› 4dww

X-ray diffraction
1.74Å resolution

Crystal Structure of Nattokinase from Bacillus subtilis natto

Released:
DOI: 10.2210/pdb4dww/pdb
PDB entry 4dww coloured by chain, front view.
PDB entry 4dww coloured by chain, side view.
PDB entry 4dww coloured by chain, top view.
Source organism: Bacillus subtilis subsp. natto
Primary publication:
Purification, crystallization and preliminary X-ray diffraction experiment of nattokinase from Bacillus subtilis natto.
Yanagisawa Y, Chatake T, Chiba-Kamoshida K, Naito S, Ohsugi T, Sumi H, Yasuda I, Morimoto Y
Acta Crystallogr Sect F Struct Biol Cryst Commun 66 1670-3 (2010)
PMID: 21139221

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:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153042 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Subtilisin NAT Chain: A
Molecule details ›
Chain: A
Length: 275 amino acids
Theoretical weight: 27.9 KDa
Source organism: Bacillus subtilis subsp. natto
UniProt:
  • 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:
Ligand CA 2 x CA
1 modified residue:
Ligand SEB 1 x SEB

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-values:
R R work R free
0.137 0.133 0.199

Quick links

Citations

4 review citations

Microbial production of nattokinase: current progress, challenge and prospect.
Cai et al. (2017)
3 more

6 mentions without citation

Microbial Fibrinolytic Enzymes as Anti-Thrombotics: Production, Characterisation and Prodigious Biopharmaceutical Applications.
Sharma et al. (2021)
5 more