4dww Summary

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Crystal Structure of Nattokinase from Bacillus subtilis natto

The structure was published by Yanagisawa, Y., Chatake, T., Chiba-Kamoshida, K., et al., Sumi, H., Yasuda, I., and Morimoto, Y., in 2010 in a paper entitled "Purification, crystallization and preliminary X-ray diffraction experiment of nattokinase from Bacillus subtilis natto" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 1.74 Å and deposited in 2012.

The experimental data on which the structure is based was also deposited.

The PDB entry contains the structure of Subtilisin NAT. This molecule has the UniProt identifier P35835 (SUBN_BACNA)search. The sample contained 275 residues which is < 90% of the natural sequence. Out of 275 residues 275 were observed and are deposited in the PDB.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule is most likely monomeric.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A Subtilisin NAT P35835 (107-381) (SUBN_BACNA)search Bacillus subtilis subsp. nattosearch < 90% 275 100%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
P35835 (107 - 381) Subtilisin NAT Bacillus subtilis subsp. natto

Chain Sequence family (Pfam)
A Subtilase familysearch

Chain ID Biological process (GO) Molecular function (GO)
A (P35835) proteolysissearch serine-type endopeptidase activitysearch

Chain InterPro annotation
A Peptidase S8/S53 domainsearch Peptidase S8, subtilisin-relatedsearch Peptidase S8, subtilisin, His-active sitesearch Peptidase S8, subtilisin, Asp-active sitesearch Peptidase S8, subtilisin, Ser-active sitesearch