4MM3

Crystal structure of SARS-CoV papain-like protease PLpro in complex with ubiquitin aldehyde

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	d4mm3a_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4mm3b2	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like viral protease catalytic domain	automated matches	SARS-CoV (Severe acute respiratory syndrome-related coronavirus ) [TaxId: 694009 ],	SCOPe (2.08)
B	d4mm3b1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	SARS-CoV (Severe acute respiratory syndrome-related coronavirus ) [TaxId: 694009 ],	SCOPe (2.08)
B	d4mm3b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	SARS-CoV (Severe acute respiratory syndrome-related coronavirus ) [TaxId: 694009 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ubiquitin-like	8043829	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	ubiquitin_1	e4mm3A1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
B	Viral_protease_N	e4mm3B1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Viral_protease_N	ECOD (1.6)
B	Viral_protease_C	e4mm3B2	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	3.10.20.540	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Papain-like viral protease, N-terminal domain	CATH (4.3.0)
B	1.10.8.1190	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	2.60.120.1680	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
B	PF08715	Coronavirus papain-like peptidase (CoV_peptidase)	Coronavirus papain-like peptidase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding RNA binding organic cyclic compound binding nucleic acid binding	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process protein ubiquitination macromolecule modification post-translational protein modification catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
B	Papain-like proteinase	3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity catalytic activity binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA 5'-3' DNA helicase activity helicase activity ATP-dependent activity RNA methyltransferase activity transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity methyltransferase activity mRNA methyltransferase activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides peptidase activity omega peptidase activity catalytic activity, acting on a protein endonuclease activity identical protein binding protein binding O-methyltransferase activity mRNA (nucleoside-2'-O-)-methyltransferase activity 5'-3' RNA polymerase activity RNA polymerase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups ubiquitin-like protein peptidase activity K48-linked deubiquitinase activity deubiquitinase activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity lyase activity RNA binding nucleic acid binding single-stranded RNA binding K63-linked deubiquitinase activity cysteine-type deubiquitinase activity G-quadruplex RNA binding 5'-3' RNA helicase activity RNA helicase activity ATP-dependent activity, acting on RNA cation binding transition metal ion binding zinc ion binding metal ion binding	cellular biosynthetic process cellular metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process cellular biosynthetic process cellular metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process cellular response to stimulus symbiont-mediated perturbation of host cellular process regulation of biological process biological process involved in interspecies interaction between organisms regulation of cellular process response to stimulus signaling biological regulation biological process involved in interaction with host canonical NF-kappaB signal transduction intracellular signal transduction biological process involved in symbiotic interaction cell communication symbiont-mediated perturbation of host NF-kappaB cascade symbiont-mediated perturbation of host process intracellular signaling cassette signal transduction symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated suppression of host NF-kappaB cascade modulation of process of another organism symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host ISG15-protein conjugation response to host defenses 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 symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response 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 viral gene expression viral protein processing modulation by virus of host process virus-mediated perturbation of host defense response modulation by virus of host cellular process symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host interferon-mediated signaling pathway viral transcription gene expression DNA-templated transcription negative regulation of biological process symbiont-mediated perturbation of host translation negative regulation of cellular metabolic process symbiont-mediated suppression of host gene expression RNA catabolic process mRNA catabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression negative regulation of macromolecule biosynthetic process symbiont-mediated degradation of host mRNA nucleic acid catabolic process symbiont-mediated suppression of host translation regulation of macromolecule biosynthetic process symbiont-mediated perturbation of host gene expression regulation of metabolic process catabolic process macromolecule catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of macromolecule metabolic process mRNA metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process symbiont-mediated perturbation of host ubiquitin-like protein modification autophagy positive regulation of biological 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 positive regulation of autophagy modulation by virus of host autophagy regulation of catabolic process positive regulation of catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process viral translational frameshifting viral translation proteolysis protein metabolic process	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part host intracellular region cellular anatomical entity host cell cytoplasm part host intracellular organelle cytoplasmic viral factory double membrane vesicle viral factory membrane host cell membrane host cell cytoplasmic vesicle membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part host intracellular region cellular anatomical entity host cell cytoplasm part host intracellular organelle cytoplasmic viral factory double membrane vesicle viral factory membrane host cell 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 endosome membrane host cell endoplasmic reticulum host cell Golgi apparatus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR019954	Ubiquitin conserved site	Conserved Site
