› 4awa

X-ray diffraction
2.5Å resolution

Crystal structure of active legumain in complex with YVAD-CMK at pH 5.0

Released:
DOI: 10.2210/pdb4awa/pdb
PDB entry 4awa coloured by chain, front view.
PDB entry 4awa coloured by chain, side view.
PDB entry 4awa coloured by chain, top view.
Source organisms:
Primary publication:
Mechanistic and structural studies on legumain explain its zymogenicity, distinct activation pathways, and regulation.
Dall E, Brandstetter H
Proc Natl Acad Sci U S A 110 10940-5 (2013)
PMID: 23776206

Function and Biology Details

Reaction catalysed: 
Hydrolysis of proteins and small molecule substrates at -Asn-|-Xaa- bonds.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-164295 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Legumain Chain: A
Molecule details ›
Chain: A
Length: 284 amino acids
Theoretical weight: 32.27 KDa
Source organism: Homo sapiens
Expression system: Leishmania tarentolae
UniProt:
  • Canonical: Q99538 (Residues: 26-309; Coverage: 68%)
Gene names: LGMN, PRSC1
Sequence domains: Peptidase C13 family
Structure domains: Rossmann fold
YVAD-CMK Chain: I
Molecule details ›
Chain: I
Length: 6 amino acids
Theoretical weight: 525 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand SO4 2 x SO4
Ligand NAG 3 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P42
Unit cell:
a: 64.3Å b: 64.3Å c: 79.09Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.238 0.237 0.256
Expression systems:
  • Leishmania tarentolae
  • Not provided

Quick links

Citations

19 review citations

Vacuolar processing enzyme in plant programmed cell death.
Hatsugai et al. (2015)
18 more

8 mentions without citation

Asparaginyl endopeptidases: enzymology, applications and limitations.
Tang et al. (2021)
7 more