3GSH

Three-dimensional structure of a post translational modified barley LTP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The crystal structure of oxylipin-conjugated barley LTP1 highlights the unique plasticity of the hydrophobic cavity of these plant lipid-binding proteins.

Bakan, B.Hamberg, M.Larue, V.Prange, T.Marion, D.Lascombe, M.B.

(2009) Biochem Biophys Res Commun 390: 780-785

  • DOI: https://doi.org/10.1016/j.bbrc.2009.10.049
  • Primary Citation of Related Structures:  
    3GSH

  • PubMed Abstract: 

    The barley lipid transfer protein (LTP1) adducted by an alpha-ketol, (9-hydroxy-10-oxo-12(Z)-octadecenoic acid) exhibits an unexpected high lipid transfer activity. The crystal structure of this oxylipin-adducted LTP1, (LTP1b) was determined at 1.8A resolution. The covalently bound oxylipin was partly exposed at the surface of the protein and partly buried within the hydrophobic cavity. The structure of the oxylipidated LTP1 emphasizes the unique plasticity of the hydrophobic cavity of these plant lipid-binding proteins when compared to the other members of the family. The plasticity of the hydrophobic cavity and increase of its surface hydrophobicity induced by the oxylipin account for the improvement of the lipid transfer activity of LTP1b. These observations open new perspectives to explore the different biological functions of LTPs, including their allergenic properties.


  • Organizational Affiliation

    INRA, Unité de recherches Biopolymères, Interactions, Assemblages, BP71627, La Géraudière, 44316 Nantes cedex 3, France. bakan@nantes.inra.fr


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-specific lipid-transfer protein 1
A, B
91Hordeum vulgareMutation(s): 0 
UniProt
Find proteins for P07597 (Hordeum vulgare)
Explore P07597 
Go to UniProtKB:  P07597
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07597
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ASY
Query on ASY

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B]
(12E)-10-oxooctadec-12-enoic acid
C18 H32 O3
IEQLMTRAAYQDSD-DHZHZOJOSA-N
TFA
Query on TFA

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B]
trifluoroacetic acid
C2 H F3 O2
DTQVDTLACAAQTR-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
K [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.74α = 90
b = 76.133β = 104.34
c = 39.402γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary