6YSA | pdb_00006ysa

Crystal structure of Arabidopsis thaliana legumain isoform beta in zymogen state

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
C	SCOP2 Family	Legumain-like	8104318	4006439	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Caspase-like	8104319	3001096	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Caspase-like	8104319	3001096	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)
L	KOG1348	e6ysaL2	A: alpha arrays	X: Legumain prodomain (From Topology)	H: Legumain prodomain (From Topology)	T: Legumain prodomain	F: KOG1348	ECOD (1.6)
L	Peptidase_C13	e6ysaL1	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C13	ECOD (1.6)
K	KOG1348	e6ysaK2	A: alpha arrays	X: Legumain prodomain (From Topology)	H: Legumain prodomain (From Topology)	T: Legumain prodomain	F: KOG1348	ECOD (1.6)
K	Peptidase_C13	e6ysaK1	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C13	ECOD (1.6)
J	KOG1348	e6ysaJ2	A: alpha arrays	X: Legumain prodomain (From Topology)	H: Legumain prodomain (From Topology)	T: Legumain prodomain	F: KOG1348	ECOD (1.6)
J	Peptidase_C13	e6ysaJ1	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C13	ECOD (1.6)
I	KOG1348	e6ysaI2	A: alpha arrays	X: Legumain prodomain (From Topology)	H: Legumain prodomain (From Topology)	T: Legumain prodomain	F: KOG1348	ECOD (1.6)
I	Peptidase_C13	e6ysaI1	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C13	ECOD (1.6)
H	KOG1348	e6ysaH1	A: alpha arrays	X: Legumain prodomain (From Topology)	H: Legumain prodomain (From Topology)	T: Legumain prodomain	F: KOG1348	ECOD (1.6)
H	Peptidase_C13	e6ysaH2	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C13	ECOD (1.6)
G	KOG1348	e6ysaG2	A: alpha arrays	X: Legumain prodomain (From Topology)	H: Legumain prodomain (From Topology)	T: Legumain prodomain	F: KOG1348	ECOD (1.6)
G	Peptidase_C13	e6ysaG1	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C13	ECOD (1.6)
F	KOG1348	e6ysaF1	A: alpha arrays	X: Legumain prodomain (From Topology)	H: Legumain prodomain (From Topology)	T: Legumain prodomain	F: KOG1348	ECOD (1.6)
F	Peptidase_C13	e6ysaF2	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C13	ECOD (1.6)
E	KOG1348	e6ysaE1	A: alpha arrays	X: Legumain prodomain (From Topology)	H: Legumain prodomain (From Topology)	T: Legumain prodomain	F: KOG1348	ECOD (1.6)
E	Peptidase_C13	e6ysaE2	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C13	ECOD (1.6)
D	KOG1348	e6ysaD1	A: alpha arrays	X: Legumain prodomain (From Topology)	H: Legumain prodomain (From Topology)	T: Legumain prodomain	F: KOG1348	ECOD (1.6)
D	Peptidase_C13	e6ysaD2	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C13	ECOD (1.6)
C	KOG1348	e6ysaC1	A: alpha arrays	X: Legumain prodomain (From Topology)	H: Legumain prodomain (From Topology)	T: Legumain prodomain	F: KOG1348	ECOD (1.6)
C	Peptidase_C13	e6ysaC2	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C13	ECOD (1.6)
B	KOG1348	e6ysaB2	A: alpha arrays	X: Legumain prodomain (From Topology)	H: Legumain prodomain (From Topology)	T: Legumain prodomain	F: KOG1348	ECOD (1.6)
B	Peptidase_C13	e6ysaB1	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C13	ECOD (1.6)
A	KOG1348	e6ysaA2	A: alpha arrays	X: Legumain prodomain (From Topology)	H: Legumain prodomain (From Topology)	T: Legumain prodomain	F: KOG1348	ECOD (1.6)
A	Peptidase_C13	e6ysaA1	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C13	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF01650	Peptidase C13 family (Peptidase_C13)	Peptidase C13 family	-	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF20985	Legumain, prodomain (Legum_prodom)	Legumain, prodomain	This domain is found in the proenzyme form of Vacuolar-processing enzyme (VPE), known as legumain. VPE is an asparagine-specific endopeptidase that plays important roles in many physiological processes, including the maturation of toll-like receptors ...	This domain is found in the proenzyme form of Vacuolar-processing enzyme (VPE), known as legumain. VPE is an asparagine-specific endopeptidase that plays important roles in many physiological processes, including the maturation of toll-like receptors 3/7/9. The mature active form of VPE is generated by autoproteolytic maturation at acidic pH. In the three-dimensional structure of the proenzyme, this prodomain is located on top of the protease domain, blocking access to the active site. It shows an entirely alpha-helical fold, with an activation peptide and a region that assemblies into a death domain-like fold at its C-terminal end [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	Vacuolar-processing enzyme beta-isozyme	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity	catabolic process proteolysis involved in protein catabolic process proteolysis metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process catabolic process proteolysis involved in protein catabolic process proteolysis metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process protein processing vacuolar protein processing	membrane-bounded organelle storage vacuole intracellular anatomical structure vacuole intracellular membrane-bounded organelle protein storage vacuole intracellular organelle cellular anatomical structure organelle plant-type vacuole cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR046427	Legumain prodomain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR048501	Legumain, prodomain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR001096	Peptidase C13, legumain	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR043577	Asparaginyl endopeptidase	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	SNN	Parent Component: ASN RESID: AA0302 , AA0593 PSI-MOD : L-aspartimide MOD:00307 , 2-(2-aminosuccinimidyl)pentanedioic acid (Asn) MOD:01940 , 2-(2-aminosuccinimidyl)pentanedioic acid (Asp) MOD:01941