binding tyrosyl-RNA phosphodiesterase activity catalytic activity, acting on RNA	cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cellular process signal transduction cell communication double-strand break repair primary metabolic process DNA metabolic process nucleic acid metabolic process cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cellular process signal transduction cell communication 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 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
A, B	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding structural molecule activity protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding structural molecule activity structural constituent of ribosome	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis ribosomal small subunit biogenesis catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis ribosomal small subunit biogenesis catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process macromolecule metabolic process protein metabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal biosynthetic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	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 protein-containing complex preribosome nuclear protein-containing complex small-subunit processome ribonucleoprotein complex cytoplasm ribosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR005135	Endonuclease/exonuclease/phosphatase	Domain
C, D	IPR051547	Tyrosyl-DNA phosphodiesterase 2-like	Family
C, D	IPR036691	Endonuclease/exonuclease/phosphatase superfamily	Homologous Superfamily
C, D	IPR009060	UBA-like superfamily	Homologous Superfamily
A, B	IPR019954	Ubiquitin conserved site	Conserved Site
A, B	IPR000626	Ubiquitin-like domain	Domain
A, B	IPR038582	Small ribosomal subunit protein eS31 eukaryotic superfamily	Homologous Superfamily
A, B	IPR002906	Small ribosomal subunit protein eS31	Domain
A, B	IPR019956	Ubiquitin domain	Domain
A, B	IPR050158	Ubiquitin and ubiquitin-like	Family
A, B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, B	IPR011332	Zinc-binding ribosomal protein	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: O95551	autosomal dominant cerebellar ataxia autosomal recessive cerebellar ataxia - epilepsy - intellectual disability syndrome due to TUD deficiency spinocerebellar ataxia type 6 cerebellar ataxia intellectual disability lymphoplasmacytic lymphoma neurodegenerative disease plasma cell myeloma spinocerebellar ataxia type 4 spinocerebellar ataxia type 7 dermatomyositis juvenile dermatomyositis malignant colon neoplasm osteogenesis imperfecta spinocerebellar ataxia type 1 autosomal dominant cerebellar ataxia autosomal recessive cerebellar ataxia - epilepsy - intellectual disability syndrome due to TUD deficiency spinocerebellar ataxia type 6 cerebellar ataxia intellectual disability lymphoplasmacytic lymphoma neurodegenerative disease plasma cell myeloma spinocerebellar ataxia type 4 spinocerebellar ataxia type 7 dermatomyositis juvenile dermatomyositis malignant colon neoplasm osteogenesis imperfecta spinocerebellar ataxia type 1 spinocerebellar ataxia type 5 ulcerative colitis breast carcinoma hereditary ataxia large cell medulloblastoma myopathy ovarian cancer spinocerebellar ataxia type 2

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.