2IO2

Crystal structure of human Senp2 in complex with RanGAP1-SUMO-1

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	d2io2b_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	SUMO-1 (smt3 homologue)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2io2a_	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	d2io2c1	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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Ubiquitin-like	8043414	3000157	SCOP2B (2022-06-29)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Rad60-SLD	e2io2B1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Rad60-SLD	ECOD (1.6)
A	Peptidase_C48	e2io2A1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C48	ECOD (1.6)
C	RanGAP1_C	e2io2C1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ras GEF (From Topology)	T: Ras GEF	F: RanGAP1_C	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 (4.3.0)
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)

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
B	Small ubiquitin-related modifier 1	protein binding binding small protein activating enzyme binding enzyme binding RNA binding organic cyclic compound binding nucleic acid binding ubiquitin-specific protease binding protease binding transcription factor binding ubiquitin-like protein ligase binding protein tag activity molecular tag activity potassium channel regulator activity protein binding binding small protein activating enzyme binding enzyme binding RNA binding organic cyclic compound binding nucleic acid binding ubiquitin-specific protease binding protease binding transcription factor binding ubiquitin-like protein ligase binding protein tag activity molecular tag activity potassium channel regulator activity channel regulator activity ion channel regulator activity molecular function regulator activity transporter regulator activity ubiquitin protein ligase binding	regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process heart process multicellular organismal process system process regulation of actin filament-based process regulation of heart contraction regulation of system process cardiac muscle contraction striated muscle contraction circulatory system process actin filament-based process regulation of multicellular organismal process blood circulation cardiac muscle cell contraction regulation of cardiac muscle contraction actin filament-based movement muscle contraction muscle system process regulation of muscle system process regulation of blood circulation regulation of striated muscle contraction regulation of actin filament-based movement regulation of muscle contraction regulation of cardiac muscle cell contraction actin-mediated cell contraction heart contraction protein localization negative regulation of protein transport regulation of localization establishment of protein localization cellular localization negative regulation of nucleocytoplasmic transport nitrogen compound transport nucleocytoplasmic transport regulation of protein localization transport nuclear transport negative regulation of intracellular protein transport regulation of protein localization to nucleus negative regulation of transport negative regulation of protein import into nucleus localization import into nucleus regulation of protein import into nucleus cellular macromolecule localization establishment of localization in cell protein import into nucleus regulation of intracellular transport negative regulation of protein localization negative regulation of intracellular transport regulation of transport regulation of establishment of protein localization negative regulation of establishment of protein localization intracellular transport regulation of nucleocytoplasmic transport protein localization to nucleus regulation of protein transport establishment of localization negative regulation of protein localization to nucleus establishment of protein localization to organelle protein transport regulation of cellular localization macromolecule localization protein localization to organelle regulation of intracellular protein transport intracellular protein transport regulation of protein stability regulation of biological quality protein stabilization negative regulation of DNA-binding transcription factor activity negative regulation of molecular function regulation of molecular function regulation of DNA-binding transcription factor activity positive regulation of cellular component organization regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of biological process regulation of cellular component biogenesis cellular component organization cellular component biogenesis positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular component organization or biogenesis positive regulation of cellular process cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus protein localization to nuclear pore protein localization to nuclear envelope organonitrogen compound metabolic process peptidyl-lysine modification protein sumoylation macromolecule modification peptidyl-amino acid modification protein 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 catabolic process positive regulation of protein metabolic process proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process proteolysis positive regulation of macromolecule metabolic process organonitrogen compound catabolic process regulation of protein metabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process positive regulation of proteolysis regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process nuclear body organization nucleus organization organelle organization PML body organization negative regulation of ion transmembrane transporter activity negative regulation of potassium ion transmembrane transporter activity regulation of delayed rectifier potassium channel activity negative regulation of voltage-gated potassium channel activity negative regulation of cation transmembrane transport monoatomic cation transport regulation of potassium ion transmembrane transporter activity regulation of monoatomic ion transport inorganic ion transmembrane transport regulation of potassium ion transmembrane transport regulation of cation channel activity inorganic cation transmembrane transport transmembrane transport regulation of transmembrane transport potassium ion transport regulation of potassium ion transport negative regulation of cation channel activity