PDBe 4dww

X-ray diffraction
1.74Å resolution

Crystal Structure of Nattokinase from Bacillus subtilis natto


Function and Biology Details

Reaction catalysed:
Hydrolysis of proteins with broad specificity for peptide bonds, and a preference for a large uncharged residue in P1. Hydrolyzes peptide amides.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Subtilisin NAT Chain: A
Molecule details ›
Chain: A
Length: 275 amino acids
Theoretical weight: 27.9 KDa
Source organism: Bacillus subtilis subsp. natto
  • Canonical: P35835 (Residues: 107-381; Coverage: 78%)
Gene name: aprN
Sequence domains: Subtilase family
Structure domains: Peptidase S8/S53 domain

Ligands and Environments

1 bound ligand:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: C2
Unit cell:
a: 74.293Å b: 49.899Å c: 56.338Å
α: 90° β: 95.24° γ: 90°
R R work R free
0.137 0.133 0.199