9W7N | pdb_00009w7n

Crystal Structure of Vaborbactam in complex with SME-1 class A Carbapenemase

• PDB DOI: https://doi.org/10.2210/pdb9W7N/pdb

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


• Deposited: 2025-08-06 Released: 2025-11-19 
• 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: 2.00 Å
• R-Value Free: 
  0.242 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

Beyond structure and activity: targeting class A carbapenemases with monocyclic and bicyclic boronic acids to counter antimicrobial resistance.

Dhankhar, K., Hazra, M., Nair, A.S.R., Alhmeidi Alkhatib, A.E., Mishra, N.C., Hazra, S.

(2025) Org Biomol Chem 

• PubMed: 41217385 
• DOI: https://doi.org/10.1039/d5ob01703c
• Primary Citation of Related Structures:  
  9W7N, 9W7O, 9W7P


• PubMed Abstract: 
  

  Bicyclic boronic acids inhibit SME-1 carbapenemase via a unique π-π stacking with His105 and covalent interaction with Ser70. Ledaborbactam shows the strongest inhibition, with the lowest k _i and enhanced structural stability. X-ray crystallography and molecular dynamics reveal key features helpful in structure-based optimization of boronates targeting class A β-lactamases.

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Organizational Affiliation: 
• Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Haridwar, Uttarakhand, 247667, India. [e-mail].
Department of Polymer and Process Engineering, Indian Institute of Technology, Roorkee, Haridwar, Uttarakhand, 247667, India.
Department of Botany and Microbiology, Gurukula Kangri (Deemed to be University), Haridwar, Uttarakhand, 249404, India.
Centre for Nanotechnology, Indian Institute of Technology, Roorkee, Haridwar, Uttarakhand, 247667, India.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59.82 kDa 
• Atom Count: 4,486 
• 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, B	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4D6 (Subject of Investigation/LOI)	C [auth A], F [auth B]	Vaborbactam C12 H16 B N O5 S IOOWNWLVCOUUEX-WPRPVWTQSA-N
PG4 (Subject of Investigation/LOI)	D [auth A], G [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.242 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.180 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.039	α = 90
b = 51.011	β = 92.799
c = 130.533	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: 2025-11-19 
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: 2025-11-19
  Type: Initial release