3HWG

Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Fe-TrenCam-hopo2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Parsing the functional specificity of Siderocalin / Lipocalin 2 / NGAL for siderophores and related small-molecule ligands

Clifton, M.C.Rupert, P.B.Hoette, T.M.Raymond, K.N.Abergel, R.J.Strong, R.K.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neutrophil gelatinase-associated lipocalin
A, B, C
198Homo sapiensMutation(s): 1 
Gene Names: LCN2 (HNL, NGAL)
Find proteins for P80188 (Homo sapiens)
Go to Gene View: LCN2
Go to UniProtKB:  P80188
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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Download CCD File 
A, B, C
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
QED
Query on QED

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Download CCD File 
A, B, C
N,N'-{[(2-{[(2,3-dihydroxyphenyl)carbonyl]amino}ethyl)imino]diethane-2,1-diyl}bis(1-hydroxy-6-oxo-1,6-dihydropyridine-2-carboxamide)
tren mono-2,3-catecholamido bis-N-hydroxypyridin-2-one-6-amide
C25 H28 N6 O9
UPWYYPIMZVCQNS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.242 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 114.084α = 90.00
b = 114.084β = 90.00
c = 118.422γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-06-17 
  • Released Date: 2010-06-02 
  • Deposition Author(s): Clifton, M.C.

Revision History 

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2019-02-27
    Type: Data collection, Database references