9VGV | pdb_00009vgv

Crystal Structure of BlaA beta-lactamase in complex with the Antifungal Agent Tavaborole.

• PDB DOI: https://doi.org/10.2210/pdb9VGV/pdb

• Classification: HYDROLASE
• Organism(s): Yersinia enterocolitica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-06-15 Released: 2025-08-06 
• Deposition Author(s): Dhankhar, K., Bhattacharya, S., Hazra, S.
• Funding Organization(s): Indian Council of Medical Research, Board of Research in Nuclear Sciences (BRNS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of BlaA beta-lactamase in complex with the Antifungal Agent Tavaborole.

Dhankhar, K., Bhattacharya, S., Hazra, S.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 28.65 kDa 
• Atom Count: 2,061 
• Modeled Residue Count: 260 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	261	Yersinia enterocolitica	Mutation(s): 0  Gene Names: blaA EC: 3.5.2.6
UniProt
Find proteins for Q01166 (Yersinia enterocolitica) Explore Q01166  Go to UniProtKB:  Q01166

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CF8 (Subject of Investigation/LOI)	B [auth A]	Tavaborole C7 H6 B F O2 LFQDNHWZDQTITF-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.494	α = 90
b = 72.98	β = 94.421
c = 43.938	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Dhankhar, K., Bhattacharya, S., Hazra, S.

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Funding Organization	Location	Grant Number
Indian Council of Medical Research	India	EM/Dev/IG/20/07/73/2023
Board of Research in Nuclear Sciences (BRNS)	India	54/14/03/2023-BRNS/12162

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release