2Q6F

Crystal structure of infectious bronchitis virus (IBV) main protease in complex with a Michael acceptor inhibitor N3

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	d2q6fa_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	automated matches	automated matches	(Infectious bronchitis virus ) [TaxId: 11120 ],	SCOPe (2.08)
B	d2q6fb_	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	SCOP2 Family	Viral cysteine protease of trypsin fold (M)Pro-like	8076486	4002259	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Trypsin-like serine proteases	8076487	3000114	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Trypsin-like serine proteases	8076487	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	PF05409	e2q6fA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF05409	ECOD (1.6)
A	PF05409	e2q6fA2	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: PF05409	ECOD (1.6)
B	PF05409	e2q6fB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF05409	ECOD (1.6)
B	PF05409	e2q6fB2	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: PF05409	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	Infectious bronchitis virus (IBV) main protease	peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity lyase activity RNA binding binding organic cyclic compound binding nucleic acid binding transferase activity peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity lyase activity RNA binding binding organic cyclic compound binding nucleic acid binding transferase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	viral genome replication viral process viral life cycle viral gene expression viral protein processing 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 positive regulation of cellular metabolic process regulation of autophagy viral genome replication viral process viral life cycle viral gene expression viral protein processing 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 positive regulation of cellular metabolic process regulation of autophagy biological process involved in symbiotic interaction cellular catabolic process positive regulation of metabolic 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 cellular metabolic process biological regulation regulation of cellular metabolic process regulation of catabolic process symbiont-mediated perturbation of host autophagy biological process involved in interaction with host positive regulation of catabolic process modulation by symbiont of host process regulation of cellular catabolic process positive regulation of cellular catabolic process cellular process metabolic process regulation of metabolic process organic substance metabolic process organonitrogen compound metabolic process proteolysis primary metabolic process protein metabolic process macromolecule metabolic process	membrane cellular anatomical entity host cellular component host intracellular part host cell perinuclear region of cytoplasm host cell cytoplasm host cell part host intracellular region host cell cytoplasm part host intracellular membrane-bounded organelle host cell endoplasmic reticulum host cell membrane host intracellular organelle host cell endomembrane system membrane cellular anatomical entity host cellular component host intracellular part host cell perinuclear region of cytoplasm host cell cytoplasm host cell part host intracellular region host cell cytoplasm part host intracellular membrane-bounded organelle host cell endoplasmic reticulum host cell membrane host intracellular organelle host cell endomembrane system host cell endoplasmic reticulum membrane
C [auth D], D [auth C]	N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR043611	Coronavirus replicase NSP3, C-terminal	Domain
A, B	IPR014822	Non-structural protein NSP9, coronavirus	Domain
A, B	IPR038123	Non-structural protein NSP4, C-terminal superfamily, coronavirus	Homologous Superfamily
A, B	IPR047566	Coronavirus replicase NSP3, Y domain	Domain
A, B	IPR044308	Non-structural protein 5, gammacoronavirus	Domain
A, B	IPR037230	Non-structural protein NSP8 superfamily, coronavirus	Homologous Superfamily
A, B	IPR014828	Non-structural protein NSP7, coronavirus	Domain
A, B	IPR043178	Papain-like protease, thumb domain superfamily, coronavirus	Homologous Superfamily
A, B	IPR032505	Non-structural protein NSP4, C-terminal, coronavirus	Domain
A, B	IPR043503	Papain-like viral protease, palm and finger domains, coronavirus	Homologous Superfamily
A, B	IPR014829	Non-structural protein NSP8, coronavirus	Domain
A, B	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
A, B	IPR036499	Non-structural protein NSP9 superfamily, coronavirus	Homologous Superfamily
A, B	IPR044353	NSP3, second ubiquitin-like (Ubl) domain, coronavirus	Domain
A, B	IPR002589	Macro domain	Domain
A, B	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B	IPR044383	Non-structural protein 2, IBV-like	Domain
A, B	IPR008740	Peptidase C30, coronavirus	Domain
A, B	IPR044368	Non-structural protein 6, gammacoronavirus	Domain
A, B	IPR036333	RNA synthesis protein NSP10 superfamily, coronavirus	Homologous Superfamily
A, B	IPR013016	Peptidase C16, coronavirus	Domain
A, B	IPR040795	Non-structural protein 2, gammacoronavirus	Domain
A, B	IPR037204	Non-structural protein NSP7 superfamily, coronavirus	Homologous Superfamily
A, B	IPR043472	Macro domain-like	Homologous Superfamily
A, B	IPR044357	NSP3, first ubiquitin-like (Ubl) domain, coronavirus	Domain
A, B	IPR043610	Non-structural protein 6, coronavirus	Domain
A, B	IPR044371	Non-structural protein 3, X-domain-like	Domain
A, B	IPR043477	Peptidase C30, domain 3, coronavirus	Homologous Superfamily
A, B	IPR018995	RNA synthesis protein NSP10, coronavirus	Domain
A, B	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily