2IO1 | pdb_00002io1

Crystal structure of human Senp2 in complex with preSUMO-3

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)
F	d2io1f_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2io1d_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2io1b_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2io1c_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Adenain-like	Sentrin-specific protease 2, SENP2	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2io1e_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Adenain-like	Sentrin-specific protease 2, SENP2	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2io1a_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Adenain-like	Sentrin-specific protease 2, SENP2	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)
F	SCOP2B Superfamily	Ubiquitin-like	8032781	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8032781	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8032781	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cysteine proteinases	8040201	3001808	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Cysteine proteinases	8040201	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8040201	3001808	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)
F	Rad60-SLD	e2io1F1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Rad60-SLD	ECOD (1.6)
D	Rad60-SLD	e2io1D1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Rad60-SLD	ECOD (1.6)
B	Rad60-SLD	e2io1B1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Rad60-SLD	ECOD (1.6)
C	Peptidase_C48	e2io1C1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C48	ECOD (1.6)
E	Peptidase_C48	e2io1E1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C48	ECOD (1.6)
A	Peptidase_C48	e2io1A1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C48	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.40.395.10	Alpha Beta	3-Layer(aba) Sandwich	Adenoviral Proteinase	Chain	CATH (4.3.0)
E	3.40.395.10	Alpha Beta	3-Layer(aba) Sandwich	Adenoviral Proteinase	Chain	CATH (4.3.0)
A	3.40.395.10	Alpha Beta	3-Layer(aba) Sandwich	Adenoviral Proteinase	Chain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F	PF11976	Ubiquitin-2 like Rad60 SUMO-like (Rad60-SLD)	Ubiquitin-2 like Rad60 SUMO-like	-	Family
A, C, E	PF02902	Ulp1 protease family, C-terminal catalytic domain (Peptidase_C48)	Ulp1 protease family, C-terminal catalytic domain	This domain contains the catalytic triad Cys-His-Asn.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F	Small ubiquitin-related modifier 3 precursor	protein binding binding ubiquitin-like protein ligase binding enzyme binding protein tag activity molecular tag activity	regulation of molecular function regulation of DNA binding regulation of binding negative regulation of binding biological regulation negative regulation of molecular function negative regulation of DNA binding peptidyl-lysine modification primary metabolic process protein sumoylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process regulation of molecular function regulation of DNA binding regulation of binding negative regulation of binding biological regulation negative regulation of molecular function negative regulation of DNA binding peptidyl-lysine modification primary metabolic process protein sumoylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of localization localization regulation of biological process regulation of protein localization macromolecule localization protein localization to organelle regulation of protein localization to nucleus intracellular protein localization protein localization to nucleus	intracellular anatomical structure intracellular membraneless organelle chromosome chromosomal region kinetochore intracellular organelle cellular anatomical structure organelle membraneless organelle chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome cytoplasm intracellular anatomical structure intracellular membraneless organelle chromosome chromosomal region kinetochore intracellular organelle cellular anatomical structure organelle membraneless organelle chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen nuclear body PML body
A, C, E	Sentrin-specific protease 2	cysteine-type peptidase activity peptidase activity ubiquitin-like protein peptidase activity catalytic activity, acting on a protein SUMO-specific endopeptidase activity cysteine-type endopeptidase activity hydrolase activity catalytic activity ubiquitin-like protein-specific endopeptidase activity endopeptidase activity deSUMOylase activity	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development regulation of cellular process cell cycle DNA replication regulation of primary metabolic process nucleobase-containing compound metabolic process cell cycle regulation of nucleobase-containing compound metabolic process developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development regulation of cellular process cell cycle DNA replication regulation of primary metabolic process nucleobase-containing compound metabolic process cell cycle regulation of nucleobase-containing compound metabolic process regulation of cell cycle cell cycle process DNA-templated DNA replication regulation of biological process DNA endoreduplication regulation of cell cycle process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process DNA replication regulation of DNA endoreduplication regulation of DNA-templated DNA replication metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process protein destabilization regulation of protein stability regulation of biological quality RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport placenta development chordate embryonic development labyrinthine layer development embryo development in utero embryonic development embryonic placenta development embryo development ending in birth or egg hatching embryonic organ development negative regulation of post-translational protein modification regulation of protein modification process negative regulation of biological process regulation of protein ubiquitination protein ubiquitination negative regulation of protein modification process negative regulation of cellular process protein metabolic process negative regulation of protein ubiquitination regulation of protein modification by small protein conjugation or removal protein modification process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process negative regulation of metabolic process macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal establishment of protein localization protein transport intracellular protein localization peptidyl-lysine modification protein sumoylation peptidyl-amino acid modification positive regulation of protein metabolic process positive regulation of biological process positive regulation of post-translational protein modification positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination protein desumoylation protein modification by small protein removal cell differentiation involved in embryonic placenta development cellular developmental process reproductive process developmental process involved in reproduction trophoblast giant cell differentiation cell differentiation cellular response to stimulus regulation of signaling regulation of Wnt signaling pathway cell surface receptor signaling pathway response to stimulus signaling regulation of signal transduction cell communication regulation of response to stimulus regulation of cell communication signal transduction Wnt signaling pathway fat cell differentiation regulation of cell cycle phase transition cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle regulation of G1/S transition of mitotic cell cycle mitotic cell cycle process G1/S transition of mitotic cell cycle mitotic cell cycle phase transition proteolysis positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription	membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane cytoplasm cytosol protein-containing complex nuclear protein-containing complex nuclear pore membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen intracellular membraneless organelle nuclear body membraneless organelle PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F	IPR000626	Ubiquitin-like domain	Domain
B, D, F	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B, D, F	IPR022617	Rad60/SUMO-like domain	Domain
A, C, E	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, C, E	IPR003653	Ulp1 protease family, C-terminal catalytic domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F	Pharos: P55854	lymphoplasmacytic lymphoma psoriasis ovarian cancer Sjogren syndrome plasma cell myeloma
A, C, E	Pharos: Q9HC62	atypical teratoid rhabdoid tumor large cell medulloblastoma malignant mesothelioma osteosarcoma drug-induced liver injury Liver Cirrhosis, Experimental medulloblastoma ovarian cancer glioblastoma malignant glioma non-small cell lung carcinoma subependymal giant cell astrocytoma

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.