› 5lub

X-ray diffraction
2.1Å resolution

Crystal structure of human legumain (AEP) in complex with compound 11

Released:
DOI: 10.2210/pdb5lub/pdb
PDB 5lub coloured by chain and viewed from the front.
PDB 5lub coloured by chain and viewed from the side.
PDB 5lub coloured by chain and viewed from the top.
Source organism: Homo sapiens
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
OpenAccess logo 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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Legumain Chains: A, B
Molecule details ›
Chains: A, B
Length: 262 amino acids
Theoretical weight: 29.94 KDa
Source organism: Homo sapiens
Expression system: Leishmania tarentolae
UniProt:
  • Canonical: Q99538 (Residues: 26-287; Coverage: 63%)
Gene names: LGMN, PRSC1
Sequence domains: Peptidase C13 family
Structure domains: Rossmann fold

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand NAG 2 x NAG
Ligand 3Y7 1 x 3Y7
1 modified residue:
Ligand SNN 2 x SNN

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P212121
Unit cell:
a: 43.52Å b: 75.04Å c: 172.97Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.221 0.253
Expression system: Leishmania tarentolae

Quick links

Citations

7 review citations

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