9IO7 | pdb_00009io7

Crystal Structure of SME-1 Carbapenemase in complex with Zidebactam

• PDB DOI: https://doi.org/10.2210/pdb9IO7/pdb

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


• Deposited: 2024-07-08 Released: 2025-07-16 
• 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: 2.40 Å
• R-Value Free: 
  0.267 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.183 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of SME-1 Carbapenemase in complex with ZIdebactam

Dhankhar, K., Hazra, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.86 kDa 
• Atom Count: 2,123 
• Modeled Residue Count: 267 
• Deposited Residue Count: 275 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-lactamase	A	275	Serratia marcescens	Mutation(s): 0  Gene Names: sme-2, blaSME-1, blaSME-4, blaSME1, SME12620_22 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
C8V (Subject of Investigation/LOI)	B [auth A]	(2S,5R)-1-formyl-N'-[(3R)-piperidine-3-carbonyl]-5-[(sulfooxy)amino]piperidine-2-carbohydrazide C13 H23 N5 O7 S KMYLRFCWFBWPGR-MXWKQRLJSA-N
EDO (Subject of Investigation/LOI)	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.267 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.183 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.884	α = 90
b = 50.18	β = 97.939
c = 60.586	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Dhankhar, K., Hazra, S.

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Funding Organization	Location	Grant Number
Indian Council of Medical Research	India	EM/Dev/IG/20/0773/2023
Board of Research in Nuclear Sciences (BRNS)	India	54/14/03/2023-BRNS

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release