2Q6D

Crystal structure of infectious bronchitis virus (IBV) main 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	d2q6da_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	automated matches	automated matches	(Infectious bronchitis virus ) [TaxId: 11120 ],	SCOPe (2.08)
B	d2q6db1	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	automated matches	automated matches	(Infectious bronchitis virus ) [TaxId: 11120 ],	SCOPe (2.08)
B	d2q6db2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Infectious bronchitis virus ) [TaxId: 11120 ],	SCOPe (2.08)
C	d2q6dc_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	automated matches	automated matches	(Infectious bronchitis virus ) [TaxId: 11120 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Trypsin-like serine proteases	8076485	3000114	SCOP2B (2022-06-29)
B	SCOP2 Family	Viral cysteine protease of trypsin fold, (M)Pro-like	8076484	4002259	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Trypsin-like serine proteases	8076485	3000114	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Trypsin-like serine proteases	8076485	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	e2q6dA1	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	e2q6dA2	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	e2q6dB1	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	e2q6dB2	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	e2q6dC1	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	e2q6dC2	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	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	Infectious bronchitis virus (IBV) main protease	peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity 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 exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity 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 exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 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 organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding helicase activity RNA helicase activity ATP-dependent activity, acting on RNA ATP-dependent activity endonuclease activity ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA 5'-3' DNA helicase activity RNA methyltransferase activity O-methyltransferase activity transferase activity, transferring one-carbon groups mRNA (nucleoside-2'-O-)-methyltransferase activity transferase activity S-adenosylmethionine-dependent methyltransferase activity methyltransferase activity mRNA methyltransferase activity 5'-3' RNA polymerase activity RNA polymerase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity lyase activity RNA binding nucleic acid 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 cation binding transition metal ion binding zinc ion binding metal 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 viral gene expression viral protein processing gene expression DNA-templated transcription symbiont-mediated perturbation of host cellular process catabolic process regulation of cellular process biological process involved in interspecies interaction between organisms autophagy positive regulation of biological process modulation by virus of host process regulation of autophagy biological process involved in symbiotic interaction positive regulation of metabolic process symbiont-mediated perturbation of host process induction by virus of host autophagy process utilizing autophagic mechanism modulation of process of another organism 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 biological regulation regulation of catabolic process biological process involved in interaction with host positive regulation of catabolic process regulation of metabolic process viral translational frameshifting viral translation proteolysis protein metabolic process	cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell endomembrane system host intracellular region host cell endoplasmic reticulum membrane cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell endomembrane system host intracellular region host cell endoplasmic reticulum membrane host cell endoplasmic reticulum-Golgi intermediate compartment host cell perinuclear region of cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR042515	Non-structural protein NSP15, N-terminal domain superfamily, coronavirus	Homologous Superfamily
