7MC9

X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d7mc9b_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d7mc9d_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d7mc9f_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d7mc9h_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d7mc9j_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
L	d7mc9l_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
N	d7mc9n_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
P	d7mc9p_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Ubiquitin-like	8101457	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8101457	3000157	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ubiquitin-like	8101457	3000157	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ubiquitin-like	8101457	3000157	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ubiquitin-like	8101457	3000157	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Ubiquitin-like	8101457	3000157	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Ubiquitin-like	8101457	3000157	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Ubiquitin-like	8101457	3000157	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	Viral_protease_C	e7mc9A1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)
C	Viral_protease_C	e7mc9C1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)
E	Viral_protease_C	e7mc9E1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)
G	Viral_protease_C	e7mc9G1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)
I	Viral_protease_C	e7mc9I1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)
K	Viral_protease_C	e7mc9K1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)
M	Viral_protease_C	e7mc9M1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)
O	Viral_protease_C	e7mc9O1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)
B	ubiquitin_1	e7mc9B1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
D	ubiquitin_1	e7mc9D1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
F	ubiquitin_1	e7mc9F1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
H	ubiquitin_1	e7mc9H1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
J	ubiquitin_1	e7mc9J1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
L	ubiquitin_1	e7mc9L1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
N	ubiquitin_1	e7mc9N1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
P	ubiquitin_1	e7mc9P1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K, M, O	PF08715	Coronavirus papain-like peptidase (CoV_peptidase)	Coronavirus papain-like peptidase	-	Family
B, D, F, H, J B, D, F, H, J, L, N, P	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K, M, O	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	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 symbiont-mediated perturbation of host process 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 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 symbiont-mediated perturbation of host process 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 symbiont-mediated perturbation of host defenses response to defenses of other organism 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 symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway viral gene expression viral protein processing viral 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 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 cellular process metabolic process regulation of metabolic process viral genome replication viral life cycle viral translational frameshifting viral translation proteolysis primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane 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
B, D, F, H, J B, D, F, H, J, L, N, P	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	developmental process multicellular organismal process reproductive system development gonad development tube development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics seminiferous tubule development developmental process multicellular organismal process reproductive system development gonad development tube development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics seminiferous tubule development anatomical structure development reproductive structure development system development regulation of mitochondrial membrane potential biological regulation regulation of biological quality regulation of membrane potential catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of biological process neuron apoptotic process regulation of cellular process regulation of apoptotic process regulation of programmed cell death cell death apoptotic process programmed cell death regulation of neuron apoptotic process multicellular organismal-level homeostasis homeostatic process energy homeostasis regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process regulation of macromolecule metabolic process macromolecule modification post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of signal transduction regulation of intrinsic apoptotic signaling pathway intracellular signal transduction cell communication positive regulation of apoptotic signaling pathway positive regulation of response to stimulus regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator signal transduction intrinsic apoptotic signaling pathway regulation of signaling positive regulation of programmed cell death positive regulation of intracellular signal transduction signal transduction by p53 class mediator positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication intrinsic apoptotic signaling pathway by p53 class mediator positive regulation of intrinsic apoptotic signaling pathway regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of apoptotic signaling pathway positive regulation of signaling cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation cellular component organization or biogenesis plasma membrane bounded cell projection organization nervous system development generation of neurons anatomical structure morphogenesis neuron development hypothalamus development forebrain development central nervous system neuron development central nervous system neuron differentiation hypothalamus cell differentiation hypothalamus gonadotrophin-releasing hormone neuron development limbic system development head development forebrain generation of neurons hypothalamus gonadotrophin-releasing hormone neuron differentiation brain development diencephalon development forebrain neuron development central nervous system development forebrain neuron differentiation sexual reproduction organelle fission meiotic cell cycle multicellular organismal reproductive process female gamete generation meiotic cell cycle process gamete generation nuclear division organelle organization meiosis I meiosis I cell cycle process female meiosis I female meiotic nuclear division meiotic nuclear division cell cycle cell cycle process positive regulation of protein monoubiquitination protein monoubiquitination regulation of protein monoubiquitination regulation of proteolysis involved in protein catabolic process regulation of proteolysis proteasomal protein catabolic process regulation of catabolic process regulation of proteasomal protein catabolic process regulation of protein catabolic process male meiosis I male meiotic nuclear division male gamete generation connective tissue development adipose tissue development fat pad development tissue development female gonad development female sex differentiation development of primary female sexual characteristics establishment of organelle localization cellular localization organelle transport along microtubule transport establishment of mitochondrion localization intracellular transport establishment of localization localization mitochondrion localization establishment of mitochondrion localization, microtubule-mediated mitochondrion transport along microtubule organelle localization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane cell projection neuron projection plasma membrane bounded cell projection intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane endocytic vesicle endosome membrane endosome mitochondrial membrane organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane somatodendritic compartment cell body neuronal cell body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K, M, O	IPR043611	Coronavirus replicase NSP3, C-terminal	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR038123	Non-structural protein NSP4, C-terminal superfamily, coronavirus	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR047566	Coronavirus replicase NSP3, Y domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR043178	Papain-like protease, thumb domain superfamily, coronavirus	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR044353	NSP3, second ubiquitin-like (Ubl) domain, coronavirus	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR013016	Peptidase C16, coronavirus	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR037204	Non-structural protein NSP7 superfamily, coronavirus	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR044357	NSP3, first ubiquitin-like (Ubl) domain, coronavirus	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR046443	NSP1, globular domain, alpha/betacoronavirus	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR043610	Non-structural protein 6, coronavirus	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR043477	Peptidase C30, domain 3, coronavirus	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR011050	Pectin lyase fold/virulence factor	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR043615	Nonstructural protein 2, N-terminal domain, coronavirus	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR044369	Non-structural protein 6, alphacoronavirus	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR014822	Non-structural protein NSP9, coronavirus	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR037230	Non-structural protein NSP8 superfamily, coronavirus	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR014828	Non-structural protein NSP7, coronavirus	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR032505	Non-structural protein NSP4, C-terminal, coronavirus	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR014829	Non-structural protein NSP8, coronavirus	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR036499	Non-structural protein NSP9 superfamily, coronavirus	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR002589	Macro domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR008740	Peptidase C30, coronavirus	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR047573	Non-structural protein 2, middle domain, coronavirus	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR049894	Coronavirus NSP3, 3Ecto domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR044309	Non-structural protein 5, alphacoronavirus	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR043472	Macro domain-like	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR044371	Non-structural protein 3, X-domain-like	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR043613	Non-structural protein 2, C-terminal domain, coronavirus	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR044385	Nonstructural protein 2, HCoV-229E-like	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L, N, P	IPR019954	Ubiquitin conserved site	Conserved Site
B, D, F, H, J B, D, F, H, J, L, N, P	IPR050158	Ubiquitin and ubiquitin-like	Family
B, D, F, H, J B, D, F, H, J, L, N, P	IPR000626	Ubiquitin-like domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR019956	Ubiquitin domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F, H, J B, D, F, H, J, L, N, P	Pharos: P0CG47	astrocytic tumor cleft soft palate lung cancer Cleft of hard palate ovarian cancer isolated cleft palate