5CP3

Crystal Structure of an Antigen-Binding Fragment of Monoclonal Antibody against Sulfonamides in Complex with Sulfathiazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Class-specific Monoclonal Antibodies and Dihydropteroate Synthase in Bioassays used for the Detection of Sulfonamides: Structural Insights into Recognition Diversity.

Li, C.Liang, X.Wen, K.Li, Y.Zhang, X.Ma, M.Yu, X.Yu, W.Shen, J.Wang, Z.

(2019) Anal. Chem. 91: 2392-2400

  • DOI: 10.1021/acs.analchem.8b05174
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Molecular recognition between a receptor and ligand is a fundamental event in bioanalytical assays, which guarantees the sensitivity and specificity of an assay for the detection of the target of interest. An intensive understanding of the interactio ...

    Molecular recognition between a receptor and ligand is a fundamental event in bioanalytical assays, which guarantees the sensitivity and specificity of an assay for the detection of the target of interest. An intensive understanding of the interaction mechanism could be useful for desirable hapten design, directed antibody evolution in vitro, and assay improvement. To illustrate the structural information on class-specific monoclonal antibodies (mAbs) and dihydropteroate synthase (DHPS) against sulfonamides (SAs) we have previously prepared, we initially measured the kinetic parameters of mAb 4C7, 4D11, and DHPS, which showed that the affinities of 4C7 and 4D11 were in the pM to μM range, while DHPS was uniformly in the μM range. Three-dimensional quantitative structure-activity relationship analysis for 4C7 and 4D11 then revealed that the contributions from the stereochemical structure and electron density of the SAs were comparable to binding with mAb. To acquire insights into the structural basis of mAbs and DHPS during the recognition process, the crystal structures of 4C7 and its complex with sulfathiazole were determined using X-ray crystallography. The results showed the SAs orientation and hydrogen bonding interactions mainly contributed to the diverse SAs-mAb affinities. However, for DHPS, a nucleophilic substitution reaction occurred during the recognition process with the SAs, which contributed to the surprisingly uniform affinity for all the SAs tested. This study verified the previous hypotheses on antibody production against SAs and enhanced our understanding of antibody-SAs interactions, which provided useful information toward the rational design of novel haptens and directed evolution to produce class-specific antibodies as DHPS.


    Organizational Affiliation

    Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine , China Agricultural University , 100193 Beijing , People's Republic of China.,Henan Animal Health Supervision Institute , 450008 Zhengzhou , People's Republic of China.,Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing Laboratory of Food Quality and Safety , Beijing Municipal Education Commission , 100193 Beijing , People's Republic of China.,College of Veterinary Medicine , Qingdao Agricultural University , 266109 Qingdao , People's Republic of China.,College of Food Science and Technology , Henan Agricultural University , 450002 Zhengzhou , People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Light Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7
A
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Heavy Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7
H
212N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 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
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
YTZ
Query on YTZ

Download SDF File 
Download CCD File 
A
4-amino-N-(1,3-thiazol-2-yl)benzenesulfonamide
Sulfathiazole
C9 H9 N3 O2 S2
JNMRHUJNCSQMMB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 126.624α = 90.00
b = 69.474β = 115.26
c = 62.009γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31372475

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2019-02-13
    Type: Data collection, Database references, Derived calculations