A, B, C	IPR048673	Nonstructural protein 13, stalk domain, coronavirus	Domain
A, B, C	IPR046435	NSP14, guanine-N7-methyltransferase domain, coronavirus	Domain
A, B, C	IPR043174	Non-structural protein NSP15, middle domain superfamily	Homologous Superfamily
A, B, C	IPR009469	RNA-dependent RNA polymerase, N-terminal, coronavirus	Domain
A, B, C	IPR043611	Coronavirus replicase NSP3, C-terminal	Domain
A, B, C	IPR038123	Non-structural protein NSP4, C-terminal superfamily, coronavirus	Homologous Superfamily
A, B, C	IPR047566	Coronavirus replicase NSP3, Y domain	Domain
A, B, C	IPR044308	Non-structural protein 5, gammacoronavirus	Domain
A, B, C	IPR044316	Nonstructural protein 14, gammacoronavirus	Domain
A, B, C	IPR043178	Papain-like protease, thumb domain superfamily, coronavirus	Homologous Superfamily
A, B, C	IPR046441	RNA-dependent RNA polymerase, coronavirus	Domain
A, B, C	IPR048672	Nonstructural protein 13, zinc-binding domain, coronavirus	Domain
A, B, C	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
A, B, C	IPR044863	Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain	Domain
A, B, C	IPR044343	Nonstructural protein 13, 1B domain, coronavirus	Domain
A, B, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C	IPR043608	Nonstructural protein 15, middle domain, coronavirus	Domain
A, B, C	IPR044328	Nonstructural protein 15, N-terminal, gammacoronavirus	Domain
A, B, C	IPR044353	NSP3, second ubiquitin-like (Ubl) domain, coronavirus	Domain
A, B, C	IPR044358	RNA-dependent RNA polymerase, gammacoronavirus	Domain
A, B, C	IPR037227	Endoribonuclease EndoU-like	Homologous Superfamily
A, B, C	IPR027352	Nonstructural protein 13, zinc-binding domain, coronavirus-like	Domain
A, B, C	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B, C	IPR044383	Non-structural protein 2, IBV-like	Domain
A, B, C	IPR013016	Peptidase C16, coronavirus	Domain
A, B, C	IPR040795	Non-structural protein 2, gammacoronavirus	Domain
A, B, C	IPR037204	Non-structural protein NSP7 superfamily, coronavirus	Homologous Superfamily
A, B, C	IPR009466	Non-structural protein 14, coronavirus	Domain
A, B, C	IPR044357	NSP3, first ubiquitin-like (Ubl) domain, coronavirus	Domain
A, B, C	IPR046436	Nidovirus 3'-5' exoribonuclease domain	Domain
A, B, C	IPR047570	NSP12, interface domain, coronavirus	Domain
A, B, C	IPR043610	Non-structural protein 6, coronavirus	Domain
A, B, C	IPR027351	(+) RNA virus helicase core domain	Domain
A, B, C	IPR009461	Non-structural protein NSP16, coronavirus-like	Domain
A, B, C	IPR043477	Peptidase C30, domain 3, coronavirus	Homologous Superfamily
A, B, C	IPR018995	RNA synthesis protein NSP10, coronavirus	Domain
A, B, C	IPR050534	Coronaviruses polyprotein 1ab	Family
A, B, C	IPR043606	Coronavirus replicase NSP15, N-terminal oligomerization	Domain
A, B, C	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
A, B, C	IPR014822	Non-structural protein NSP9, coronavirus	Domain
A, B, C	IPR037230	Non-structural protein NSP8 superfamily, coronavirus	Homologous Superfamily
A, B, C	IPR046440	Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain	Domain
A, B, C	IPR014828	Non-structural protein NSP7, coronavirus	Domain
A, B, C	IPR032505	Non-structural protein NSP4, C-terminal, coronavirus	Domain
A, B, C	IPR043503	Papain-like viral protease, palm and finger domains, coronavirus	Homologous Superfamily
A, B, C	IPR014829	Non-structural protein NSP8, coronavirus	Domain
A, B, C	IPR044325	Nonstructural protein 15, middle domain, gammacoronavirus	Domain
A, B, C	IPR046438	Nidovirus 2-O-methyltransferase	Domain
A, B, C	IPR036499	Non-structural protein NSP9 superfamily, coronavirus	Homologous Superfamily
A, B, C	IPR002589	Macro domain	Domain
A, B, C	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C	IPR008740	Peptidase C30, coronavirus	Domain
A, B, C	IPR044368	Non-structural protein 6, gammacoronavirus	Domain
A, B, C	IPR036333	RNA synthesis protein NSP10 superfamily, coronavirus	Homologous Superfamily
A, B, C	IPR049894	Coronavirus NSP3, 3Ecto domain	Domain
A, B, C	IPR043472	Macro domain-like	Homologous Superfamily
A, B, C	IPR043609	NendoU domain, nidovirus	Domain
A, B, C	IPR044371	Non-structural protein 3, X-domain-like	Domain
A, B, C	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A, B, C	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain