3FOR | pdb_00003for

Thermolysin Complexed with BNPA (2-Benzyl-3-Nitro Propanoic Acid Amide)

• PDB DOI: https://doi.org/10.2210/pdb3FOR/pdb

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


• Deposited: 2008-12-31 Released: 2010-01-12 
• Deposition Author(s): Wang, S.-F., Jin, J.-Y., Tian, G.-R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.213 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Nitro as ZBG in the inhibition of Thermolysin

Wang, S.-F., Jin, J.-Y., Tian, G.-R.

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)

Macromolecule Content 

• Total Structure Weight: 34.87 kDa 
• Atom Count: 2,663 
• Modeled 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
ZNP	H [auth A]	(2R)-2-benzyl-3-nitropropanamide C10 H12 N2 O3 JJVMCABGSUOHSC-SECBINFHSA-N
DMS	G [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-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: 1.93 Å
• R-Value Free:  0.213 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.094	α = 90
b = 93.094	β = 90
c = 129.28	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-12 
Deposition Author(s): Wang, S.-F., Jin, J.-Y., Tian, G.-R.

Revision History  

• Version 1.0: 2010-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description