4GQP

Structure based design of sub-nanomolar affinity anti-methamphetamine single chain antibodies.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Affinity improvement of a therapeutic antibody to methamphetamine and amphetamine through structure-based antibody engineering.

Thakkar, S.Nanaware-Kharade, N.Celikel, R.Peterson, E.C.Varughese, K.I.

(2014) Sci Rep 4: 3673-3673

  • DOI: 10.1038/srep03673

  • PubMed Abstract: 
  • Methamphetamine (METH) abuse is a worldwide threat, without any FDA approved medications. Anti-METH IgGs and single chain fragments (scFvs) have shown efficacy in preclinical studies. Here we report affinity enhancement of an anti-METH scFv for METH ...

    Methamphetamine (METH) abuse is a worldwide threat, without any FDA approved medications. Anti-METH IgGs and single chain fragments (scFvs) have shown efficacy in preclinical studies. Here we report affinity enhancement of an anti-METH scFv for METH and its active metabolite amphetamine (AMP), through the introduction of point mutations, rationally designed to optimize the shape and hydrophobicity of the antibody binding pocket. The binding affinity was measured using saturation binding technique. The mutant scFv-S93T showed 3.1 fold enhancement in affinity for METH and 26 fold for AMP. The scFv-I37M and scFv-Y34M mutants showed enhancement of 94, and 8 fold for AMP, respectively. Structural analysis of scFv-S93T:METH revealed that the substitution of Ser residue by Thr caused the expulsion of a water molecule from the cavity, creating a more hydrophobic environment for the binding that dramatically increases the affinities for METH and AMP.


    Organizational Affiliation

    Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Anti-METH scFv
H
249N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B40
Query on B40

Download SDF File 
Download CCD File 
H
(2S)-N-methyl-1-phenylpropan-2-amine
Methamphetamine
C10 H15 N
MYWUZJCMWCOHBA-VIFPVBQESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B40Kd: 0.79 nM BINDINGMOAD
B40Kd: 0.25 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 34.516α = 90.00
b = 65.265β = 98.20
c = 48.483γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
HKL-2000data scaling
HKL-2000data collection
CCP4model building
HKL-2000data reduction
REFMACrefinement
CCP4phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Database references
  • Version 1.2: 2018-05-02
    Type: Data collection