5O77

Klebsiella pneumoniae OmpK35


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Getting Drugs into Gram-Negative Bacteria: Rational Rules for Permeation through General Porins.

Acosta-Gutierrez, S.Ferrara, L.Pathania, M.Masi, M.Wang, J.Bodrenko, I.Zahn, M.Winterhalter, M.Stavenger, R.A.Pages, J.M.Naismith, J.H.van den Berg, B.Page, M.G.P.Ceccarelli, M.

(2018) ACS Infect Dis 4: 1487-1498

  • DOI: https://doi.org/10.1021/acsinfecdis.8b00108
  • Primary Citation of Related Structures:  
    5O77, 5O79, 6ENE

  • PubMed Abstract: 

    Small, hydrophilic molecules, including most important antibiotics in clinical use, cross the Gram-negative outer membrane through the water-filled channels provided by porins. We have determined the X-ray crystal structures of the principal general porins from three species of Enterobacteriaceae, namely Enterobacter aerogenes, Enterobacter cloacae, and Klebsiella pneumoniae, and determined their antibiotic permeabilities as well as those of the orthologues from Escherichia coli. Starting from the structure of the porins and molecules, we propose a physical mechanism underlying transport and condense it in a computationally efficient scoring function. The scoring function shows good agreement with in vitro penetration data and will enable the screening of virtual databases to identify molecules with optimal permeability through porins and help to guide the optimization of antibiotics with poor permeation.


  • Organizational Affiliation

    Department of Physics , University of Cagliari, Cittadella Universitaria di Monserrato , SP Monserrato-Sestu Km 0.8 , Monserrato , 09042 , Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OmpK35337Klebsiella pneumoniaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1P8FCM7 (Klebsiella pneumoniae)
Explore A0A1P8FCM7 
Go to UniProtKB:  A0A1P8FCM7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1P8FCM7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.312α = 90
b = 77.312β = 90
c = 114.044γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description