2IO3 | pdb_00002io3

Crystal structure of human Senp2 in complex with RanGAP1-SUMO-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)
A	d2io3a1	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)
C	d2io3c1	All alpha proteins	alpha-alpha superhelix	Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain	Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain	Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2io3b1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	SUMO-2	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	Cysteine proteinases	8040201	3001808	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain	8081380	3001897	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8043638	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)
A		e2io3A1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
C		e2io3C1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Propep_M14	F:	ECOD (20:10:01)
B		e2io3B1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.395.10	Alpha Beta	3-Layer(aba) Sandwich	Adenoviral Proteinase	Chain	CATH (4.3.0)
C	1.25.40.200	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ran-GTPase activating protein 1, C-terminal domain	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
A	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
C	Ran GTPase-activating protein 1	small GTPase binding protein binding binding enzyme binding GTPase binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity RNA binding nucleic acid binding small GTPase binding protein binding binding enzyme binding GTPase binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity RNA binding nucleic acid binding cell adhesion molecule binding cadherin binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding	response to stimulus response to stress response to wounding response to axon injury negative regulation of protein transport regulation of localization establishment of protein localization negative regulation of nucleocytoplasmic transport regulation of cellular process nucleocytoplasmic transport nuclear transport negative regulation of biological process negative regulation of intracellular protein transport negative regulation of transport response to stimulus response to stress response to wounding response to axon injury negative regulation of protein transport regulation of localization establishment of protein localization negative regulation of nucleocytoplasmic transport regulation of cellular process nucleocytoplasmic transport nuclear transport negative regulation of biological process negative regulation of intracellular protein transport negative regulation of transport localization establishment of localization in cell intracellular protein localization nuclear export regulation of protein export from nucleus regulation of intracellular transport regulation of biological process negative regulation of establishment of protein localization intracellular transport regulation of nucleocytoplasmic transport protein localization to nucleus protein export from nucleus establishment of localization maintenance of location regulation of intracellular protein transport intracellular protein transport maintenance of protein location cellular localization regulation of protein localization transport maintenance of location in cell maintenance of protein location in cell negative regulation of cellular process negative regulation of protein export from nucleus negative regulation of protein localization negative regulation of intracellular transport regulation of transport biological regulation regulation of establishment of protein localization maintenance of protein location in nucleus regulation of protein transport protein transport regulation of cellular localization macromolecule localization protein localization to organelle cellular process maintenance of protein localization in organelle cellular response to stimulus cellular response to nitrogen compound cellular response to vasopressin response to endogenous stimulus response to peptide hormone cellular response to peptide hormone stimulus response to oxygen-containing compound response to nitrogen compound response to vasopressin cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical cellular response to hormone stimulus peptidyl-lysine modification primary metabolic process protein sumoylation macromolecule modification peptidyl-amino acid modification metabolic 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 signaling signal transduction cell communication activation of GTPase activity positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity	membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system nuclear membrane membrane organelle membrane microtubule organizing center membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system nuclear membrane membrane organelle membrane microtubule organizing center cytoskeleton membraneless organelle centriole intracellular membraneless organelle microtubule cytoskeleton cytoplasmic periphery of the nuclear pore complex perinuclear region of cytoplasm cytoplasm cytosol protein-containing complex nuclear protein-containing complex nuclear pore somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection mitotic spindle spindle inclusion body aggresome membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen catalytic complex SUMO ligase complex transferase complex chromosome chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome neuron projection cytoplasm axon axon cytoplasm nuclear pore cytoplasmic filaments
B	Small ubiquitin-related modifier 2	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO transferase activity transferase activity catalytic activity protein binding binding ubiquitin-like protein ligase binding enzyme binding protein tag activity molecular tag activity ubiquitin protein ligase binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO transferase activity transferase activity catalytic activity protein binding binding ubiquitin-like protein ligase binding enzyme binding protein tag activity molecular tag activity ubiquitin protein ligase binding RNA binding nucleic acid 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 positive regulation of proteasomal protein catabolic process 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 positive regulation of proteasomal protein catabolic process regulation of cellular process catabolic process positive regulation of protein metabolic process positive regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biological process regulation of protein metabolic process biological regulation proteasomal protein catabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of metabolic process regulation of protein catabolic process positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic 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 nucleobase-containing compound metabolic 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 nucleic acid metabolic 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	cellular anatomical structure neuron to neuron synapse synapse cell junction hippocampal mossy fiber to CA3 synapse presynapse presynaptic cytosol intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical structure neuron to neuron synapse synapse cell junction hippocampal mossy fiber to CA3 synapse presynapse presynaptic cytosol intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen GABA-ergic synapse glutamatergic synapse intracellular membraneless organelle nuclear body membraneless organelle PML body postsynapse postsynaptic cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A	IPR003653	Ulp1 protease family, C-terminal catalytic domain	Domain
C	IPR036720	Ran-GTPase activating protein 1, C-terminal domain superfamily	Homologous Superfamily
C	IPR027038	Ran GTPase-activating protein	Family
C	IPR001611	Leucine-rich repeat	Repeat
C	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
C	IPR009109	Ran-GTPase activating protein 1, C-terminal	Domain
B	IPR000626	Ubiquitin-like domain	Domain
B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B	IPR022617	Rad60/SUMO-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	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
C	Pharos: P46060	diffuse large B-cell lymphoma autism spectrum disorder endogenous depression Pick disease tuberculosis bipolar disorder non-small cell lung carcinoma psoriasis vitiligo osteoarthritis subependymal giant cell astrocytoma
B	Pharos: P61956	malignant ependymoma psoriasis non-alcoholic fatty liver disease systemic sclerosis osteosarcoma

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.