1LVO

Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain

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	d1lvoa_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Viral cysteine protease of trypsin fold	Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)	(Transmissible gastroenteritis virus ) [TaxId: 11149 ],	SCOPe (2.08)
B	d1lvob_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Viral cysteine protease of trypsin fold	Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)	(Transmissible gastroenteritis virus ) [TaxId: 11149 ],	SCOPe (2.08)
C	d1lvoc_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Viral cysteine protease of trypsin fold	Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)	(Transmissible gastroenteritis virus ) [TaxId: 11149 ],	SCOPe (2.08)
D	d1lvod_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Viral cysteine protease of trypsin fold	Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)	(Transmissible gastroenteritis virus ) [TaxId: 11149 ],	SCOPe (2.08)
E	d1lvoe_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Viral cysteine protease of trypsin fold	Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)	(Transmissible gastroenteritis virus ) [TaxId: 11149 ],	SCOPe (2.08)
F	d1lvof_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Viral cysteine protease of trypsin fold	Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)	(Transmissible gastroenteritis virus ) [TaxId: 11149 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Viral cysteine protease of trypsin fold, (M)Pro-like	8029094	4002259	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Trypsin-like serine proteases	8041473	3000114	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Trypsin-like serine proteases	8041473	3000114	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Trypsin-like serine proteases	8041473	3000114	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Trypsin-like serine proteases	8041473	3000114	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Trypsin-like serine proteases	8041473	3000114	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Trypsin-like serine proteases	8041473	3000114	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	Peptidase_C30_N	e1lvoA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_C30_N	ECOD (1.6)
A	Peptidase_C30_C	e1lvoA2	A: alpha arrays	X: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain (From Topology)	H: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain (From Topology)	T: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain	F: Peptidase_C30_C	ECOD (1.6)
B	Peptidase_C30_N	e1lvoB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_C30_N	ECOD (1.6)
B	Peptidase_C30_C	e1lvoB2	A: alpha arrays	X: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain (From Topology)	H: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain (From Topology)	T: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain	F: Peptidase_C30_C	ECOD (1.6)
C	Peptidase_C30_N	e1lvoC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_C30_N	ECOD (1.6)
C	Peptidase_C30_C	e1lvoC2	A: alpha arrays	X: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain (From Topology)	H: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain (From Topology)	T: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain	F: Peptidase_C30_C	ECOD (1.6)
D	Peptidase_C30_N	e1lvoD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_C30_N	ECOD (1.6)
D	Peptidase_C30_C	e1lvoD2	A: alpha arrays	X: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain (From Topology)	H: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain (From Topology)	T: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain	F: Peptidase_C30_C	ECOD (1.6)
E	Peptidase_C30_N	e1lvoE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_C30_N	ECOD (1.6)
E	Peptidase_C30_C	e1lvoE2	A: alpha arrays	X: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain (From Topology)	H: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain (From Topology)	T: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain	F: Peptidase_C30_C	ECOD (1.6)
F	Peptidase_C30_N	e1lvoF1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_C30_N	ECOD (1.6)
F	Peptidase_C30_C	e1lvoF2	A: alpha arrays	X: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain (From Topology)	H: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain (From Topology)	T: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) C-terminal domain	F: Peptidase_C30_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
A	1.10.1840.10	Mainly Alpha	Orthogonal Bundle	main proteinase (3clpro) structure, domain 3	main proteinase (3clpro) structure, domain 3	CATH (4.3.0)
B	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
B	1.10.1840.10	Mainly Alpha	Orthogonal Bundle	main proteinase (3clpro) structure, domain 3	main proteinase (3clpro) structure, domain 3	CATH (4.3.0)
C	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
C	1.10.1840.10	Mainly Alpha	Orthogonal Bundle	main proteinase (3clpro) structure, domain 3	main proteinase (3clpro) structure, domain 3	CATH (4.3.0)
D	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
D	1.10.1840.10	Mainly Alpha	Orthogonal Bundle	main proteinase (3clpro) structure, domain 3	main proteinase (3clpro) structure, domain 3	CATH (4.3.0)
E	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
E	1.10.1840.10	Mainly Alpha	Orthogonal Bundle	main proteinase (3clpro) structure, domain 3	main proteinase (3clpro) structure, domain 3	CATH (4.3.0)
F	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
F	1.10.1840.10	Mainly Alpha	Orthogonal Bundle	main proteinase (3clpro) structure, domain 3	main proteinase (3clpro) structure, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF05409	Coronavirus endopeptidase C30 (Peptidase_C30)	Coronavirus endopeptidase C30	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Replicase, hydrolase domain	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 RNA helicase activity ATP-dependent activity, acting on RNA endonuclease activity 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 cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity lyase activity RNA binding nucleic acid binding ubiquitin-like protein peptidase activity cysteine-type deubiquitinase activity deubiquitinase activity cation binding transition metal ion binding zinc ion binding metal ion binding	viral gene expression viral protein processing viral process symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process modulation by virus of host process virus-mediated perturbation of host defense response modulation of process of another organism biological process involved in interaction with host modulation by virus of host cellular process biological process involved in symbiotic interaction symbiont-mediated perturbation of host cellular process response to stimulus viral gene expression viral protein processing viral process symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process modulation by virus of host process virus-mediated perturbation of host defense response modulation of process of another organism biological process involved in interaction with host modulation by virus of host cellular process biological process involved in symbiotic interaction