1QJQ | pdb_00001qjq

FERRIC HYDROXAMATE RECEPTOR FROM ESCHERICHIA COLI (FHUA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.278 (Depositor) 
  • R-Value Work: 
    0.225 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Crystal structure of the antibiotic albomycin in complex with the outer membrane transporter FhuA.

Ferguson, A.D.Braun, V.Fiedler, H.P.Coulton, J.W.Diederichs, K.Welte, W.

(2000) Protein Sci 9: 956-963

  • DOI: https://doi.org/10.1110/ps.9.5.956
  • Primary Citation Related Structures: 
    1QJQ, 1QKC

  • PubMed Abstract: 

    One alternative method for drug delivery involves the use of siderophore-antibiotic conjugates. These compounds represent a specific means by which potent antimicrobial agents, covalently linked to iron-chelating siderophores, can be actively transported across the outer membrane of gram-negative bacteria. These "Trojan Horse" antibiotics may prove useful as an efficient means to combat multi-drug-resistant bacterial infections. Here we present the crystallographic structures of the natural siderophore-antibiotic conjugate albomycin and the siderophore phenylferricrocin, in complex with the active outer membrane transporter FhuA from Escherichia coli. To our knowledge, this represents the first structure of an antibiotic bound to its cognate transporter. Albomycins are broad-host range antibiotics that consist of a hydroxamate-type iron-chelating siderophore, and an antibiotically active, thioribosyl pyrimidine moiety. As observed with other hydroxamate-type siderophores, the three-dimensional structure of albomycin reveals an identical coordination geometry surrounding the ferric iron atom. Unexpectedly, this antibiotic assumes two conformational isomers in the binding site of FhuA, an extended and a compact form. The structural information derived from this study provides novel insights into the diverse array of antibiotic moieties that can be linked to the distal portion of iron-chelating siderophores and offers a structural platform for the rational design of hydroxamate-type siderophore-antibiotic conjugates.


  • Organizational Affiliation
    • Fachbereich Biologie, Universität Konstanz, Germany.

Macromolecule Content 

  • Total Structure Weight: 84.92 kDa 
  • Atom Count: 6,218 
  • Modeled Residue Count: 707 
  • Deposited Residue Count: 725 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FERRIC HYDROXAMATE RECEPTOR725Escherichia coli K-12Mutation(s): 0 
Gene Names: FHUA
Membrane Entity: Yes 
UniProt
Find proteins for P06971 (Escherichia coli (strain K12))
Explore P06971 
Go to UniProtKB:  P06971
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06971
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-[alpha-D-galactopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-[L-glycero-alpha-D-manno-heptopyranose-(1-7)]L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2,3-dideoxy-alpha-D-glucoyranose-(1-6)-2-amino-2,3-dideoxy-alpha-D-glucoyranose
B
11N/A
Glycosylation Resources
GlyTouCan: G89342MM
GlyCosmos: G89342MM

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PFC

Query on PFC



Download:Ideal Coordinates CCD File
N [auth A]PHENYLFERRICROCIN-IRON
C34 H48 Fe N9 O12
CYHYTMBFIKKRSE-OVSNALSBSA-N
FTT

Query on FTT



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
3-HYDROXY-TETRADECANOIC ACID
C14 H28 O3
ATRNZOYKSNPPBF-CYBMUJFWSA-N
DPO

Query on DPO



Download:Ideal Coordinates CCD File
I [auth A],
K [auth A]
DIPHOSPHATE
O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-J
PO4

Query on PO4



Download:Ideal Coordinates CCD File
J [auth A],
L [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
NI

Query on NI



Download:Ideal Coordinates CCD File
M [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.278 (Depositor) 
  • R-Value Work:  0.225 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.1α = 90
b = 172.1β = 90
c = 87.65γ = 120
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-17
    Changes: Data collection
  • Version 1.4: 2019-10-09
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.5: 2020-07-01
    Changes: Advisory, Data collection, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Structure summary