8CX9

Structure of the SARS-COV2 PLpro (C111S) in complex with a dimeric Ubv that inhibits activity by an unusual allosteric mechanism

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
F [auth I]	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
H [auth G]	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
I [auth K]	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
J [auth L]	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
K [auth H]	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
L [auth J]	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	Ubiquitin-like	8066187	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 [auth B]	PF08715	e8cx9B1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF08715	ECOD (1.6)
A [auth B]	PF08715	e8cx9B2	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF08715	ECOD (1.6)
B [auth A]	PF08715	e8cx9A2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF08715	ECOD (1.6)
B [auth A]	PF08715	e8cx9A1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF08715	ECOD (1.6)
C	PF08715	e8cx9C1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF08715	ECOD (1.6)
C	PF08715	e8cx9C2	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF08715	ECOD (1.6)
D	PF08715	e8cx9D1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF08715	ECOD (1.6)
D	PF08715	e8cx9D2	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF08715	ECOD (1.6)
E	PF00240	e8cx9E1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
F [auth I]	PF00240	e8cx9I1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
H [auth G]	PF00240	e8cx9G1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
I [auth K]	PF00240	e8cx9K1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
J [auth L]	PF00240	e8cx9L1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
K [auth H]	PF00240	e8cx9H1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
L [auth J]	PF00240	e8cx9J1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
G [auth F]	PF00240	e8cx9F1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth A], C, D	PF08715	Coronavirus papain-like peptidase (CoV_peptidase)	Coronavirus papain-like peptidase	-	Family
E, F [auth I], G [auth F], H [auth G], I [auth K], E, F [auth I], G [auth F], H [auth G], I [auth K], J [auth L], K [auth H], L [auth J]	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 [auth B], B [auth A], C, D	Papain-like protease nsp3	peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity endonuclease activity nuclease activity hydrolase activity, acting on ester bonds cysteine-type peptidase activity ubiquitin-like protein peptidase activity ISG15-specific peptidase activity peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity endonuclease activity nuclease activity hydrolase activity, acting on ester bonds cysteine-type peptidase activity ubiquitin-like protein peptidase activity ISG15-specific peptidase activity cysteine-type endopeptidase activity endopeptidase activity RNA binding binding organic cyclic compound binding nucleic acid binding single-stranded RNA binding cysteine-type deubiquitinase activity deubiquitinase activity G-quadruplex RNA binding lipid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	methylation metabolic process symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host ISG15-protein conjugation response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism symbiont-mediated perturbation of host defenses response to external stimulus response to biotic stimulus biological process involved in interaction with host methylation metabolic process symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host ISG15-protein conjugation response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism symbiont-mediated perturbation of host defenses response to external stimulus response to biotic stimulus biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response modulation by symbiont of host process response to host immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus modulation of process of another organism viral gene expression viral protein processing viral process symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity symbiont-mediated suppression of host signal transduction pathway cellular process symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway catabolic process regulation of cellular process autophagy positive regulation of biological process modulation by virus of host process positive regulation of cellular metabolic process regulation of autophagy cellular catabolic process positive regulation of metabolic process induction by virus of host autophagy process utilizing autophagic mechanism positive regulation of cellular process modulation by virus of host cellular process positive regulation of autophagy regulation of biological process modulation by virus of host autophagy cellular metabolic process biological regulation regulation of cellular metabolic process regulation of catabolic process symbiont-mediated perturbation of host autophagy positive regulation of catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process regulation of metabolic process symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated perturbation of host translation symbiont-mediated suppression of host gene expression symbiont-mediated degradation of host mRNA symbiont-mediated suppression of host translation symbiont-mediated perturbation of host gene expression symbiont-mediated perturbation of host ubiquitin-like protein modification viral genome replication viral life cycle organic substance metabolic process organonitrogen compound metabolic process proteolysis primary metabolic process protein metabolic process macromolecule metabolic process	membrane cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell endomembrane system host intracellular region host cell endoplasmic reticulum membrane membrane cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell endomembrane system host intracellular region host cell endoplasmic reticulum membrane cytoplasmic viral factory double membrane vesicle viral factory membrane host cell cytoplasmic vesicle membrane host cell cytoplasmic vesicle viral factory double membrane vesicle viral factory outer membrane double membrane vesicle viral factory host cell perinuclear region of cytoplasm host cell Golgi apparatus host cell endosome
E, F [auth I], G [auth F], H [auth G], I [auth K], E, F [auth I], G [auth F], H [auth G], I [auth K], J [auth L], K [auth H], L [auth J]	Ubiquitin variant UbV.CV2.1	structural molecule activity structural constituent of ribosome protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	organic substance metabolic process organonitrogen compound metabolic process macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process organic substance metabolic process organonitrogen compound metabolic process macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis organic substance catabolic process protein ubiquitination post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process translation gene expression macromolecule biosynthetic process biosynthetic process organic substance biosynthetic process cytoplasmic translation cellular process	membrane-bounded organelle organelle cellular anatomical entity vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery membrane-bounded organelle organelle cellular anatomical entity vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane endocytic vesicle vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome cytosolic ribosome intracellular non-membrane-bounded organelle ribosome non-membrane-bounded organelle endosome membrane endosome mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane protein-containing complex ribosomal subunit cytosolic large ribosomal subunit ribonucleoprotein complex large ribosomal subunit cytosolic small ribosomal subunit small ribosomal subunit