monoatomic ion transmembrane transport negative regulation of monoatomic ion transport regulation of transmembrane transporter activity potassium ion transmembrane transport regulation of monoatomic ion transmembrane transport negative regulation of transmembrane transport metal ion transport regulation of transporter activity monoatomic cation transmembrane transport negative regulation of monoatomic ion transmembrane transport negative regulation of delayed rectifier potassium channel activity monoatomic ion transport regulation of metal ion transport negative regulation of potassium ion transport regulation of monoatomic ion transmembrane transporter activity negative regulation of transporter activity negative regulation of potassium ion transmembrane transport regulation of monoatomic cation transmembrane transport regulation of action potential negative regulation of action potential action potential regulation of membrane potential DNA metabolic process DNA damage response DNA repair regulation of DNA binding regulation of binding negative regulation of binding negative regulation of DNA binding cellular response to metal ion cellular response to chemical stimulus response to metal ion response to chemical cellular response to cadmium ion response to cadmium ion regulation of calcium ion transport calcium ion transport regulation of calcium ion transmembrane transport calcium ion transmembrane transport negative regulation of transcription by transcription factor localization developmental process anatomical structure development roof of mouth development	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle nuclear speck nuclear body nucleoplasm nuclear membrane membrane endomembrane system organelle envelope nuclear envelope organelle membrane cytoplasm cytosol XY body sex chromosome chromosome cell periphery plasma membrane protein-containing complex nuclear protein-containing complex nuclear pore nuclear stress granule ribonucleoprotein granule supramolecular complex PML body
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	cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process regulation of Wnt signaling pathway cell surface receptor signaling pathway response to stimulus signaling biological regulation regulation of signal transduction cell communication regulation of response to stimulus regulation of cell communication cellular process cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process regulation of Wnt signaling pathway cell surface receptor signaling pathway response to stimulus signaling biological regulation regulation of signal transduction cell communication regulation of response to stimulus regulation of cell communication cellular process signal transduction Wnt signaling pathway 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 developmental process fat cell differentiation cellular developmental process cell differentiation negative regulation of post-translational protein modification regulation of protein modification process negative regulation of biological process regulation of protein ubiquitination regulation of primary metabolic process protein ubiquitination negative regulation of protein modification 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 organonitrogen compound 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 primary metabolic process regulation of macromolecule metabolic process macromolecule modification metabolic process macromolecule metabolic process post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal protein localization establishment of protein localization cellular localization protein transport cellular macromolecule 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 protein modification by small protein conjugation or removal positive regulation of protein ubiquitination protein desumoylation protein modification by small protein removal proteolysis	membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope 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
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 organic cyclic compound 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 organic cyclic compound 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 protein localization negative regulation of protein transport regulation of localization establishment of protein localization negative regulation of nucleocytoplasmic transport nitrogen compound transport regulation of cellular process nucleocytoplasmic transport nuclear transport negative regulation of biological process response to stimulus response to stress response to wounding response to axon injury protein localization negative regulation of protein transport regulation of localization establishment of protein localization negative regulation of nucleocytoplasmic transport nitrogen compound 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 cellular macromolecule 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 organonitrogen compound 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 cellular response to organonitrogen compound response to hormone response to chemical cellular response to hormone stimulus organonitrogen compound metabolic process 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 intracellular anatomical structure organelle nuclear envelope nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system nuclear membrane membrane organelle membrane cytoplasmic periphery of the nuclear pore complex membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system nuclear membrane membrane organelle membrane 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 cytoskeleton spindle intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle 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 cytoplasmic region plasma membrane bounded cell projection cytoplasm nuclear pore cytoplasmic filaments

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR046332	Small ubiquitin-related modifier 1, Ubl domain	Domain
B	IPR000626	Ubiquitin-like domain	Domain
B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B	IPR022617	Rad60/SUMO-like domain	Domain
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P63165	orofacial cleft 10 cleft palate Neoplasm Invasiveness cleft lip pancreatic intraductal papillary-mucinous neoplasm
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

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 R01GM133198.