5MXC

Aleuria aurantia lectin (AAL) N224Q mutant in complex with alpha-methyl-L-fucoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL.

Houser, J.Kozmon, S.Mishra, D.Mishra, S.K.Romano, P.R.Wimmerova, M.Koca, J.

(2017) PLoS ONE 12: e0189375-e0189375

  • DOI: 10.1371/journal.pone.0189375

  • PubMed Abstract: 
  • Protein-carbohydrate interactions are very often mediated by the stacking CH-π interactions involving the side chains of aromatic amino acids such as tryptophan (Trp), tyrosine (Tyr) or phenylalanine (Phe). Especially suitable for stacking is the Trp ...

    Protein-carbohydrate interactions are very often mediated by the stacking CH-π interactions involving the side chains of aromatic amino acids such as tryptophan (Trp), tyrosine (Tyr) or phenylalanine (Phe). Especially suitable for stacking is the Trp residue. Analysis of the PDB database shows Trp stacking for 265 carbohydrate or carbohydrate like ligands in 5 208 Trp containing motives. An appropriate model system to study such an interaction is the AAL lectin family where the stacking interactions play a crucial role and are thought to be a driving force for carbohydrate binding. In this study we present data showing a novel finding in the stacking interaction of the AAL Trp side chain with the carbohydrate. High resolution X-ray structure of the AAL lectin from Aleuria aurantia with α-methyl-l-fucoside ligand shows two possible Trp side chain conformations with the same occupation in electron density. The in silico data shows that the conformation of the Trp side chain does not influence the interaction energy despite the fact that each conformation creates interactions with different carbohydrate CH groups. Moreover, the PDB data search shows that the conformations are almost equally distributed across all Trp-carbohydrate complexes, which would suggest no substantial preference for one conformation over another.


    Organizational Affiliation

    CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fucose-specific lectin
A
325Aleuria aurantiaMutation(s): 1 
Find proteins for P18891 (Aleuria aurantia)
Go to UniProtKB:  P18891
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
A
ALPHA-L-METHYL-FUCOSE
C7 H14 O5
OHWCAVRRXKJCRB-CXNFULCWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.138 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 132.250α = 90.00
b = 48.630β = 103.19
c = 57.580γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release