3TF6

Crystal structure of Neutrophil gelatinase-associated lipocalin (C87S mutant) in complex with Europium and the siderophore analog tren(cam)(1,2-hopo)2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.191 

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
179Homo 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DBH
Query on DBH

Download SDF File 
Download CCD File 
A, B, C
2,3-DIHYDROXY-BENZOIC ACID
C7 H6 O4
GLDQAMYCGOIJDV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
A, B, C
EUROPIUM ION
Eu
MGVUQZZTJGLWJV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DBHKd: 400 nM PDBBIND
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 114.090α = 90.00
b = 114.090β = 90.00
c = 118.190γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACphasing
PDB_EXTRACTdata extraction
REFMACrefinement
ADSCdata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-07
    Type: Initial release
  • Version 1.1: 2013-10-09
    Type: Database references
  • Version 1.2: 2019-02-13
    Type: Data collection, Database references