Annotations: 2BKR

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2bkra_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Adenain-like	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2bkrb2	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	d2bkrb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	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	SCOP2 Family	Adenain-like	8025903	4000883	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cysteine proteinases	8038282	3001808	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8034470	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	PF02902	e2bkrA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF02902	ECOD (1.6)
B	PF00240	e2bkrB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	SENTRIN-SPECIFIC PROTEASE 8	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity ubiquitin-like protein peptidase activity deNEDDylase activity	organic substance metabolic process organonitrogen compound metabolic process macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein deneddylation protein modification by small protein removal protein modification by small protein conjugation or removal proteolysis	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol
B	NEDDYLIN	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process protein metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process macromolecule modification protein modification process protein localization localization cellular localization cellular macromolecule localization macromolecule localization cellular process regulation of biological process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process regulation of primary metabolic process regulation of proteolysis regulation of metabolic process regulation of cellular process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription post-translational protein modification protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal developmental process anatomical structure morphogenesis anatomical structure development	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol nucleus extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR044613	NEDD8-specific protease 1/2-like	Family
A	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A	IPR003653	Ulp1 protease family, C-terminal catalytic domain	Domain
B	IPR019954	Ubiquitin conserved site	Conserved Site
B	IPR000626	Ubiquitin-like domain	Domain
B	IPR019956	Ubiquitin domain	Domain
B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B	IPR038738	Nedd8-like ubiquitin	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q96LD8	dengue disease ulcerative colitis interstitial cystitis malignant ependymoma
B	Pharos: Q15843	language disorder

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	Ulp1 peptidase M-CSA #820	NEDP1 is a 211 residue cysteine-type peptidase of the Ulp family expressed in homo sapiens. It is a deneddylase enzyme involved in the processing of preNEDD8 to its mature form and the deconjugation of NEDD8 from modified substrates (eg. cullin). NEDP1 discrimates between NEDD8 and homologous ubiquitin, involving highly precise molecular recognition due to a single residue change in the C-terminus of NEDD8.	Defined by 5 residues: TRP:A-26HIS:A-102TRP:A-103ASP:A-119CYS:A-163 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.4.22 (PDB Primary Data) Search M-CSA Motif + EC 3.4.22

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