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A], C, D	IPR022733	DPUP/SUD, C-terminal, betacoronavirus	Domain
A [auth B], B [auth A], C, D	IPR024358	Non-structural protein NSP3, N-terminal, betacoronavirus	Domain
A [auth B], B [auth A], C, D	IPR043611	Coronavirus replicase NSP3, C-terminal	Domain
A [auth B], B [auth A], C, D	IPR044864	Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus	Domain
A [auth B], B [auth A], C, D	IPR038123	Non-structural protein NSP4, C-terminal superfamily, coronavirus	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR042570	Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR047566	Coronavirus replicase NSP3, Y domain	Domain
A [auth B], B [auth A], C, D	IPR043178	Papain-like protease, thumb domain superfamily, coronavirus	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
A [auth B], B [auth A], C, D	IPR038166	Polyprotein cleavage domain PL2pro superfamily, betacoronavirus	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR044353	NSP3, second ubiquitin-like (Ubl) domain, coronavirus	Domain
A [auth B], B [auth A], C, D	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR013016	Peptidase C16, coronavirus	Domain
A [auth B], B [auth A], C, D	IPR037204	Non-structural protein NSP7 superfamily, coronavirus	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR044357	NSP3, first ubiquitin-like (Ubl) domain, coronavirus	Domain
A [auth B], B [auth A], C, D	IPR046443	NSP1, globular domain, alpha/betacoronavirus	Domain
A [auth B], B [auth A], C, D	IPR043610	Non-structural protein 6, coronavirus	Domain
A [auth B], B [auth A], C, D	IPR043477	Peptidase C30, domain 3, coronavirus	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR018995	RNA synthesis protein NSP10, coronavirus	Domain
A [auth B], B [auth A], C, D	IPR043478	Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR038400	Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR046442	NSP1, C-terminal domain, betacoronavirus	Domain
A [auth B], B [auth A], C, D	IPR043615	Nonstructural protein 2, N-terminal domain, coronavirus	Domain
A [auth B], B [auth A], C, D	IPR043177	Papain-like protease, N-terminal domain superfamily, coronavirus	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR014822	Non-structural protein NSP9, coronavirus	Domain
A [auth B], B [auth A], C, D	IPR038030	NSP1 globular domain superfamily, betacoronavirus	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR021590	NSP1, globular domain, betacoronavirus	Domain
A [auth B], B [auth A], C, D	IPR024375	Non-structural protein NSP3, SUD-M domain, betacoronavirus	Domain
A [auth B], B [auth A], C, D	IPR044367	Non-structural protein 6, betacoronavirus	Domain
A [auth B], B [auth A], C, D	IPR037230	Non-structural protein NSP8 superfamily, coronavirus	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR014828	Non-structural protein NSP7, coronavirus	Domain
A [auth B], B [auth A], C, D	IPR032505	Non-structural protein NSP4, C-terminal, coronavirus	Domain
A [auth B], B [auth A], C, D	IPR043503	Papain-like viral protease, palm and finger domains, coronavirus	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR014829	Non-structural protein NSP8, coronavirus	Domain
A [auth B], B [auth A], C, D	IPR036499	Non-structural protein NSP9 superfamily, coronavirus	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR002589	Macro domain	Domain
A [auth B], B [auth A], C, D	IPR047567	Non-structural protein NSP3, group 2-specific marker domain, betacoronavirus	Domain
A [auth B], B [auth A], C, D	IPR044389	Non-structural protein 2, SARS-CoV-like	Domain
A [auth B], B [auth A], C, D	IPR008740	Peptidase C30, coronavirus	Domain
A [auth B], B [auth A], C, D	IPR036333	RNA synthesis protein NSP10 superfamily, coronavirus	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR047573	Non-structural protein 2, middle domain, coronavirus	Domain
A [auth B], B [auth A], C, D	IPR043472	Macro domain-like	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR044371	Non-structural protein 3, X-domain-like	Domain
A [auth B], B [auth A], C, D	IPR032592	Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus	Domain
A [auth B], B [auth A], C, D	IPR043613	Non-structural protein 2, C-terminal domain, coronavirus	Domain
A [auth B], B [auth A], C, D	IPR038083	Non-structural protein NSP3A domain-like superfamily	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
E, F [auth I], G [auth F], H [auth G], I [auth K], E, F [auth I], G [auth F], H [auth G], I [auth K], J [auth L], K [auth H], L [auth J]	IPR019954	Ubiquitin conserved site	Conserved Site
E, F [auth I], G [auth F], H [auth G], I [auth K], E, F [auth I], G [auth F], H [auth G], I [auth K], J [auth L], K [auth H], L [auth J]	IPR038587	Large ribosomal subunit protein eL40 superfamily	Homologous Superfamily
E, F [auth I], G [auth F], H [auth G], I [auth K], E, F [auth I], G [auth F], H [auth G], I [auth K], J [auth L], K [auth H], L [auth J]	IPR000626	Ubiquitin-like domain	Domain
E, F [auth I], G [auth F], H [auth G], I [auth K], E, F [auth I], G [auth F], H [auth G], I [auth K], J [auth L], K [auth H], L [auth J]	IPR019956	Ubiquitin domain	Domain
E, F [auth I], G [auth F], H [auth G], I [auth K], E, F [auth I], G [auth F], H [auth G], I [auth K], J [auth L], K [auth H], L [auth J]	IPR001975	Large ribosomal subunit protein eL40 domain	Domain
E, F [auth I], G [auth F], H [auth G], I [auth K], E, F [auth I], G [auth F], H [auth G], I [auth K], J [auth L], K [auth H], L [auth J]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F [auth I], G [auth F], H [auth G], I [auth K], E, F [auth I], G [auth F], H [auth G], I [auth K], J [auth L], K [auth H], L [auth J]	Pharos: P62987	attention deficit hyperactivity disorder, inattentive type heart disease dental caries lung cancer gastroesophageal reflux disease plasma cell myeloma