symbiont-mediated perturbation of host cellular process response to stimulus symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus symbiont-mediated perturbation of host signal transduction pathway response to host defenses response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host defenses response to defenses of other organism response to external stimulus symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process symbiont-mediated perturbation of host ubiquitin-like protein modification catabolic process regulation of cellular process autophagy positive regulation of biological process regulation of autophagy positive regulation of metabolic process induction by virus of host autophagy process utilizing autophagic mechanism positive regulation of cellular process positive regulation of autophagy regulation of biological process modulation by virus of host autophagy biological regulation regulation of catabolic process positive regulation of catabolic process regulation of metabolic process viral genome replication viral life cycle 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 cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell cytoplasm part host intracellular organelle host cell perinuclear region of cytoplasm membrane host cell membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR042515	Non-structural protein NSP15, N-terminal domain superfamily, coronavirus	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR043174	Non-structural protein NSP15, middle domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR038123	Non-structural protein NSP4, C-terminal superfamily, coronavirus	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR032039	Alphacoronavirus nsp1	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043178	Papain-like protease, thumb domain superfamily, coronavirus	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR046441	RNA-dependent RNA polymerase, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR038634	Alphacoronavirus nsp1 domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR044863	Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR044343	Nonstructural protein 13, 1B domain, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR037227	Endoribonuclease EndoU-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR027352	Nonstructural protein 13, zinc-binding domain, coronavirus-like	Domain
A, B, C, D, E A, B, C, D, E, F	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR013016	Peptidase C16, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR009466	Non-structural protein 14, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR044357	NSP3, first ubiquitin-like (Ubl) domain, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR046436	Nidovirus 3'-5' exoribonuclease domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR047570	NSP12, interface domain, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR018995	RNA synthesis protein NSP10, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043615	Nonstructural protein 2, N-terminal domain, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR050534	Coronaviruses polyprotein 1ab	Family
A, B, C, D, E A, B, C, D, E, F	IPR043177	Papain-like protease, N-terminal domain superfamily, coronavirus	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR043606	Coronavirus replicase NSP15, N-terminal oligomerization	Domain
A, B, C, D, E A, B, C, D, E, F	IPR044330	Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR044369	Non-structural protein 6, alphacoronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR041679	DNA2/NAM7 helicase-like, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR044356	RNA-dependent RNA polymerase, alphacoronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR014828	Non-structural protein NSP7, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR014829	Non-structural protein NSP8, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036499	Non-structural protein NSP9 superfamily, coronavirus	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR008740	Peptidase C30, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036333	RNA synthesis protein NSP10 superfamily, coronavirus	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR047573	Non-structural protein 2, middle domain, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR049894	Coronavirus NSP3, 3Ecto domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR044309	Non-structural protein 5, alphacoronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043472	Macro domain-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR043609	NendoU domain, nidovirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043613	Non-structural protein 2, C-terminal domain, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR048673	Nonstructural protein 13, stalk domain, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR046435	NSP14, guanine-N7-methyltransferase domain, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR009469	RNA-dependent RNA polymerase, N-terminal, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043611	Coronavirus replicase NSP3, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR047566	Coronavirus replicase NSP3, Y domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR048672	Nonstructural protein 13, zinc-binding domain, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR043608	Nonstructural protein 15, middle domain, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR044353	NSP3, second ubiquitin-like (Ubl) domain, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR037204	Non-structural protein NSP7 superfamily, coronavirus	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR047912	Non-structural protein 13, helicase domain, alphacoronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR046443	NSP1, globular domain, alpha/betacoronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR044313	Nonstructural protein 14, alphacoronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043610	Non-structural protein 6, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027351	(+) RNA virus helicase core domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR044322	Nonstructural protein 15, middle domain, alpha/betacoronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR009461	Non-structural protein NSP16, coronavirus-like	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043477	Peptidase C30, domain 3, coronavirus	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR044401	NSP15, NendoU domain, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR014822	Non-structural protein NSP9, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR037230	Non-structural protein NSP8 superfamily, coronavirus	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR046440	Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR032505	Non-structural protein NSP4, C-terminal, coronavirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR046438	Nidovirus 2-O-methyltransferase	Domain
A, B, C, D, E A, B, C, D, E, F	IPR002589	Macro domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR044371	Non-structural protein 3, X-domain-like	Domain
A, B, C, D, E A, B, C, D, E, F	IPR044385	Nonstructural protein 2, HCoV-229E-like	Domain