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)

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
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

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

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

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q01166
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CF8 (Subject of Investigation/LOI) Query on A1CF8 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	Tavaborole C₇ H₆ B F O₂ LFQDNHWZDQTITF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-06

Deposition Author(s):

Bhattacharya, S.

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.