› 5lu9

X-ray diffraction
2.27Å resolution

Crystal structure of YVAD-cmk bound human legumain (AEP) in complex with compound 11

Released:
DOI: 10.2210/pdb5lu9/pdb
PDB entry 5lu9 coloured by chain, front view.
PDB entry 5lu9 coloured by chain, side view.
PDB entry 5lu9 coloured by chain, top view.
Source organisms:
Primary publication:
Inhibition of delta-secretase improves cognitive functions in mouse models of Alzheimer's disease.
Zhang Z, Obianyo O, Dall E, Du Y, Fu H, Liu X, Kang SS, Song M, Yu SP, Cabrele C, Schubert M, Li X, Wang JZ, Brandstetter H, Ye K
Nat Commun 8 14740 (2017)
PMID: 28345579

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-165964 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
AC-TYR-VAL-ALA-ASP-CHLOROMETHYLKETONE Chain: C
Molecule details ›
Chain: C
Length: 6 amino acids
Theoretical weight: 525 Da
Source organism: synthetic construct
Expression system: Not provided
Legumain Chain: A
Molecule details ›
Chain: A
Length: 263 amino acids
Theoretical weight: 30.1 KDa
Source organism: Homo sapiens
Expression system: Leishmania tarentolae
UniProt:
  • Canonical: Q99538 (Residues: 26-288; Coverage: 63%)
Gene names: LGMN, PRSC1
Sequence domains: Peptidase C13 family
Structure domains: Rossmann fold

Ligands and Environments

3 bound ligands:
Ligand NAG 2 x NAG
Ligand SO4 2 x SO4
Ligand 3Y7 1 x 3Y7
1 modified residue:
Ligand SNN 1 x SNN

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P42
Unit cell:
a: 64.39Å b: 64.39Å c: 79.33Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.245 0.244 0.273
Expression systems:
  • Not provided
  • Leishmania tarentolae

Quick links

Citations

14 review citations

Molecular and cellular mechanisms underlying the pathogenesis of Alzheimer's disease.
Guo et al. (2020)
13 more

2 mentions without citation

Inhibition of delta-secretase improves cognitive functions in mouse models of Alzheimer's disease.
Zhang et al. (2017)
1 more