4F49

2.25A resolution structure of Transmissible Gastroenteritis Virus Protease containing a covalently bound Dipeptidyl Inhibitor

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	d4f49a1	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)	TGEV (Porcine transmissible gastroenteritis coronavirus strain Purdue ) [TaxId: 11151 ],	SCOPe (2.08)
A	d4f49a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	TGEV (Porcine transmissible gastroenteritis coronavirus strain Purdue ) [TaxId: 11151 ],	SCOPe (2.08)
B	d4f49b_	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)	TGEV (Porcine transmissible gastroenteritis coronavirus strain Purdue ) [TaxId: 11151 ],	SCOPe (2.08)
C	d4f49c1	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)	TGEV (Porcine transmissible gastroenteritis coronavirus strain Purdue ) [TaxId: 11151 ],	SCOPe (2.08)
C	d4f49c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	TGEV (Porcine transmissible gastroenteritis coronavirus strain Purdue ) [TaxId: 11151 ],	SCOPe (2.08)
D	d4f49d1	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)	TGEV (Porcine transmissible gastroenteritis coronavirus strain Purdue ) [TaxId: 11151 ],	SCOPe (2.08)
D	d4f49d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	TGEV (Porcine transmissible gastroenteritis coronavirus strain Purdue ) [TaxId: 11151 ],	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	8076462	4002259	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Trypsin-like serine proteases	8076463	3000114	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Trypsin-like serine proteases	8076463	3000114	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Trypsin-like serine proteases	8076463	3000114	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Trypsin-like serine proteases	8076463	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	e4f49A1	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	e4f49A2	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	e4f49B1	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	e4f49B2	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	e4f49C1	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	e4f49C2	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	e4f49D1	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	e4f49D2	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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	3C-like proteinase	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 RNA binding binding organic cyclic compound binding nucleic acid binding transferase activity ubiquitin-like protein peptidase 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 RNA binding binding organic cyclic compound binding nucleic acid binding transferase activity ubiquitin-like protein peptidase activity cysteine-type deubiquitinase activity deubiquitinase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	viral gene expression viral protein processing viral process symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms response to stimulus symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway response to biotic stimulus biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response response to host immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response viral gene expression viral protein processing viral process symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms response to stimulus symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway response to biotic stimulus biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response response to host 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 modulation of process of another organism symbiont-mediated perturbation of host defense response response to host defenses response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism symbiont-mediated perturbation of host defenses response to external stimulus biological process involved in interaction with host symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity symbiont-mediated suppression of host signal transduction pathway modulation by symbiont of host process cellular process symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway catabolic process regulation of cellular process autophagy positive regulation of biological process modulation by virus of host process positive regulation of cellular metabolic process regulation of autophagy cellular catabolic process positive regulation of metabolic process induction by virus of host autophagy process utilizing autophagic mechanism 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 positive regulation of catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process metabolic process regulation of metabolic process symbiont-mediated perturbation of host ubiquitin-like protein modification viral genome replication viral life cycle 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 cell membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR043611	Coronavirus replicase NSP3, C-terminal	Domain
A, B, C, D	IPR038123	Non-structural protein NSP4, C-terminal superfamily, coronavirus	Homologous Superfamily
A, B, C, D	IPR032039	Alphacoronavirus nsp1	Domain
A, B, C, D	IPR047566	Coronavirus replicase NSP3, Y domain	Domain
A, B, C, D	IPR043178	Papain-like protease, thumb domain superfamily, coronavirus	Homologous Superfamily
A, B, C, D	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
A, B, C, D	IPR038634	Alphacoronavirus nsp1 domain superfamily	Homologous Superfamily
A, B, C, D	IPR044353	NSP3, second ubiquitin-like (Ubl) domain, coronavirus	Domain
A, B, C, D	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B, C, D	IPR013016	Peptidase C16, coronavirus	Domain
A, B, C, D	IPR037204	Non-structural protein NSP7 superfamily, coronavirus	Homologous Superfamily
A, B, C, D	IPR044357	NSP3, first ubiquitin-like (Ubl) domain, coronavirus	Domain
A, B, C, D	IPR046443	NSP1, globular domain, alpha/betacoronavirus	Domain
A, B, C, D	IPR043610	Non-structural protein 6, coronavirus	Domain
A, B, C, D	IPR043477	Peptidase C30, domain 3, coronavirus	Homologous Superfamily
A, B, C, D	IPR018995	RNA synthesis protein NSP10, coronavirus	Domain
A, B, C, D	IPR043615	Nonstructural protein 2, N-terminal domain, coronavirus	Domain
A, B, C, D	IPR043177	Papain-like protease, N-terminal domain superfamily, coronavirus	Homologous Superfamily
A, B, C, D	IPR044369	Non-structural protein 6, alphacoronavirus	Domain
A, B, C, D	IPR014822	Non-structural protein NSP9, coronavirus	Domain
A, B, C, D	IPR037230	Non-structural protein NSP8 superfamily, coronavirus	Homologous Superfamily
A, B, C, D	IPR014828	Non-structural protein NSP7, coronavirus	Domain
A, B, C, D	IPR032505	Non-structural protein NSP4, C-terminal, coronavirus	Domain
A, B, C, D	IPR014829	Non-structural protein NSP8, coronavirus	Domain
A, B, C, D	IPR036499	Non-structural protein NSP9 superfamily, coronavirus	Homologous Superfamily
A, B, C, D	IPR002589	Macro domain	Domain
A, B, C, D	IPR008740	Peptidase C30, coronavirus	Domain
A, B, C, D	IPR036333	RNA synthesis protein NSP10 superfamily, coronavirus	Homologous Superfamily
A, B, C, D	IPR047573	Non-structural protein 2, middle domain, coronavirus	Domain
A, B, C, D	IPR044309	Non-structural protein 5, alphacoronavirus	Domain
A, B, C, D	IPR043472	Macro domain-like	Homologous Superfamily
A, B, C, D	IPR044371	Non-structural protein 3, X-domain-like	Domain
A, B, C, D	IPR043613	Non-structural protein 2, C-terminal domain, coronavirus	Domain
A, B, C, D	IPR044385	Nonstructural protein 2, HCoV-229E-like	Domain
A, B, C, D	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily