6V8H | pdb_00006v8h

Crystal structure of Ara h 8.0201


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 
    0.268 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.227 (Depositor) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Structural analysis of 8-anilino-1-naphthalene sulfonate (ANS) binding to the PR-10 allergen Ara h 8.

O'Malley, A.Offermann, L.R.Khatri, K.Linn, C.Pote, S.McBride, J.K.Perdue, M.L.Hurlburt, B.K.Maleki, S.J.Mias, G.I.Chruszcz, M.

(2025) Biochem Biophys Res Commun 793: 153013-153013

  • DOI: https://doi.org/10.1016/j.bbrc.2025.153013
  • Primary Citation Related Structures: 
    6AWR, 6V8H, 6V8J, 6V8M, 6V8S

  • PubMed Abstract: 

    We previously determined crystal structures of peanut allergen Ara h 8.0101 in the apo form as well as in complex with model ligands. These structures illustrated the varied ligand binding capabilities of PR-10s and Ara h 8's structural similarity to the major birch allergen Bet v 1. Here, we expanded on those structural studies with structures of Ara h 8.0101 and Ara h 8.0201 in complex with 8-anilino-1-naphthalene sulfonate (ANS), as well as the apo form of Ara h 8.0201. Structural studies revealed that both proteins may bind more than one ANS molecule. We also examined the impact of ANS on the ligand binding cavities of Ara h 8.0101 and Ara h 8.0201 with fluorescence assays and compared the results to prototypic PR-10 Bet v 1.0101. Moreover, as ANS is often used in fluorescence-based ligand binding assays, we analyzed structures from the PDB and provided a summary on experimentally determined ANS binding sites. These analyses show that ANS is useful for investigation of ligand binding sites, but it may also participate in non-specific reactions on nonpolar surfaces of proteins.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.

Macromolecule Content 

  • Total Structure Weight: 131.65 kDa 
  • Atom Count: 9,326 
  • Modeled Residue Count: 1,214 
  • Deposited Residue Count: 1,224 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ara h 8 allergen isoform153Arachis hypogaeaMutation(s): 0 
Gene Names: Ahy_Scaffold6g108211
UniProt
Find proteins for B0YIU5 (Arachis hypogaea)
Explore B0YIU5 
Go to UniProtKB:  B0YIU5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0YIU5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free:  0.268 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.227 (Depositor) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.997α = 90
b = 111.275β = 93.7
c = 80.021γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2025-12-03
    Changes: Database references, Structure summary