3FW4

Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric Catechol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Iron traffics in circulation bound to a siderocalin (Ngal)-catechol complex.

Bao, G.Clifton, M.Hoette, T.M.Mori, K.Deng, S.X.Qiu, A.Viltard, M.Williams, D.Paragas, N.Leete, T.Kulkarni, R.Li, X.Lee, B.Kalandadze, A.Ratner, A.J.Pizarro, J.C.Schmidt-Ott, K.M.Landry, D.W.Raymond, K.N.Strong, R.K.Barasch, J.

(2010) Nat Chem Biol 6: 602-609

  • DOI: https://doi.org/10.1038/nchembio.402
  • Primary Citation of Related Structures:  
    3FW4, 3FW5

  • PubMed Abstract: 

    The lipocalins are secreted proteins that bind small organic molecules. Scn-Ngal (also known as neutrophil gelatinase associated lipocalin, siderocalin, lipocalin 2) sequesters bacterial iron chelators, called siderophores, and consequently blocks bacterial growth. However, Scn-Ngal is also prominently expressed in aseptic diseases, implying that it binds additional ligands and serves additional functions. Using chemical screens, crystallography and fluorescence methods, we report that Scn-Ngal binds iron together with a small metabolic product called catechol. The formation of the complex blocked the reactivity of iron and permitted its transport once introduced into circulation in vivo. Scn-Ngal then recycled its iron in endosomes by a pH-sensitive mechanism. As catechols derive from bacterial and mammalian metabolism of dietary compounds, the Scn-Ngal-catechol-Fe(III) complex represents an unforeseen microbial-host interaction, which mimics Scn-Ngal-siderophore interactions but instead traffics iron in aseptic tissues. These results identify an endogenous siderophore, which may link the disparate roles of Scn-Ngal in different diseases.


  • Organizational Affiliation

    College of Physicians and Surgeons of Columbia University, New York, New York, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neutrophil gelatinase-associated lipocalin
A, B, C
178Homo sapiensMutation(s): 1 
Gene Names: HNLLCN2NGAL
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens)
Explore P80188 
Go to UniProtKB:  P80188
PHAROS:  P80188
GTEx:  ENSG00000148346 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80188
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CAQ
Query on CAQ

Download Ideal Coordinates CCD File 
E [auth A],
T [auth C]
CATECHOL
C6 H6 O2
YCIMNLLNPGFGHC-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
I [auth A],
J [auth A],
K [auth A],
Y [auth C],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
D [auth A],
P [auth B],
S [auth C]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
GA [auth C]
H [auth A]
L [auth A]
M [auth A]
N [auth A]
GA [auth C],
H [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
Q [auth B],
R [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
U [auth C]
V [auth C]
W [auth C]
F [auth A],
G [auth A],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CAQ PDBBind:  3FW4 Kd: 0.4 (nM) from 1 assay(s)
Binding MOAD:  3FW4 Kd: 0.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.421α = 90
b = 115.421β = 90
c = 118.801γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description