24TN | pdb_000024tn

Crystal structure of class C beta-lactamase PDC-16 in complex with imipenem

• PDB DOI: https://doi.org/10.2210/pdb24TN/pdb

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


• Deposited: 2026-03-19 Released: 2026-10-07 
• Deposition Author(s): Liji, S.S., Dhanasingh, I.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.245 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.189 (DCC) 

Starting Model: experimental

Literature

Crystal structure of class C beta-lactamase PDC-16 in complex with imipenem

Liji, S.S., Dhanasingh, I.

(2026) Int J Biol Macromol 

• DOI: https://doi.org/10.1016/j.ijbiomac.2026.154709

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 79.49 kDa 
• Atom Count: 5,940 
• Modeled Residue Count: 718 
• Deposited Residue Count: 718 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A [auth B], B [auth A]	359	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: blaPDC EC: 3.5.2.6
UniProt
Find proteins for A0A1Z1VQP5 (Pseudomonas aeruginosa) Explore A0A1Z1VQP5  Go to UniProtKB:  A0A1Z1VQP5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IM2 (Subject of Investigation/LOI)	C [auth B], E [auth A]	(5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid C12 H19 N3 O4 S UACUABDJLSUFFC-IWSPIJDZSA-N
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.245 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.189 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.82	α = 90
b = 90.02	β = 90
c = 103.11	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-07 
Deposition Author(s): Liji, S.S., Dhanasingh, I.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-10-07
  Type: Initial release