4ESP | pdb_00004esp

Crystal Structure of Peanut Allergen Ara h 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 
    0.183 (Depositor), 0.168 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4ESP

This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Peanut ( Arachis hypogaea ) Allergen Ara h 5.

Wang, Y.Fu, T.J.Howard, A.Kothary, M.H.McHugh, T.H.Zhang, Y.

(2013) J Agric Food Chem 61: 1573-1578

  • DOI: https://doi.org/10.1021/jf303861p
  • Primary Citation Related Structures: 
    4ESP

  • PubMed Abstract: 

    Profilins from numerous species are known to be allergens, including food allergens, such as peanut ( Arachis hypogaea ) allergen Ara h 5, and pollen allergens, such as birch allergen Bet v 2. Patients with pollen allergy can also cross-react to peanut. Structural characterization of allergens will allow a better understanding of the allergenicity of food allergens and their cross-reactivities. The three-dimensional structures of most known food allergens remain to be elucidated. Here, we report the first crystallographic study of a food allergen in the profilin family. The structure of peanut allergen Ara h 5 was determined, and the resolution of the final refined structure was 1.1 Å. Structure alignment revealed that Ara h 5 is more similar to Bet v 2 than to Hev b 8, although sequence alignment suggested that Ara h 5 is more closely related to Hev b 8 than to Bet v 2, indicating that homology-model-based prediction of immunoglobulin E epitopes needs to be interpreted with caution.


  • Organizational Affiliation
    • Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, United States.

Macromolecule Content 

  • Total Structure Weight: 14.6 kDa 
  • Atom Count: 1,298 
  • Modeled Residue Count: 130 
  • Deposited Residue Count: 130 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Profilin130Arachis hypogaeaMutation(s): 0 
Gene Names: profilin
UniProt
Find proteins for D3K177 (Arachis hypogaea)
Explore D3K177 
Go to UniProtKB:  D3K177
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3K177
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO

Query on EDO



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA

Query on IPA



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free:  0.183 (Depositor), 0.168 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.574α = 90
b = 58.574β = 90
c = 101.717γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations