9XFY | pdb_00009xfy

Crystal structure of Class A beta-lactamase BlaA in complex with ertapenem (imine form)

• PDB DOI: https://doi.org/10.2210/pdb9XFY/pdb
• Entry: 9XFY supersedes: 8IXX

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


• Deposited: 2025-10-29 Released: 2025-11-12 
• Deposition Author(s): Bhattacharya, 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: 1.70 Å
• R-Value Free: 
  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.195 (DCC) 

Starting Model: experimental

Literature

Crystal structure of Class A beta-lactamase BlaA in complex with ertapenem (imine form)

Bhattacharya, S., 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

Macromolecule Content 

• Total Structure Weight: 32.73 kDa 
• Atom Count: 2,264 
• Modeled Residue Count: 262 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	294	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
2RG (Subject of Investigation/LOI)	B [auth A]	(2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid C22 H27 N3 O7 S RALHTEQYPKBGFO-SAGZMZRGSA-N
PO4 (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.195 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.743	α = 90
b = 72.818	β = 95.776
c = 43.7	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: 2025-11-12 
Deposition Author(s): Bhattacharya, S., Dhankhar, K., Hazra, S.
• This entry supersedes: 8IXX

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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: 2025-11-12
  Type: Initial release