8RKY | pdb_00008rky

X-ray structure of the drug binding domain of AlbA in complex with the KMR-14-14 compound of the pyrrolobenzodiazepines class

• PDB DOI: https://doi.org/10.2210/pdb8RKY/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Klebsiella oxytoca
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-01-01 Released: 2025-01-15 
• Deposition Author(s): Di Palma, M., Surani, Y.M., Rahman, K.M., Steiner, R.A.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Ministero dell Universita e della Ricerca

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.234 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.212 (DCC) 

Starting Model: experimental

Literature

Convergent evolution of antibiotic resistance mechanisms between pyrrolobenzodiazepines and albicidin in multidrug resistant Klebsiella pneumoniae.

Surani, Y.M., Wand, M.E., Picconi, P., Di Palma, M., Zenezini Chiozzi, R., Hasan, M.M., Andriollo, P., Gratz, S., Nahar, K.S., Maynard-Smith, M., Sussmuth, R.D., Steiner, R.A., Rahman, K.M., Hind, C.K., Sutton, J.M.

(2025) NPJ Antimicrob Resist 3: 52-52

• PubMed: 40481275 
• DOI: https://doi.org/10.1038/s44259-025-00104-4
• Primary Citation Related Structures: 
  8RKY


• PubMed Abstract: 
  

  Pyrrolobenzodiazepines (PBDs) containing C8-linked aliphatic heterocycles have been developed as a new class of potent antibacterial compounds. They are active against multidrug resistant Gram-negative pathogens, including Klebsiella pneumoniae. When isolates were exposed to PBDs, they acquired resistance, with significant increases in inhibitory concentrations. Resistant strains showed mutations in genes associated with resistance to albicidin, specifically tsx and merR-family regulator albA. Heterologous expression of AlbA in E. coli and introducing the L120Q AlbA resistance-mediating modification into the genome of a sensitive K. pneumoniae strain conferred PBD and albicidin resistance. Proteomic analysis of the resistant strains showed elevated AlbA protein levels compared to isogenic wild-type strains. Crystallographic studies with the antibiotic binding domain of AlbA show binding of KMR-14-14 to the same groove shown to bind albicidin. Given the parallels between these two structurally unrelated compound classes, AlbA may offer resistance to further antibiotics and should be considered in future antibiotic discovery.

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Organizational Affiliation: 
• UK Health Security Agency, Research and Evaluation, Porton Down, Salisbury, SP4 0JG, Wiltshire, UK.
Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK.
Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy.
UCL Mass Spectrometry Science Technology Platform, Division of Biosciences, Darwin Building, University College London, Gower Street, London, WC1E 6BT, UK.
Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, 4331, Bangladesh.
Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany.
Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London, SE1 1UL, UK.
Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK. [e-mail].
UK Health Security Agency, Research and Evaluation, Porton Down, Salisbury, SP4 0JG, Wiltshire, UK. [e-mail].
Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK. [e-mail].

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 83.61 kDa 
• Atom Count: 6,088 
• Modeled Residue Count: 650 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Albicidin resistance protein	A [auth BBB], B [auth CCC], C [auth AAA]	224	Klebsiella oxytoca	Mutation(s): 0  Gene Names: albA
UniProt
Find proteins for Q8KRS7 (Klebsiella oxytoca) Explore Q8KRS7  Go to UniProtKB:  Q8KRS7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1H1Q (Subject of Investigation/LOI)	E [auth BBB], H [auth CCC]	~{S}-[(2~{S},3~{S})-2,3-bis(oxidanyl)-4-sulfanyl-butyl] 4-[[5-[[4-[4-[[(6~{a}~{S})-2-methoxy-11-oxidanylidene-6~{a},7,8,9-tetrahydropyrrolo[2,1-c][1,4]benzodiazepin-3-yl]oxy]butanoylamino]-1-methyl-pyrrol-2-yl]carbonylamino]-1-benzothiophen-2-yl]carbonylamino]-1-methyl-imidazole-2-carbothioate C41 H44 N8 O9 S3 KAPRUVBCCMGSEO-UHFFFAOYSA-N
A1H1R (Subject of Investigation/LOI)	D [auth BBB], G [auth CCC], I [auth AAA], J [auth AAA]	ethyl 4-[[5-[[4-[4-[[(6~{a}~{S})-2-methoxy-11-oxidanylidene-6~{a},7,8,9-tetrahydropyrrolo[2,1-c][1,4]benzodiazepin-3-yl]oxy]butanoylamino]-1-methyl-pyrrol-2-yl]carbonylamino]-1-benzothiophen-2-yl]carbonylamino]-1-methyl-imidazole-2-carboxylate C39 H40 N8 O8 S FOOOXHGRWPRUKF-RUZDIDTESA-N
DTV	F [auth BBB], K [auth AAA], L [auth AAA]	(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL C4 H10 O2 S2 VHJLVAABSRFDPM-QWWZWVQMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.234 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.212 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.631	α = 90
b = 118.95	β = 92.073
c = 57.702	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Di Palma, M., Surani, Y.M., Rahman, K.M., Steiner, R.A.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M009513/1
Ministero dell Universita e della Ricerca	Italy	--

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release
  
• Version 1.1: 2026-07-01
  Changes: Database references