6WUU

Crystal structure of the SARS CoV-2 Papain-like protease in complex with peptide inhibitor VIR250

Present annotations:

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Product Annotation
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

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)
C	SCOP2B Superfamily	PLpro Zn-binding domain-like	8092568	3002538	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cysteine proteinases	8092567	3001808	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cysteine proteinases	8092567	3001808	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8092569	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cysteine proteinases	8092567	3001808	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cysteine proteinases	8092567	3001808	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PLpro Zn-binding domain-like	8092568	3002538	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8092569	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cysteine proteinases	8092567	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cysteine proteinases	8092567	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLpro Zn-binding domain-like	8092568	3002538	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8092569	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	Viral_protease_N	e6wuuA1	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	e6wuuA2	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)
C	Viral_protease_N	e6wuuC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Viral_protease_N	ECOD (1.6)
C	Viral_protease_C	e6wuuC2	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)
D	Viral_protease_N	e6wuuD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Viral_protease_N	ECOD (1.6)
D	Viral_protease_C	e6wuuD2	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	Viral_protease_N	e6wuuB1	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	e6wuuB2	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	3.10.20.540	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Papain-like viral protease, N-terminal domain	CATH (utative)
A	1.10.8.1190	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (utative)
A	2.60.120.1680	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
C	3.10.20.540	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Papain-like viral protease, N-terminal domain	CATH (utative)
C	1.10.8.1190	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (utative)
C	2.60.120.1680	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
D	3.10.20.540	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Papain-like viral protease, N-terminal domain	CATH (utative)
D	1.10.8.1190	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (utative)
D	2.60.120.1680	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
B	3.10.20.540	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Papain-like viral protease, N-terminal domain	CATH (utative)
B	1.10.8.1190	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (utative)
B	2.60.120.1680	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Identifier	Description	Comments	Source
A, B, C, D	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, C, D	Non-structural protein 3	RNA helicase activity catalytic activity helicase activity ATP-dependent activity, acting on RNA 5'-3' RNA helicase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid ATP-dependent activity pyrophosphatase activity hydrolase activity hydrolase activity, acting on acid anhydrides hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity cysteine-type deubiquitinase activity peptidase activity cysteine-type peptidase activity ubiquitin-like protein peptidase activity deubiquitinase activity catalytic activity, acting on a protein endopeptidase activity cysteine-type endopeptidase activity DNA helicase activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA nuclease activity endonuclease activity hydrolase activity, acting on ester bonds binding protein binding identical protein binding ISG15-specific peptidase activity lyase activity mRNA (nucleoside-2'-O-)-methyltransferase activity methyltransferase activity O-methyltransferase activity RNA methyltransferase activity mRNA methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity transferase activity transferase activity, transferring one-carbon groups omega peptidase activity protein dimerization activity protein homodimerization activity RNA-dependent RNA polymerase activity transferase activity, transferring phosphorus-containing groups nucleotidyltransferase activity 5'-3' RNA polymerase activity RNA polymerase activity nucleic acid binding RNA binding single-stranded RNA binding organic cyclic compound binding heterocyclic compound binding zinc ion binding ion binding cation binding metal ion binding transition metal ion binding	viral process viral life cycle viral genome replication regulation of viral genome replication positive regulation of viral genome replication positive regulation of biological process positive regulation of viral process regulation of biological process regulation of viral process biological regulation regulation of viral life cycle metabolic process negative regulation of metabolic process cellular process gene expression regulation of gene expression negative regulation of macromolecule metabolic process negative regulation of gene expression modulation by virus of host process modulation by virus of host cellular process regulation of metabolic process modulation of process of another organism modulation by virus of host gene expression suppression by virus of host gene expression macromolecule metabolic process modulation by symbiont of host process modulation by symbiont of host cellular process biological process involved in symbiotic interaction biological process involved in interspecies interaction between organisms negative regulation of biological process regulation of cellular process biological process involved in interaction with host regulation of macromolecule metabolic process organic substance metabolic process response to external stimulus response to biotic stimulus mitigation of host antiviral defense response suppression by virus of host NF-kappaB cascade response to external biotic stimulus response to stimulus response to other organism modulation by symbiont of host defense response response to defenses of other organism response to host defenses response to host viral gene expression viral protein processing viral replication complex formation and maintenance viral transcription	host cellular component host cell cytoplasm host cell part host intracellular part host cell cytoplasm part viral factory cytoplasmic viral factory host intracellular region host cell cellular anatomical entity host cell membrane host intracellular organelle host intracellular membrane-bounded organelle double membrane vesicle viral factory host cell cytoplasmic vesicle host cell cytoplasmic vesicle membrane double membrane vesicle viral factory membrane double membrane vesicle viral factory outer membrane protein-containing complex catalytic complex peptidase complex endopeptidase complex intracellular protein-containing complex endoribonuclease complex endonuclease complex exoribonuclease complex host cell endoplasmic reticulum host cell endoplasmic reticulum-Golgi intermediate compartment host cell endosome host cell Golgi apparatus host cell nucleus host cell perinuclear region of cytoplasm mRNA cap binding complex RNA cap binding complex intracellular anatomical structure nucleus mRNA cap methyltransferase complex methyltransferase complex organelle membrane-bounded organelle intracellular organelle intracellular membrane-bounded organelle nuclear protein-containing complex transferase complex RNA polymerase complex RNA-directed RNA polymerase complex viral RNA-directed RNA polymerase complex transferase complex, transferring phosphorus-containing groups
E [auth G], F [auth H], G [auth I], H [auth J]	VIR250	none	none	none

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E [auth G], F [auth H], G [auth I], H [auth J]	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359
E [auth G], F [auth H], G [auth I], H [auth J]	DPP	Parent Component: ALA RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354
E [auth G], F [auth H], G [auth I], H [auth J]	GVE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354
E [auth G], F [auth H], G [auth I], H [auth J]	UB4	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354

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.