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	Ldh_1_C	e6ysaL1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)
K	Ldh_1_C	e6ysaK1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)
J	Ldh_1_C	e6ysaJ1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)
I	Ldh_1_C	e6ysaI1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)
H	Ldh_1_C	e6ysaH1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)
G	Ldh_1_C	e6ysaG1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)
F	Ldh_1_C	e6ysaF1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)
E	Ldh_1_C	e6ysaE1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)
D	Ldh_1_C	e6ysaD1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)
C	WD40, Beta-prop_WDR3_2nd	e6ysaC1	A: beta barrels	X: Tail specific protease helical domain	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: WD40, Beta-prop_WDR3_2nd	ECOD (v294.2)
B	Ldh_1_C	e6ysaB1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)
A	Ldh_1_C	e6ysaA1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)

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	primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process 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 : AA0302 , AA0593 : L-aspartimide MOD:00307 , 2-(2-aminosuccinimidyl)pentanedioic acid (Asn) MOD:01940 , 2-(2-aminosuccinimidyl)pentanedioic acid (Asp) MOD:01941

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.