8RMI | pdb_00008rmi

Crystal structure of ferrioxamine transporter FoxA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 
    0.268 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

Synthesis and antibacterial properties under blue LED light of conjugates between the siderophore desferrioxamine B (DFOB) and an Iridium(III) complex.

Faucon, A.Renault, J.Josts, I.Couchot, J.Renaud, J.L.Hoegy, F.Plesiat, P.Tidow, H.Gaillard, S.Mislin, G.L.A.

(2024) Bioorg Med Chem 112: 117842-117842

  • DOI: https://doi.org/10.1016/j.bmc.2024.117842
  • Primary Citation Related Structures: 
    8RM3, 8RMI

  • PubMed Abstract: 

    The decline of antibiotics efficacy worldwide has recently reached a critical point urging for the development of new strategies to regain upper hand on multidrug resistant bacterial strains. In this context, the raise of photodynamic therapy (PDT), initially based on organic photosensitizers (PS) and more recently on organometallic PS, offers promising perspectives. Many PS exert their biological effects through the generation of reactive oxygen species (ROS) able to freely diffuse into and to kill surrounding bacteria. Hijacking of the bacterial iron-uptake systems with siderophore-PS conjugates would specifically target pathogens. Here, we report the synthesis of unprecedented conjugates between the siderophore desferrioxamine B (DFOB) and an antibacterial iridium(III) PS. Redox properties of the new conjugates have been determined at excited states and compared to that of an antibacterial iridium PS previously reported by our groups. Tested on nosocomial pathogen Pseudomonas aeruginosa and other bacteria, these conjugates demonstrated significant inhibitory activity when activated with blue LED light. Ir(III) conjugate and iridium free DFOB-2,2'-dipyridylamine ligands were crystallized in complex with FoxA, the outer membrane transporter involved in DFOB uptake in P. aeruginosa and revealed details of the binding mode of these unprecedented conjugates.


  • Organizational Affiliation
    • CNRS, UMR7242 Biotechnologie et Signalisation Cellulaire, 300 Boulevard Sébastien Brant, F-67412 Illkirch, Strasbourg, France; Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), 300 Boulevard Sébastien Brant, F-67412 Illkirch, Strasbourg, France.

Macromolecule Content 

  • Total Structure Weight: 92.48 kDa 
  • Atom Count: 5,519 
  • Modeled Residue Count: 677 
  • Deposited Residue Count: 820 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferrioxamine receptor FoxA820Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: foxAPA2466
UniProt
Find proteins for Q9I116 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I116 
Go to UniProtKB:  Q9I116
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I116
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H1Z
(Subject of Investigation/LOI)

Query on A1H1Z



Download:Ideal Coordinates CCD File
D [auth A][1-[2-[2-[2-[2-[2-(dipyridin-2-ylamino)ethanoylamino]ethoxy]ethoxy]ethoxy]ethyl]-1,2,3-triazol-4-yl]methyl ~{N}-[5-[[4-[5-[[4-[5-[ethanoyl(oxidanyl)amino]pentylamino]-4-oxidanylidene-butanoyl]-oxidanyl-amino]pentylamino]-4-oxidanylidene-butanoyl]-oxidanyl-amino]pentyl]carbamate
C49 H77 N13 O14
UJSWWURLJJYLAP-UHFFFAOYSA-N
BOG

Query on BOG



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
G [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
N [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
NH4

Query on NH4



Download:Ideal Coordinates CCD File
F [auth A]AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free:  0.268 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.515α = 90
b = 93.515β = 90
c = 177.817γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release