5GL8

The crystal structure of Nattokinase fragments

• PDB DOI: https://doi.org/10.2210/pdb5GL8/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis subsp. natto
• Mutation(s): No 


• Deposited: 2016-07-10 Released: 2017-10-25 
• Deposition Author(s): Liu, W.
• Funding Organization(s): National Natural Science Foundation of China

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.291 
• R-Value Work: 0.231 
• R-Value Observed: 0.234 

Starting Model: experimental

Literature

unpublished

Ren, Y., Pan, X., Lyu, Q., Liu, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55.54 kDa 
• Atom Count: 4,747 
• Modelled Residue Count: 550 
• Deposited Residue Count: 550 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Subtilisin NAT	A, B	275	Bacillus subtilis subsp. natto	Mutation(s): 0  EC: 3.4.21.62
UniProt
Find proteins for P35835 (Bacillus subtilis subsp. natto) Explore P35835  Go to UniProtKB:  P35835

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth B], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.291 
• R-Value Work: 0.231 
• R-Value Observed: 0.234 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.284	α = 90
b = 73.959	β = 97.47
c = 67.811	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-10-25 
Deposition Author(s): Liu, W.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	8130268

Revision History  

• Version 1.0: 2017-10-25
  Type: Initial release
  
• Version 1.1: 2018-07-18
  Changes: Data collection, Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description