3FYX

The Structure of OmpF porin with a synthetic dibenzo-18-crown-6 as modulator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

On the function and structure of synthetically modified porins.

Reitz, S.Cebi, M.Reiss, P.Studnik, G.Linne, U.Koert, U.Essen, L.O.

(2009) Angew Chem Int Ed Engl 48: 4853-4857

  • DOI: 10.1002/anie.200900457
  • Primary Citation of Related Structures:  
    3FYX

  • PubMed Abstract: 
  • The attachment of modulators to a trimeric porin ion channel was investigated (see picture of the trimer with a crown ether modulator (orange)). The interplay of modulator and protein is essential for the conformational heterogeneity of the hybrid channel ...

    The attachment of modulators to a trimeric porin ion channel was investigated (see picture of the trimer with a crown ether modulator (orange)). The interplay of modulator and protein is essential for the conformational heterogeneity of the hybrid channel. Single-site attachment in large pores is not sufficient to change the electrophysiological characteristics of the pores-such change requires additional noncovalent interactions or second-site attachments.


    Organizational Affiliation

    Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Outer membrane protein FA340Escherichia coli K-12Mutation(s): 1 
Gene Names: b0929cmlBcoacryJW0912ompFtolF
Membrane Entity: Yes 
UniProt
Find proteins for P02931 (Escherichia coli (strain K12))
Explore P02931 
Go to UniProtKB:  P02931
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
451 (Subject of Investigation/LOI)
Query on 451

Download Ideal Coordinates CCD File 
B [auth A]N-(6,7,9,10,17,18,20,21-octahydrodibenzo[b,k][1,4,7,10,13,16]hexaoxacyclooctadecin-2-yl)acetamide
C22 H27 N O7
YHKGWOJTUMJPNW-UHFFFAOYSA-N
 Ligand Interaction
EPE
Query on EPE

Download Ideal Coordinates CCD File 
C [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.52α = 90
b = 135.52β = 90
c = 47.52γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance