4YLU

X-ray structure of MERS-CoV nsp5 protease bound with a non-covalent 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	d4ylua_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	automated matches	automated matches	(Middle East respiratory syndrome-related coronavirus ) [TaxId: 1335626 ],	SCOPe (2.08)
B	d4ylub_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	automated matches	automated matches	(Middle East respiratory syndrome-related coronavirus ) [TaxId: 1335626 ],	SCOPe (2.08)
C	d4yluc_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	automated matches	automated matches	(Middle East respiratory syndrome-related coronavirus ) [TaxId: 1335626 ],	SCOPe (2.08)
D	d4ylud_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	automated matches	automated matches	(Middle East respiratory syndrome-related coronavirus ) [TaxId: 1335626 ],	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	8076473	3000114	SCOP2B (2022-06-29)
B	SCOP2 Family	Viral cysteine protease of trypsin fold, (M)Pro-like	8076472	4002259	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Trypsin-like serine proteases	8076473	3000114	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Trypsin-like serine proteases	8076473	3000114	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Trypsin-like serine proteases	8076473	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	e4yluA2	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	e4yluA1	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	e4yluB1	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	e4yluB2	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	e4yluC2	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	e4yluC1	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	e4yluD2	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	e4yluD1	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	ORF1a protein	peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity RNA binding binding organic cyclic compound binding peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity RNA binding binding organic cyclic compound binding nucleic acid binding single-stranded RNA binding ubiquitin-like protein peptidase activity cysteine-type deubiquitinase activity deubiquitinase activity G-quadruplex RNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	methylation metabolic process symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host ISG15-protein conjugation response to host defenses biological process involved in interspecies interaction between organisms response to stimulus 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 response to biotic stimulus biological process involved in interaction with host methylation metabolic process symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host ISG15-protein conjugation response to host defenses biological process involved in interspecies interaction between organisms response to stimulus 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 response to biotic stimulus biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process 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 modulation of process of another organism viral gene expression viral protein processing viral process regulation of cellular process negative regulation of biological process symbiont-mediated perturbation of host translation negative regulation of cellular metabolic process nucleobase-containing compound metabolic process symbiont-mediated suppression of host gene expression RNA catabolic process mRNA catabolic process regulation of biological process cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process primary metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process symbiont-mediated degradation of host mRNA nucleic acid catabolic process symbiont-mediated suppression of host translation regulation of macromolecule biosynthetic process symbiont-mediated perturbation of host gene expression macromolecule metabolic process regulation of metabolic process symbiont-mediated perturbation of host cellular process catabolic process cellular biosynthetic process RNA metabolic process macromolecule catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process modulation by virus of host process virus-mediated perturbation of host defense response modulation by virus of host cellular process symbiont-mediated perturbation of host ubiquitin-like protein modification autophagy positive regulation of biological 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 positive regulation of autophagy modulation by virus of host autophagy regulation of catabolic process positive regulation of catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated perturbation of host signal transduction pathway viral genome replication viral life cycle viral translational frameshifting viral translation proteolysis protein 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	IPR022733	DPUP/SUD, C-terminal, betacoronavirus	Domain
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	IPR042570	Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus	Homologous Superfamily
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	IPR044388	Non-structural protein 2, MERS-CoV-like	Domain
A, B, C, D	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
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	IPR044382	NSP3, SUD-C domain, MERS-CoV-like	Domain
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	IPR038400	Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus	Homologous Superfamily
A, B, C, D	IPR046442	NSP1, C-terminal domain, betacoronavirus	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	IPR014822	Non-structural protein NSP9, coronavirus	Domain
A, B, C, D	IPR021590	NSP1, globular domain, betacoronavirus	Domain
A, B, C, D	IPR024375	Non-structural protein NSP3, SUD-M domain, betacoronavirus	Domain
A, B, C, D	IPR044367	Non-structural protein 6, betacoronavirus	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	IPR043503	Papain-like viral protease, palm and finger domains, coronavirus	Homologous Superfamily
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	IPR047567	Non-structural protein NSP3, group 2-specific marker domain, betacoronavirus	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	IPR049894	Coronavirus NSP3, 3Ecto domain	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	IPR032592	Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus	Domain
A, B, C, D	IPR043613	Non-structural protein 2, C-terminal domain, coronavirus	Domain
A, B, C, D	IPR038083	Non-structural protein NSP3A domain-like superfamily	Homologous Superfamily
A, B, C, D	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily