2IY0 | pdb_00002iy0

SENP1 (mutant) SUMO1 RanGAP

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)
C	d2iy0c1	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	d2iy0b_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2iy0a1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Adenain-like	Sentrin-specific protease 1	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)
C	SCOP2B Superfamily	Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain	8081380	3001897	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8043414	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8033184	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)
C		e2iy0C1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: tRNA-binding arm	T: tRNA-binding arm	F:	ECOD (v294.1)
B	S4	e2iy0B1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: S4	ECOD (v294.1)
A	Phage_lysozyme	e2iy0A1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Phage_lysozyme	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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
C	PF07834	RanGAP1 C-terminal domain (RanGAP1_C)	RanGAP1 C-terminal domain	Ran-GTPase activating protein 1 (RanGAP1, Swiss:P46061) is a GTPase activator for the nuclear Ras-related regulatory protein Ran, converting it to the putatively inactive GDP-bound state. Its C-terminal domain is required for RanGAP1 localisation at ...	Ran-GTPase activating protein 1 (RanGAP1, Swiss:P46061) is a GTPase activator for the nuclear Ras-related regulatory protein Ran, converting it to the putatively inactive GDP-bound state. Its C-terminal domain is required for RanGAP1 localisation at the vertebrate nuclear pore complex, and is sumoylated by the small ubiquitin-related modifier protein (SUMO-1, Swiss:Q93068). This domain is composed almost entirely of helical substructures that are organised into an alpha-alpha superhelix fold, with the exception of the peptide containing the lysine residue required for SUMO-1 conjugation [1].	Domain
B	PF11976	Ubiquitin-2 like Rad60 SUMO-like (Rad60-SLD)	Ubiquitin-2 like Rad60 SUMO-like	-	Family
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
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 intercellular transport 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 1	protein binding binding small protein activating enzyme binding enzyme binding RNA binding nucleic acid binding ubiquitin-specific protease binding protease binding ubiquitin-like protein ligase binding transporter activator activity molecular function activator activity molecular function regulator activity transporter regulator activity protein tag activity protein binding binding small protein activating enzyme binding enzyme binding RNA binding nucleic acid binding ubiquitin-specific protease binding protease binding ubiquitin-like protein ligase binding transporter activator activity molecular function activator activity molecular function regulator activity transporter regulator activity protein tag activity molecular tag activity potassium channel regulator activity channel regulator activity ion channel regulator activity ubiquitin protein ligase binding	regulation of cellular process negative regulation of biological process RNA 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 regulation of cellular process negative regulation of biological process RNA 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 negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic 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 negative regulation of transcription initiation by RNA polymerase II regulation of DNA-templated transcription initiation transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II DNA-templated transcription initiation regulation of transcription initiation by RNA polymerase II negative regulation of DNA-templated transcription initiation 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 negative regulation of protein transport regulation of localization establishment of protein localization cellular localization negative regulation of nucleocytoplasmic 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 intercellular transport import into nucleus regulation of protein import into nucleus establishment of localization in cell protein import into nucleus intracellular protein localization 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 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 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 proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic 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 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 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 protein catabolic process nuclear body organization nucleus organization organelle organization PML body organization regulation of action potential negative regulation of action potential action potential regulation of membrane potential DNA metabolic process DNA damage response DNA repair 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 monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport monoatomic ion transport monoatomic cation transport regulation of metal ion transport regulation of monoatomic ion transport transmembrane transport regulation of transmembrane transport regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport developmental process anatomical structure development roof of mouth 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 nuclear speck ribonucleoprotein granule nuclear body nucleoplasm supramolecular complex nuclear ribonucleoprotein granule nuclear membrane membrane endomembrane system organelle envelope nuclear envelope organelle membrane cytoplasm cytosol XY body sex chromosome chromosome presynapse presynaptic cytosol synapse cell junction cell periphery plasma membrane protein-containing complex nuclear protein-containing complex nuclear pore glutamatergic synapse nuclear stress granule PML body postsynapse postsynaptic cytosol
A	SENTRIN-SPECIFIC PROTEASE 1	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity cysteine-type peptidase activity ubiquitin-like protein peptidase activity SUMO-specific endopeptidase activity cysteine-type endopeptidase activity ubiquitin-like protein-specific endopeptidase activity deSUMOylase activity	multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process homeostatic process cell development regulation of cell differentiation regulation of cell development multicellular organism development cell differentiation anatomical structure development regulation of immune system process regulation of multicellular organismal process myeloid cell homeostasis multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process homeostatic process cell development regulation of cell differentiation regulation of cell development multicellular organism development cell differentiation anatomical structure development regulation of immune system process regulation of multicellular organismal process myeloid cell homeostasis erythrocyte homeostasis developmental process regulation of biological process regulation of multicellular organismal development definitive hemopoiesis hemopoiesis regulation of myeloid cell differentiation biological regulation regulation of definitive erythrocyte differentiation erythrocyte differentiation definitive erythrocyte differentiation regulation of erythrocyte differentiation multicellular organismal-level homeostasis myeloid cell differentiation immune system process regulation of hemopoiesis homeostasis of number of cells cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process regulation of mRNA catabolic process negative regulation of cellular process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process regulation of catabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of mRNA stability regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of RNA stability nucleic acid catabolic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of mRNA metabolic process regulation of metabolic process regulation of cellular component organization cellular component organization cellular component biogenesis cellular component assembly regulation of postsynapse assembly cell junction assembly regulation of synapse structure or activity synapse organization cellular component organization or biogenesis regulation of synapse assembly system development postsynapse organization postsynapse assembly regulation of postsynapse organization nervous system development regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly 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 protein desumoylation protein modification by small protein removal positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process negative regulation of protein catabolic process negative regulation of protein metabolic process negative regulation of ubiquitin-dependent protein catabolic process negative regulation of catabolic process negative regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of protein metabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process negative regulation of proteasomal protein catabolic process regulation of proteasomal protein catabolic process regulation of protein catabolic process	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane presynapse presynaptic cytosol synapse cytoplasm cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen glutamatergic synapse postsynapse postsynaptic cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
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: P63165	orofacial cleft 10 cleft palate Neoplasm Invasiveness cleft lip pancreatic intraductal papillary-mucinous neoplasm
A	Pharos: Q9P0U3	atypical teratoid rhabdoid tumor malignant glioma primitive neuroectodermal tumor glioblastoma medulloblastoma prostate carcinoma large cell medulloblastoma 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.