1KRO

Thermolysin complexed with Z-D-Threonine (benzyloxycarbonyl-D-Threonine)

• PDB DOI: https://doi.org/10.2210/pdb1KRO/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Bacillus thermoproteolyticus
• Mutation(s): No 


• Deposited: 2002-01-10 Released: 2003-01-10 
• Deposition Author(s): Senda, M., Senda, T., Kidokoro, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.182 
• R-Value Work: 0.166 
• R-Value Observed: 0.171 

Literature

Crystal structure analyses of thermolysin in complex with its inhibitors.

Senda, M., Senda, T., Kidokoro, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.88 kDa 
• Atom Count: 2,637 
• Modelled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermolysin	A	316	Bacillus thermoproteolyticus	Mutation(s): 0  EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus) Explore P00800  Go to UniProtKB:  P00800

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PHQ	G [auth A]	benzyl chlorocarbonate C8 H7 Cl O2 HSDAJNMJOMSNEV-UHFFFAOYSA-N
DTH	H [auth A]	D-THREONINE C4 H9 N O3 AYFVYJQAPQTCCC-STHAYSLISA-N
ZN	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.182 
• R-Value Work: 0.166 
• R-Value Observed: 0.171 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.759	α = 90
b = 93.759	β = 90
c = 131.34	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-10 
Deposition Author(s): Senda, M., Senda, T., Kidokoro, S.

Revision History  

• Version 1.0: 2003-01-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations