Crystal structure of AlbA in complex with albicidin

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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This is version 1.1 of the entry. See complete history


Molecular insights into antibiotic resistance - how a binding protein traps albicidin.

Rostock, L.Driller, R.Gratz, S.Kerwat, D.von Eckardstein, L.Petras, D.Kunert, M.Alings, C.Schmitt, F.J.Friedrich, T.Wahl, M.C.Loll, B.Mainz, A.Sussmuth, R.D.

(2018) Nat Commun 9: 3095-3095

  • DOI: https://doi.org/10.1038/s41467-018-05551-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The worldwide emergence of antibiotic resistance poses a serious threat to human health. A molecular understanding of resistance strategies employed by bacteria is obligatory to generate less-susceptible antibiotics. Albicidin is a highly potent antibacterial compound synthesized by the plant-pathogenic bacterium Xanthomonas albilineans. The drug-binding protein AlbA confers albicidin resistance to Klebsiella oxytoca. Here we show that AlbA binds albicidin with low nanomolar affinity resulting in full inhibition of its antibacterial activity. We report on the crystal structure of the drug-binding domain of AlbA (AlbAS) in complex with albicidin. Both α-helical repeat domains of AlbAS are required to cooperatively clamp albicidin, which is unusual for drug-binding proteins of the MerR family. Structure-guided NMR binding studies employing synthetic albicidin derivatives give valuable information about ligand promiscuity of AlbAS. Our findings thus expand the general understanding of antibiotic resistance mechanisms and support current drug-design efforts directed at more effective albicidin analogs.

  • Organizational Affiliation

    Institut für Chemie, Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Albicidin resistance protein
A, B
222Klebsiella oxytocaMutation(s): 0 
Gene Names: albA
Find proteins for Q8KRS7 (Klebsiella oxytoca)
Explore Q8KRS7 
Go to UniProtKB:  Q8KRS7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KRS7
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Binding Affinity Annotations 
IDSourceBinding Affinity
BWH Binding MOAD:  6ET8 Kd: 5.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.07α = 90
b = 123.35β = 90
c = 159.2γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references