Annotations: 7JIR

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d7jira2	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like viral protease catalytic domain	automated matches	2019-nCoV (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ],	SCOPe (2.08)
A	d7jira1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	2019-nCoV (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ],	SCOPe (2.08)

Chains

Domain Info

Class

Fold

Superfamily

Family

Domain

Species

Provenance Source (Version)

d7jira2

Alpha and beta proteins (a+b)

Cysteine proteinases

Papain-like viral protease catalytic domain

automated matches

2019-nCoV (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ],

SCOPe (2.08)

d7jira1

Alpha and beta proteins (a+b)

beta-Grasp (ubiquitin-like)

Ubiquitin-like

automated matches

2019-nCoV (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ],

SCOPe (2.08)

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PLpro Zn-binding domain-like	8092568	3002538	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8092567	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8092567	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8092569	3000157	SCOP2B (2022-06-29)

Chains

Type

Family Name

Domain Identifier

Family Identifier

Provenance Source (Version)

SCOP2B Superfamily

PLpro Zn-binding domain-like

8092568

3002538

SCOP2B (2022-06-29)

SCOP2B Superfamily

Cysteine proteinases

8092567

3001808

SCOP2B (2022-06-29)

SCOP2B Superfamily

Cysteine proteinases

8092567

3001808

SCOP2B (2022-06-29)

SCOP2B Superfamily

Ubiquitin-like

8092569

3000157

SCOP2B (2022-06-29)

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Viral_protease_N	e7jirA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Viral_protease_N	ECOD (1.6)
A	Viral_protease_C	e7jirA2	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)

Chains

Family Name

Domain Identifier

Architecture

Possible Homology

Homology

Topology

Family

Provenance Source (Version)

Viral_protease_N

e7jirA1

A: a+b two layers

X: beta-Grasp

H: Ubiquitin-related

T: Ubiquitin-like

F: Viral_protease_N

ECOD (1.6)

Viral_protease_C

e7jirA2

A: a+b complex topology

X: Cysteine proteinases-like

H: Cysteine proteinases (From Topology)

T: Cysteine proteinases

F: Viral_protease_C

ECOD (1.6)

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Papain-like protease	protein guanylyltransferase activity guanylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups nucleic acid conformation isomerase activity forked DNA-dependent helicase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity ATP-dependent activity, acting on DNA protein guanylyltransferase activity guanylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups nucleic acid conformation isomerase activity forked DNA-dependent helicase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA macromolecular conformation isomerase activity 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity nuclease activity hydrolase activity, acting on ester bonds exonuclease activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding double-stranded DNA helicase activity 5'-3' DNA helicase activity RNA methyltransferase activity transferase activity, transferring one-carbon groups S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity methyltransferase activity mRNA methyltransferase activity lipid binding four-way junction helicase 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 endonuclease activity RNA endonuclease activity RNA endonuclease activity, producing 3'-phosphomonoesters peptidase activity omega peptidase activity catalytic activity, acting on a protein cation binding transition metal ion binding copper ion binding metal ion binding O-methyltransferase activity mRNA (nucleoside-2'-O-)-methyltransferase activity RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity RNA polymerase activity mRNA guanylyltransferase activity RNA guanylyltransferase activity cysteine-type peptidase activity ubiquitin-like protein peptidase activity ISG15-specific peptidase activity cysteine-type endopeptidase activity endopeptidase activity lyase activity RNA binding nucleic acid binding single-stranded RNA binding cysteine-type deubiquitinase activity deubiquitinase activity single-stranded DNA helicase activity 3'-5' DNA helicase activity single-stranded 3'-5' DNA helicase activity G-quadruplex RNA binding RNA helicase activity ATP-dependent activity, acting on RNA 5'-3' RNA helicase activity zinc ion binding	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 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 symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host NF-kappaB cascade symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated suppression of host NF-kappaB cascade modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host ISG15-protein conjugation symbiont-mediated perturbation of host immune response symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host innate immune response viral gene expression viral protein processing symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated suppression of host gene expression symbiont-mediated perturbation of host gene expression symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity gene expression DNA-templated transcription symbiont-mediated degradation of host mRNA symbiont-mediated perturbation of host ubiquitin-like protein modification symbiont-mediated perturbation of host autophagy symbiont-mediated activation of host autophagy symbiont-mediated suppression of host toll-like receptor signaling pathway viral translational frameshifting viral translation regulation of biological process catabolic process regulation of cellular process autophagy biological regulation regulation of catabolic process regulation of autophagy process utilizing autophagic mechanism regulation of metabolic process proteolysis protein metabolic process	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum-Golgi intermediate compartment cellular anatomical structure host cell cytoplasm host cell part host intracellular region 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 cellular anatomical structure host cell cytoplasm host cell part host intracellular region 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 host cell nucleus membrane host cell endoplasmic reticulum host cell endomembrane system host cell endoplasmic reticulum membrane host cell Golgi apparatus

Chains

Polymer

Molecular Function

Biological Process

Cellular Component

Papain-like protease

protein guanylyltransferase activity

guanylyltransferase activity

transferase activity

nucleotidyltransferase activity

catalytic activity

transferase activity, transferring phosphorus-containing groups

nucleic acid conformation isomerase activity

forked DNA-dependent helicase activity

isomerase activity

DNA helicase activity

catalytic activity, acting on a nucleic acid

helicase activity

ATP-dependent activity

ATP-dependent activity, acting on DNA

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

host intracellular membrane-bounded organelle

host cellular component

host intracellular part

host cell endoplasmic reticulum-Golgi intermediate compartment

cellular anatomical structure

host cell cytoplasm

host cell part

host intracellular region

host cell cytoplasm part

host intracellular organelle

cytoplasmic viral factory

double membrane vesicle viral factory membrane

host cell membrane

host cell cytoplasmic vesicle membrane

InterPro: Protein Family Classification InterPro Database Homepage

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

7JIR | pdb_00007jir

The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder457 inhibitor

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 7JIR | pdb_00007jir

The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder457 inhibitor

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

7JIR | pdb_00007jir