4R3D

Crystal structure of MERS Coronavirus papain like protease

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth B]	d4r3db2	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like viral protease catalytic domain	automated matches	HCoV-EMC (Betacoronavirus England 1 ) [TaxId: 1263720 ],	SCOPe (2.08)
A [auth B]	d4r3db1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	HCoV-EMC (Betacoronavirus England 1 ) [TaxId: 1263720 ],	SCOPe (2.08)
B [auth A]	d4r3da2	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like viral protease catalytic domain	automated matches	HCoV-EMC (Betacoronavirus England 1 ) [TaxId: 1263720 ],	SCOPe (2.08)
B [auth A]	d4r3da1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	HCoV-EMC (Betacoronavirus England 1 ) [TaxId: 1263720 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	PLpro Zn-binding domain-like	8091712	3002538	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	Cysteine proteinases	8091711	3001808	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	Ubiquitin-like	8091713	3000157	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	Cysteine proteinases	8091711	3001808	SCOP2B (2022-06-29)
B [auth A]	SCOP2 Family	Papain-like protease PLpro-like	8051167	4007227	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	PLpro Zn-binding domain-like	8091712	3002538	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Ubiquitin-like	8091713	3000157	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Cysteine proteinases	8091711	3001808	SCOP2 (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	e4r3dB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF08715	ECOD (1.6)
A [auth B]	PF08715	e4r3dB2	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	e4r3dA2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF08715	ECOD (1.6)
B [auth A]	PF08715	e4r3dA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF08715	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	3.10.20.540	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Papain-like viral protease, N-terminal domain	CATH (4.3.0)
A [auth B]	1.10.8.1190	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A [auth B]	2.60.120.1680	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B [auth A]	3.10.20.540	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Papain-like viral protease, N-terminal domain	CATH (4.3.0)
B [auth A]	1.10.8.1190	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B [auth A]	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 [auth B], B [auth A]	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 [auth B], B [auth A]	Non-structural protein 3	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 cysteine-type endopeptidase activity endopeptidase 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 cysteine-type endopeptidase activity endopeptidase activity RNA binding binding organic cyclic compound binding nucleic acid binding single-stranded RNA binding ubiquitin-like protein peptidase activity cysteine-type deubiquitinase activity deubiquitinase activity G-quadruplex RNA 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 cellular component host intracellular part host cell perinuclear region of cytoplasm host cell cytoplasm host cell part host intracellular region host cell cytoplasm part host cell membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A]	IPR022733	DPUP/SUD, C-terminal, betacoronavirus	Domain
A [auth B], B [auth A]	IPR043611	Coronavirus replicase NSP3, C-terminal	Domain
A [auth B], B [auth A]	IPR038123	Non-structural protein NSP4, C-terminal superfamily, coronavirus	Homologous Superfamily
A [auth B], B [auth A]	IPR042570	Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus	Homologous Superfamily
A [auth B], B [auth A]	IPR047566	Coronavirus replicase NSP3, Y domain	Domain
A [auth B], B [auth A]	IPR043178	Papain-like protease, thumb domain superfamily, coronavirus	Homologous Superfamily
A [auth B], B [auth A]	IPR044388	Non-structural protein 2, MERS-CoV-like	Domain
A [auth B], B [auth A]	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
A [auth B], B [auth A]	IPR044353	NSP3, second ubiquitin-like (Ubl) domain, coronavirus	Domain
A [auth B], B [auth A]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A [auth B], B [auth A]	IPR044382	NSP3, SUD-C domain, MERS-CoV-like	Domain
A [auth B], B [auth A]	IPR013016	Peptidase C16, coronavirus	Domain
A [auth B], B [auth A]	IPR037204	Non-structural protein NSP7 superfamily, coronavirus	Homologous Superfamily
A [auth B], B [auth A]	IPR044357	NSP3, first ubiquitin-like (Ubl) domain, coronavirus	Domain
A [auth B], B [auth A]	IPR046443	NSP1, globular domain, alpha/betacoronavirus	Domain
A [auth B], B [auth A]	IPR043610	Non-structural protein 6, coronavirus	Domain
A [auth B], B [auth A]	IPR043477	Peptidase C30, domain 3, coronavirus	Homologous Superfamily
A [auth B], B [auth A]	IPR018995	RNA synthesis protein NSP10, coronavirus	Domain
A [auth B], B [auth A]	IPR038400	Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus	Homologous Superfamily
A [auth B], B [auth A]	IPR046442	NSP1, C-terminal domain, betacoronavirus	Domain
A [auth B], B [auth A]	IPR043615	Nonstructural protein 2, N-terminal domain, coronavirus	Domain
A [auth B], B [auth A]	IPR043177	Papain-like protease, N-terminal domain superfamily, coronavirus	Homologous Superfamily
A [auth B], B [auth A]	IPR014822	Non-structural protein NSP9, coronavirus	Domain
A [auth B], B [auth A]	IPR021590	NSP1, globular domain, betacoronavirus	Domain
A [auth B], B [auth A]	IPR024375	Non-structural protein NSP3, SUD-M domain, betacoronavirus	Domain
A [auth B], B [auth A]	IPR044367	Non-structural protein 6, betacoronavirus	Domain
A [auth B], B [auth A]	IPR037230	Non-structural protein NSP8 superfamily, coronavirus	Homologous Superfamily
A [auth B], B [auth A]	IPR014828	Non-structural protein NSP7, coronavirus	Domain
A [auth B], B [auth A]	IPR032505	Non-structural protein NSP4, C-terminal, coronavirus	Domain
A [auth B], B [auth A]	IPR043503	Papain-like viral protease, palm and finger domains, coronavirus	Homologous Superfamily
A [auth B], B [auth A]	IPR014829	Non-structural protein NSP8, coronavirus	Domain
A [auth B], B [auth A]	IPR036499	Non-structural protein NSP9 superfamily, coronavirus	Homologous Superfamily
A [auth B], B [auth A]	IPR002589	Macro domain	Domain
A [auth B], B [auth A]	IPR047567	Non-structural protein NSP3, group 2-specific marker domain, betacoronavirus	Domain
A [auth B], B [auth A]	IPR008740	Peptidase C30, coronavirus	Domain
A [auth B], B [auth A]	IPR036333	RNA synthesis protein NSP10 superfamily, coronavirus	Homologous Superfamily
A [auth B], B [auth A]	IPR047573	Non-structural protein 2, middle domain, coronavirus	Domain
A [auth B], B [auth A]	IPR043472	Macro domain-like	Homologous Superfamily
A [auth B], B [auth A]	IPR044371	Non-structural protein 3, X-domain-like	Domain
A [auth B], B [auth A]	IPR032592	Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus	Domain
A [auth B], B [auth A]	IPR043613	Non-structural protein 2, C-terminal domain, coronavirus	Domain
A [auth B], B [auth A]	IPR038083	Non-structural protein NSP3A domain-like superfamily	Homologous Superfamily
A [auth B], B [auth A]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily