7JRN

Crystal structure of the wild type SARS-CoV-2 papain-like protease (PLPro) with inhibitor GRL0617

Present annotations:

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Product Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d7jrna2	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	d7jrna1	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)
B [auth J]	d7jrnj2	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)
B [auth J]	d7jrnj1	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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Cysteine proteinases	8092567	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8092569	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8092567	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLpro Zn-binding domain-like	8092568	3002538	SCOP2B (2022-06-29)
B [auth J]	SCOP2B Superfamily	PLpro Zn-binding domain-like	8092568	3002538	SCOP2B (2022-06-29)
B [auth J]	SCOP2B Superfamily	Ubiquitin-like	8092569	3000157	SCOP2B (2022-06-29)
B [auth J]	SCOP2B Superfamily	Cysteine proteinases	8092567	3001808	SCOP2B (2022-06-29)
B [auth J]	SCOP2B Superfamily	Cysteine proteinases	8092567	3001808	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	Viral_protease_N	e7jrnA2	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	e7jrnA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)
B [auth J]	Viral_protease_N	e7jrnJ2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Viral_protease_N	ECOD (1.6)
B [auth J]	Viral_protease_C	e7jrnJ1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth J]	PF08715	Coronavirus papain-like peptidase (CoV_peptidase)	Coronavirus papain-like peptidase	-	Family

Gene Product Annotation Gene Product Annotation

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth J]	Non-structural protein 3	protein guanylyltransferase activity guanylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 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 protein guanylyltransferase activity guanylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 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 cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein 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 protein binding protein dimerization activity identical protein binding protein homodimerization activity lipid binding 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 ATP-dependent activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters endonuclease activity RNA endonuclease activity, producing 3'-phosphomonoesters RNA endonuclease activity omega peptidase activity RNA methyltransferase activity transferase activity, transferring one-carbon groups S-adenosylmethionine-dependent methyltransferase activity mRNA (guanine-N7-)-methyltransferase activity N-methyltransferase activity methyltransferase activity mRNA methyltransferase activity cation binding transition metal ion binding copper ion binding metal ion binding O-methyltransferase activity mRNA (nucleoside-2'-O-)-methyltransferase activity helicase activity 5'-3' RNA polymerase activity RNA polymerase activity RNA-dependent RNA polymerase 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 G-quadruplex RNA binding 5'-3' RNA helicase activity RNA helicase activity ATP-dependent activity, acting on RNA zinc ion binding	cellular biosynthetic process RNA metabolic process viral life cycle cellular nitrogen compound biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process organic substance metabolic process heterocycle metabolic process viral RNA genome replication viral process organic substance biosynthetic process nitrogen compound metabolic process cellular metabolic process cellular nitrogen compound metabolic process cellular biosynthetic process RNA metabolic process viral life cycle cellular nitrogen compound biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process organic substance metabolic process heterocycle metabolic process viral RNA genome replication viral process organic substance biosynthetic process nitrogen compound metabolic process cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process viral genome replication biosynthetic process aromatic compound biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process cellular aromatic compound metabolic process regulation of defense response regulation of cellular process biological process involved in interspecies interaction between organisms response to stimulus suppression of host defenses by symbiont negative regulation of biological process modulation by virus of host process mitigation of host antiviral defense response perturbation by virus of host immune response response to biotic stimulus perturbation of host innate immune response biological process involved in symbiotic interaction regulation of response to stress response to stress response to host immune response regulation of immune system process response to host response to external biotic stimulus modulation of process of another organism modulation by virus of host cellular process regulation of biological process response to host defenses suppression of host innate immune response response to other organism negative regulation of response to stimulus defense response immune response response to defenses of other organism biological regulation response to external stimulus modulation by symbiont of host cellular process modulation by symbiont of host defense response biological process involved in interaction with host mitigation of host defenses by symbiont suppression by virus of host ISG15-protein conjugation regulation of response to stimulus modulation by symbiont of host process immune system process suppression by virus of host innate immune response negative regulation of defense response perturbation of host immune response regulation of immune response suppression by symbiont of host immune response viral gene expression viral protein processing suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway symbiont-mediated suppression of host receptor-mediated signal transduction perturbation of host receptor-mediated signal transduction perturbation of signal transduction in another organism symbiont-mediated suppression of host signal transduction pathway perturbation of host signal transduction pathway cellular response to stimulus response to organic substance regulation of type I interferon-mediated signaling pathway response to cytokine regulation of signal transduction cell communication interferon-mediated signaling pathway cellular response to type I interferon cellular response to cytokine stimulus signal transduction regulation of innate immune response negative regulation of immune response suppression by virus of host type I interferon-mediated signaling pathway regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus response to chemical defense response to other organism negative regulation of response to external stimulus response to type I interferon suppression of host interferon-mediated signaling pathway regulation of response to biotic stimulus regulation of response to external stimulus negative regulation of response to biotic stimulus negative regulation of signaling signaling negative regulation of cell communication cytokine-mediated signaling pathway negative regulation of cellular process innate immune response cellular response to organic substance regulation of signaling cell surface receptor signaling pathway regulation of cytokine-mediated signaling pathway negative regulation of signal transduction cellular response to chemical stimulus negative regulation of immune system process negative regulation of cytokine-mediated signaling pathway type I interferon-mediated signaling pathway regulation of cell communication negative regulation of type I interferon-mediated signaling pathway negative regulation of innate immune response pertubation of host canonical NF-kappaB cascade suppression by virus of host NF-kappaB cascade symbiont-mediated suppression of host canonical NF-kappaB cascade modulation by symbiont of host protein ubiquitination protein ubiquitination protein metabolic process protein modification process organonitrogen compound metabolic process macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal viral replication complex formation and maintenance modulation by virus of host autophagy positive stranded viral RNA replication viral transcription positive regulation of macromolecule biosynthetic process regulation of primary metabolic process regulation of nitrogen compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process regulation of cellular metabolic process positive regulation of RNA metabolic process regulation of macromolecule biosynthetic process regulation of metabolic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process positive regulation of nitrogen compound metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process gene expression protein maturation protein autoprocessing proteolysis protein processing regulation of amide metabolic process organonitrogen compound biosynthetic process cellular catabolic process post-transcriptional regulation of gene expression RNA catabolic process modulation by virus of host gene expression negative regulation of metabolic process regulation of protein metabolic process positive regulation of mRNA metabolic process cellular nitrogen compound catabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression negative regulation of macromolecule biosynthetic process heterocycle catabolic process peptide metabolic process induction by virus of catabolism of host mRNA amide metabolic process mRNA metabolic process organic cyclic compound catabolic process positive regulation of catabolic process negative regulation of biosynthetic process regulation of translation modulation by virus of host translation organic substance catabolic process negative regulation of cellular metabolic process suppression by virus of host gene expression mRNA catabolic process amide biosynthetic process aromatic compound catabolic process negative regulation of cellular biosynthetic process peptide biosynthetic process catabolic process macromolecule catabolic process regulation of mRNA catabolic process negative regulation of macromolecule metabolic process modulation by symbiont of host translation regulation of catabolic process translation suppression by virus of host translation positive regulation of mRNA catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process regulation of mRNA metabolic process DNA-templated transcription positive regulation of viral genome replication positive regulation of viral process regulation of viral process regulation of viral life cycle regulation of viral genome replication autophagy regulation of autophagy induction by virus of host autophagy process utilizing autophagic mechanism positive regulation of autophagy symbiont-mediated perturbation of host autophagy suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity multicellular organismal process cytokine production type I interferon production negative regulation of multicellular organismal process suppression by virus of host type I interferon production negative regulation of type I interferon production regulation of cytokine production regulation of multicellular organismal process suppression by virus of host cytokine production negative regulation of cytokine production modulation by virus of host cytokine production regulation of type I interferon production protein deubiquitination protein K63-linked deubiquitination protein modification by small protein removal disruption by virus of host TRAF-mediated signal transduction symbiont-mediated suppression of host TRAF-mediated signal transduction RNA-templated transcription mRNA modification macromolecule methylation RNA modification methylation mRNA methylation RNA methylation protein K48-linked deubiquitination suppression by virus of host toll-like receptor signaling pathway 7-methylguanosine RNA capping RNA capping mRNA processing RNA processing 7-methylguanosine mRNA capping	protein-containing complex endoribonuclease complex catalytic complex intracellular protein-containing complex endonuclease complex exoribonuclease complex cytoplasmic viral factory host cellular component host intracellular part viral factory host cell cytoplasm host cell part host cell host intracellular region protein-containing complex endoribonuclease complex catalytic complex intracellular protein-containing complex endonuclease complex exoribonuclease complex cytoplasmic viral factory host cellular component host intracellular part viral factory host cell cytoplasm host cell part host cell host intracellular region cellular anatomical entity host cell cytoplasm part host intracellular membrane-bounded organelle host intracellular organelle host cell endoplasmic reticulum-Golgi intermediate compartment double membrane vesicle viral factory membrane host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasmic vesicle double membrane vesicle viral factory outer membrane double membrane vesicle viral factory host cell perinuclear region of cytoplasm membrane-bounded organelle intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle organelle methyltransferase complex mRNA cap methyltransferase complex transferase complex, transferring phosphorus-containing groups viral RNA-directed RNA polymerase complex RNA polymerase complex RNA-directed RNA polymerase complex host cell endosome RNA cap binding complex mRNA cap binding complex host cell nucleus membrane host cell endoplasmic reticulum host cell endomembrane system host cell endoplasmic reticulum membrane peptidase complex endopeptidase complex host cell Golgi apparatus

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.