9NHT | pdb_00009nht

Crystal structure of structure of WT BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor KM-5-35


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.185 (Depositor), 0.193 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Inhibitors of the Bacterioferritin Ferredoxin Complex Dysregulate Iron Homeostasis and Kill Acinetobacter baumannii and Biofilm-Embedded Pseudomonas aeruginosa Cells.

Behm, A.M.Yao, H.Eze, E.C.Alli, S.A.Baugh, S.D.P.Ametsetor, E.Powell, K.M.Battaile, K.P.Seibold, S.Lovell, S.Bunce, R.A.Reitz, A.B.Rivera, M.

(2025) ACS Infect Dis 11: 1983-1993

  • DOI: https://doi.org/10.1021/acsinfecdis.5c00209
  • Primary Citation of Related Structures:  
    9NHR, 9NHT

  • PubMed Abstract: 

    In Pseudomonas aeruginosa , the iron storage protein bacterioferritin (Bfr) contributes to buffering cytosolic free iron concentrations by oxidizing Fe 2+ and storing the resultant Fe 3+ in its internal cavity, and by forming a complex with a cognate ferredoxin (Bfd) to reduce the stored Fe 3+ and mobilize Fe 2+ to the cytosol. Small molecule derivatives of 4-aminoisoindoline-1,3-dione designed to bind P. aeruginosa Bfr (Pa Bfr) at the Bfd binding site accumulate in the P. aeruginosa cell, block the Pa Bfr-Bfd complex, inhibit iron mobilization from Pa Bfr, elicit an iron starvation response, are bacteriostatic to planktonic cells, and are bactericidal to biofilm-entrenched cells. A structural alignment of Pa Bfr and Acinetobacter baumannii Bfr (Ab Bfr) showed strong conservation of the Bfd binding site on Ab Bfr. Accordingly, the small molecule inhibitors of the Pa Bfr-Bfd complex accumulate in the A. baumannii cells, elicit an iron starvation response, are bactericidal to planktonic cells, and exhibit synergy with existing antibiotics. These findings indicate that the inhibition of iron mobilization from Bfr may be an antimicrobial strategy applicable to other Gram-negative pathogens.


  • Organizational Affiliation
    • Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferroxidase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
158Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: bfrBPA3531
EC: 1.16.3.1
UniProt
Find proteins for Q9HY79 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HY79 
Go to UniProtKB:  Q9HY79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HY79
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
DA [auth D]
DB [auth J]
M [auth A]
NB [auth L]
T [auth B]
DA [auth D],
DB [auth J],
M [auth A],
NB [auth L],
T [auth B],
TA [auth H],
ZA [auth I]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
A1BYC (Subject of Investigation/LOI)
Query on A1BYC

Download Ideal Coordinates CCD File 
AB [auth I]
EA [auth D]
EB [auth J]
IB [auth K]
LA [auth F]
AB [auth I],
EA [auth D],
EB [auth J],
IB [auth K],
LA [auth F],
N [auth A],
OB [auth L],
QA [auth G],
U [auth B],
UA [auth H],
Z [auth C]
4-{[(5-bromo-2-hydroxyphenyl)methyl]amino}-1H-isoindole-1,3(2H)-dione
C15 H11 Br N2 O3
ICZMDDCYEUQOMT-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
CB [auth I]
GA [auth D]
HB [auth J]
BA [auth C],
CA [auth C],
CB [auth I],
GA [auth D],
HB [auth J],
KA [auth E],
LB [auth K],
MB [auth K],
PA [auth F],
QB [auth L],
S [auth A],
SA [auth G],
Y [auth B],
YA [auth H]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
HA [auth E],
O [auth A],
VA [auth H]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth C]
BB [auth I]
FA [auth D]
FB [auth J]
GB [auth J]
AA [auth C],
BB [auth I],
FA [auth D],
FB [auth J],
GB [auth J],
IA [auth E],
JA [auth E],
JB [auth K],
KB [auth K],
MA [auth F],
NA [auth F],
OA [auth F],
P [auth A],
PB [auth L],
Q [auth A],
R [auth A],
RA [auth G],
V [auth B],
W [auth B],
WA [auth H],
X [auth B],
XA [auth H]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.185 (Depositor), 0.193 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.97α = 90
b = 194.956β = 90
c = 203.565γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesS10 OD030394
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI169344

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Database references