2XZC

Crystal Structure of phosphonate-modified recombinant A.17 antibody FAB fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Reactibodies Generated by Kinetic Selection Couple Chemical Reactivity with Favorable Protein Dynamics.

Smirnov, I.Carletti, E.Kurkova, I.Nachon, F.Nicolet, Y.Mitkevich, V.A.Debat, H.Avalle, B.Belogurov, A.A.Kuznetsov, N.Reshetnyak, A.Masson, P.Tonevitsky, A.G.Ponomarenko, N.Makarov, A.A.Friboulet, A.Tramontano, A.Gabibov, A.

(2011) Proc.Natl.Acad.Sci.USA 108: 15954

  • DOI: 10.1073/pnas.1108460108
  • Primary Citation of Related Structures:  2XZA

  • PubMed Abstract: 
  • Igs offer a versatile template for combinatorial and rational design approaches to the de novo creation of catalytically active proteins. We have used a covalent capture selection strategy to identify biocatalysts from within a human semisynthetic an ...

    Igs offer a versatile template for combinatorial and rational design approaches to the de novo creation of catalytically active proteins. We have used a covalent capture selection strategy to identify biocatalysts from within a human semisynthetic antibody variable fragment library that uses a nucleophilic mechanism. Specific phosphonylation at a single tyrosine within the variable light-chain framework was confirmed in a recombinant IgG construct. High-resolution crystallographic structures of unmodified and phosphonylated Fabs display a 15-Å-deep two-chamber cavity at the interface of variable light (V(L)) and variable heavy (V(H)) fragments having a nucleophilic tyrosine at the base of the site. The depth and structure of the pocket are atypical of antibodies in general but can be compared qualitatively with the catalytic site of cholinesterases. A structurally disordered heavy chain complementary determining region 3 loop, constituting a wall of the cleft, is stabilized after covalent modification by hydrogen bonding to the phosphonate tropinol moiety. These features and presteady state kinetics analysis indicate that an induced fit mechanism operates in this reaction. Mutations of residues located in this stabilized loop do not interfere with direct contacts to the organophosphate ligand but can interrogate second shell interactions, because the H3 loop has a conformation adjusted for binding. Kinetic and thermodynamic parameters along with computational docking support the active site model, including plasticity and simple catalytic components. Although relatively uncomplicated, this catalytic machinery displays both stereo- and chemical selectivity. The organophosphate pesticide paraoxon is hydrolyzed by covalent catalysis with rate-limiting dephosphorylation. This reactibody is, therefore, a kinetically selected protein template that has enzyme-like catalytic attributes.


    Organizational Affiliation

    Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow 117997, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FAB A.17 HEAVY CHAIN
H
222N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FAB A.17 LIGHT CHAIN
L
216N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
XOP
Query on XOP

Download SDF File 
Download CCD File 
L
8-METHYL-8-AZABICYCLO[3.2.1]OCTAN-3-YL PHENYLPHOSPHONATE
C14 H20 N O3 P
DUXLOXDDMDLSLH-ITGUQSILSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
H, L
L-PEPTIDE LINKINGC5 H7 N O3GLU
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XOPKd: 2300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.560α = 90.00
b = 66.950β = 107.65
c = 66.210γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-10-05
    Type: Database references