Crystal structure of the OmpK36 TD insertion chimera from Klebsiella pneumonia

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae.

David, S.Wong, J.L.C.Sanchez-Garrido, J.Kwong, H.S.Low, W.W.Morecchiato, F.Giani, T.Rossolini, G.M.Brett, S.J.Clements, A.Beis, K.Aanensen, D.M.Frankel, G.

(2022) PLoS Pathog 18: e1010334-e1010334

  • DOI: https://doi.org/10.1371/journal.ppat.1010334
  • Primary Citation of Related Structures:  
    7PZF, 7Q3T

  • PubMed Abstract: 

    Mutations in outer membrane porins act in synergy with carbapenemase enzymes to increase carbapenem resistance in the important nosocomial pathogen, Klebsiella pneumoniae (KP). A key example is a di-amino acid insertion, Glycine-Aspartate (GD), in the extracellular loop 3 (L3) region of OmpK36 which constricts the pore and restricts entry of carbapenems into the bacterial cell. Here we combined genomic and experimental approaches to characterise the diversity, spread and impact of different L3 insertion types in OmpK36. We identified L3 insertions in 3588 (24.1%) of 14,888 KP genomes with an intact ompK36 gene from a global collection. GD insertions were most common, with a high concentration in the ST258/512 clone that has spread widely in Europe and the Americas. Aspartate (D) and Threonine-Aspartate (TD) insertions were prevalent in genomes from Asia, due in part to acquisitions by KP sequence types ST16 and ST231 and subsequent clonal expansions. By solving the crystal structures of novel OmpK36 variants, we found that the TD insertion causes a pore constriction of 41%, significantly greater than that achieved by GD (10%) or D (8%), resulting in the highest levels of resistance to selected antibiotics. We show that in the absence of antibiotics KP mutants harbouring these L3 insertions exhibit both an in vitro and in vivo competitive disadvantage relative to the isogenic parental strain expressing wild type OmpK36. We propose that this explains the reversion of GD and TD insertions observed at low frequency among KP genomes. Finally, we demonstrate that strains expressing L3 insertions remain susceptible to drugs targeting carbapenemase-producing KP, including novel beta lactam-beta lactamase inhibitor combinations. This study provides a contemporary global view of OmpK36-mediated resistance mechanisms in KP, integrating surveillance and experimental data to guide treatment and drug development strategies.

  • Organizational Affiliation

    Centre for Genomic Pathogen Surveillance, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
347Klebsiella pneumoniaeMutation(s): 0 
Gene Names: ompK36
Membrane Entity: Yes 
Find proteins for D6QLY2 (Klebsiella pneumoniae)
Explore D6QLY2 
Go to UniProtKB:  D6QLY2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6QLY2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on C14

Download Ideal Coordinates CCD File 
BA [auth E]
CA [auth E]
DA [auth E]
EA [auth E]
FA [auth E]
BA [auth E],
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth E],
I [auth A],
J [auth A],
JA [auth F],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth C],
V [auth D],
W [auth D],
X [auth D],
Y [auth D]
C14 H30
Query on LI

Download Ideal Coordinates CCD File 
AA [auth E]
G [auth A]
GA [auth F]
H [auth A]
HA [auth F]
AA [auth E],
G [auth A],
GA [auth F],
H [auth A],
HA [auth F],
IA [auth F],
K [auth B],
U [auth D],
Z [auth E]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.106α = 91.12
b = 73.428β = 97.17
c = 158.837γ = 103.09
Software Package:
Software NamePurpose
xia2data reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/N020103/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description