9VXS | pdb_00009vxs

Crystal structure of Antifungal agent Tavaborole in complex with SME-1 class A carbapenemase

• PDB DOI: https://doi.org/10.2210/pdb9VXS/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Serratia marcescens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-07-20 Released: 2025-08-06 
• Deposition Author(s): Dhankhar, K., 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: 
  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.189 (DCC) 

Starting Model: experimental

Literature

Crystal structure of Antifungal agent Tavaborole in complex with SME-1 class A carbapenemase

Dhankhar, K., 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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.32 kDa 
• Atom Count: 4,268 
• Modeled Residue Count: 534 
• Deposited Residue Count: 534 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase SME-1	A [auth B], B [auth A]	267	Serratia marcescens	Mutation(s): 0  Gene Names: SME-1, blaSME-1, blaSME-4, blaSME1, bpl-1, bplA, sme-2, smeA EC: 3.5.2.6
UniProt
Find proteins for P52682 (Serratia marcescens) Explore P52682  Go to UniProtKB:  P52682

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG (Subject of Investigation/LOI)	D [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	F [auth A], G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.189 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.235	α = 90
b = 51.153	β = 114.896
c = 78.318	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., Hazra, S.

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Funding Organization	Location	Grant Number
Indian Council of Medical Research	India	--
Board of Research in Nuclear Sciences (BRNS)	India	--

Revision History  

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