9KAS | pdb_00009kas

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

• PDB DOI: https://doi.org/10.2210/pdb9KAS/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2024-10-29 Released: 2025-04-16 
• Deposition Author(s): Yu, X.T., Gao, Y.G., Lei, H.T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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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

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

• PubMed: 40173361 
• DOI: https://doi.org/10.1021/acs.jafc.5c00655
• Primary Citation 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.

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Organizational Affiliation: 
• Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China.
School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
Tropical Medicine Institute & South China Chinese Medicine Collaborative Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China.
College of Mathematics and Informatics, South China Agricultural University, Guangzhou 510642, China.
Wuzhou Institute for Food and Drug Control, Wuzhou 543099, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 55.55 kDa 
• Atom Count: 3,321 
• Modeled Residue Count: 431 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-sulfonylurea antibody scFv	A [auth B], B [auth A]	260	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EEY (Subject of Investigation/LOI)	C [auth B], D [auth A]	Chlorpropamide C10 H13 Cl N2 O3 S RKWGIWYCVPQPMF-UHFFFAOYSA-N

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 = 69.917	α = 90
b = 73.456	β = 90
c = 87.525	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Yu, X.T., Gao, Y.G., Lei, H.T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32472433

Revision History  

• 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