A	IPR000626	Ubiquitin-like domain	Domain
A	IPR019956	Ubiquitin domain	Domain
A	IPR050158	Ubiquitin and ubiquitin-like	Family
A	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B	IPR022733	DPUP/SUD, C-terminal, betacoronavirus	Domain
B	IPR042515	Non-structural protein NSP15, N-terminal domain superfamily, coronavirus	Homologous Superfamily
B	IPR043174	Non-structural protein NSP15, middle domain superfamily	Homologous Superfamily
B	IPR044315	Nonstructural protein 14, betacoronavirus	Domain
B	IPR038123	Non-structural protein NSP4, C-terminal superfamily, coronavirus	Homologous Superfamily
B	IPR042570	Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus	Homologous Superfamily
B	IPR043178	Papain-like protease, thumb domain superfamily, coronavirus	Homologous Superfamily
B	IPR046441	RNA-dependent RNA polymerase, coronavirus	Domain
B	IPR044863	Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain	Domain
B	IPR044343	Nonstructural protein 13, 1B domain, coronavirus	Domain
B	IPR038166	Polyprotein cleavage domain PL2pro superfamily, betacoronavirus	Homologous Superfamily
B	IPR037227	Endoribonuclease EndoU-like	Homologous Superfamily
B	IPR027352	Nonstructural protein 13, zinc-binding domain, coronavirus-like	Domain
B	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B	IPR013016	Peptidase C16, coronavirus	Domain
B	IPR009466	Non-structural protein 14, coronavirus	Domain
B	IPR044357	NSP3, first ubiquitin-like (Ubl) domain, coronavirus	Domain
B	IPR046436	Nidovirus 3'-5' exoribonuclease domain	Domain
B	IPR047570	NSP12, interface domain, coronavirus	Domain
B	IPR018995	RNA synthesis protein NSP10, coronavirus	Domain
B	IPR043615	Nonstructural protein 2, N-terminal domain, coronavirus	Domain
B	IPR050534	Coronaviruses polyprotein 1ab	Family
B	IPR043177	Papain-like protease, N-terminal domain superfamily, coronavirus	Homologous Superfamily
B	IPR043606	Coronavirus replicase NSP15, N-terminal oligomerization	Domain
B	IPR044330	Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus	Domain
B	IPR041679	DNA2/NAM7 helicase-like, C-terminal	Domain
B	IPR024375	Non-structural protein NSP3, SUD-M domain, betacoronavirus	Domain
B	IPR014828	Non-structural protein NSP7, coronavirus	Domain
B	IPR043503	Papain-like viral protease, palm and finger domains, coronavirus	Homologous Superfamily
B	IPR014829	Non-structural protein NSP8, coronavirus	Domain
B	IPR036499	Non-structural protein NSP9 superfamily, coronavirus	Homologous Superfamily
B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
B	IPR044389	Non-structural protein 2, SARS-CoV-like	Domain
B	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
B	IPR008740	Peptidase C30, coronavirus	Domain
B	IPR036333	RNA synthesis protein NSP10 superfamily, coronavirus	Homologous Superfamily
B	IPR047573	Non-structural protein 2, middle domain, coronavirus	Domain
B	IPR049894	Coronavirus NSP3, 3Ecto domain	Domain
B	IPR043472	Macro domain-like	Homologous Superfamily
B	IPR043609	NendoU domain, nidovirus	Domain
B	IPR032592	Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus	Domain
B	IPR043613	Non-structural protein 2, C-terminal domain, coronavirus	Domain
B	IPR038083	Non-structural protein NSP3A domain-like superfamily	Homologous Superfamily
B	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
B	IPR044351	RNA-dependent RNA polymerase, SARS-CoV-like	Domain
B	IPR024358	Non-structural protein NSP3, N-terminal, betacoronavirus	Domain
B	IPR048673	Nonstructural protein 13, stalk domain, coronavirus	Domain
B	IPR046435	NSP14, guanine-N7-methyltransferase domain, coronavirus	Domain
B	IPR009469	RNA-dependent RNA polymerase, N-terminal, coronavirus	Domain
B	IPR043611	Coronavirus replicase NSP3, C-terminal	Domain
B	IPR044864	Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus	Domain
B	IPR047566	Coronavirus replicase NSP3, Y domain	Domain
B	IPR048672	Nonstructural protein 13, zinc-binding domain, coronavirus	Domain
B	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR043608	Nonstructural protein 15, middle domain, coronavirus	Domain
B	IPR044353	NSP3, second ubiquitin-like (Ubl) domain, coronavirus	Domain
B	IPR037204	Non-structural protein NSP7 superfamily, coronavirus	Homologous Superfamily
B	IPR044374	Non-structural protein 3, SUD-N macrodomain, SARS-CoV	Domain
B	IPR046443	NSP1, globular domain, alpha/betacoronavirus	Domain
B	IPR043610	Non-structural protein 6, coronavirus	Domain
B	IPR027351	(+) RNA virus helicase core domain	Domain
B	IPR044322	Nonstructural protein 15, middle domain, alpha/betacoronavirus	Domain
B	IPR009461	Non-structural protein NSP16, coronavirus-like	Domain
B	IPR043477	Peptidase C30, domain 3, coronavirus	Homologous Superfamily
B	IPR043478	Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus	Homologous Superfamily
B	IPR038400	Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus	Homologous Superfamily
B	IPR046442	NSP1, C-terminal domain, betacoronavirus	Domain
B	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
B	IPR044401	NSP15, NendoU domain, coronavirus	Domain
B	IPR014822	Non-structural protein NSP9, coronavirus	Domain
B	IPR038030	NSP1 globular domain superfamily, betacoronavirus	Homologous Superfamily
B	IPR021590	NSP1, globular domain, betacoronavirus	Domain
B	IPR044367	Non-structural protein 6, betacoronavirus	Domain
B	IPR037230	Non-structural protein NSP8 superfamily, coronavirus	Homologous Superfamily
B	IPR046440	Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain	Domain
B	IPR032505	Non-structural protein NSP4, C-terminal, coronavirus	Domain
B	IPR046438	Nidovirus 2-O-methyltransferase	Domain
B	IPR002589	Macro domain	Domain
B	IPR047567	Non-structural protein NSP3, group 2-specific marker domain, betacoronavirus	Domain
B	IPR044371	Non-structural protein 3, X-domain-like	Domain
B	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm ovarian cancer