1BH6

SUBTILISIN DY IN COMPLEX WITH THE SYNTHETIC INHIBITOR N-BENZYLOXYCARBONYL-ALA-PRO-PHE-CHLOROMETHYL KETONE

• PDB DOI: https://doi.org/10.2210/pdb1BH6/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus licheniformis
• Mutation(s): No 


• Deposited: 1998-06-15 Released: 1998-11-04 
• Deposition Author(s): Eschenburg, S., Genov, N., Wilson, K.S., Betzel, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Work: 
  0.140 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of subtilisin DY, a random mutant of subtilisin Carlsberg.

Eschenburg, S., Genov, N., Peters, K., Fittkau, S., Stoeva, S., Wilson, K.S., Betzel, C.

(1998) Eur J Biochem 257: 309-318

• PubMed: 9826175 
• DOI: https://doi.org/10.1046/j.1432-1327.1998.2570309.x
• Primary Citation of Related Structures:  
  1BH6


• PubMed Abstract: 
  

  The crystal structure of subtilisin DY inhibited by N-benzyloxycarbonyl-Ala-Pro-Phe-chloromethyl ketone has been solved by molecular replacement with subtilisin Carlsberg as the starting model. The model has been refined to a crystallographic R factor (= sigma absolute value [(absolute value Fo) - (absolute value Fc)] / sigma (absolute value of Fo) of 15.1% using X-ray diffraction data to 0.175 nm resolution. Subtilisin DY is an alkaline proteinase from the X-irradiated Japanese strain DY of Bacillus licheniformis, which normally produces subtilisin Carlsberg. It has very similar properties to subtilisin Carlsberg, with a slightly enhanced resistance to heat and guanidine hydrochloride-induced denaturation, in spite of the fact that the sequences of the two enzymes differ in 31 positions out of 274 residues. The close similarity in overall three-dimensional structure of subtilisins DY and Carlsberg and also their physicochemical properties, such as activity and stability, shows that nature aided by X-irradiation for rapid 'evolution' is able to accommodate considerable changes in sequence without substantial changes in property.

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Organizational Affiliation: 

European Molecular Biology Laboratory, Institute of Physiological Chemistry, Hamburg, Germany. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.03 kDa 
• Atom Count: 2,210 
• Modelled Residue Count: 274 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUBTILISIN DY	A	274	Bacillus licheniformis	Mutation(s): 0  EC: 3.4.21.62
UniProt
Find proteins for P00781 (Bacillus licheniformis) Explore P00781  Go to UniProtKB:  P00781

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1BH	D [auth A]	N-BENZYLOXYCARBONYL-ALA-PRO-3-AMINO-4-PHENYL-BUTAN-2-OL C26 H33 N3 O5 MACLRJNEKXUAJK-YDLSIGKMSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Work:  0.140 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.83	α = 90
b = 72.75	β = 90
c = 59.89	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CCP4	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-11-04 
Deposition Author(s): Eschenburg, S., Genov, N., Wilson, K.S., Betzel, C.

Revision History  

• Version 1.0: 1998-11-04
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-02
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary