9KAS | pdb_00009kas

Crystal structure of anti-sulfonylurea antibody scFv in complex with chlorpropamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.261 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure Profiling of Broad-Specificity Immunoassays: Multitarget Recognition for Sulfonylurea Adulteration in Food.

Yu, X.Zhou, T.Pan, K.Fan, M.H.Yan, X.Huang, X.A.Zhang, H.Shen, X.Xie, H.Gao, Y.G.Lei, H.

(2025) J Agric Food Chem 73: 9348-9358

  • DOI: https://doi.org/10.1021/acs.jafc.5c00655
  • Primary Citation of Related Structures:  
    9KAS, 9KAT

  • PubMed Abstract: 

    The limited understanding of the broad-specific antibody recognition mechanism significantly hinders the development of immunoassays for simultaneously detecting illegal adulterants. Herein, a recombinant antisulfonylureas (SUs) single-chain variable fragment (scFv), which retained the properties of its parental monoclonal antibody, was successfully generated. X-ray crystallography, molecular docking, functional assays, and mutation validation were used to investigate the structure-function relationships underlying antibody-SUs binding. Our study revealed three key mechanisms for broad specificity: (1) the conformational adaptability of the scFv, which enabled various SUs to access the binding pocket; (2) the role of the Trp98 residue in CDR-L3 in modulating binding affinities among multiple SUs; and (3) the design of haptens with common structures and more rigid R substituents, which emerged as a promising strategy for generating broad-specific antibodies. This study provides a comprehensive analysis of the broad-specific recognition mechanism, offering valuable insights for rational hapten design and targeted antibody evolution to advance multitarget immunoassays.


  • Organizational Affiliation
    • Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
anti-sulfonylurea antibody scFvA [auth B],
B [auth A]
260Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.261 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.917α = 90
b = 73.456β = 90
c = 87.525γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32472433

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Database references
  • Version 1.2: 2025-11-19
    Changes: Derived calculations, Structure summary