5ADO

Crystal structure of the paraoxon-modified A.17 antibody FAB fragment - Light chain S35R mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Robotic Qm/Mm-Driven Maturation of Antibody Combining Sites.

Smirnov, I.V.Golovin, A.V.Chatziefthimiou, S.D.Stepanova, A.V.Peng, Y.Zolotareva, O.I.Belogurov, A.A.Kurkova, I.N.Ponomarenko, N.A.Wilmanns, M.Blackburn, G.M.Gabibov, A.G.Lerner, R.A.

(2016) Sci.Adv. 2: 01695

  • DOI: 10.1126/sciadv.1501695
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In vitro selection of antibodies from large repertoires of immunoglobulin (Ig) combining sites using combinatorial libraries is a powerful tool, with great potential for generating in vivo scavengers for toxins. However, addition of a maturation func ...

    In vitro selection of antibodies from large repertoires of immunoglobulin (Ig) combining sites using combinatorial libraries is a powerful tool, with great potential for generating in vivo scavengers for toxins. However, addition of a maturation function is necessary to enable these selected antibodies to more closely mimic the full mammalian immune response. We approached this goal using quantum mechanics/molecular mechanics (QM/MM) calculations to achieve maturation in silico. We preselected A17, an Ig template, from a naïve library for its ability to disarm a toxic pesticide related to organophosphorus nerve agents. Virtual screening of 167,538 robotically generated mutants identified an optimum single point mutation, which experimentally boosted wild-type Ig scavenger performance by 170-fold. We validated the QM/MM predictions via kinetic analysis and crystal structures of mutant apo-A17 and covalently modified Ig, thereby identifying the displacement of one water molecule by an arginine as delivering this catalysis.


    Organizational Affiliation

    Lomonosov Moscow State University, Moscow 119991, Russian Federation.,European Molecular Biology Laboratory, Hamburg Unit, c/o German Synchrotron Research Center, Notkestrasse 85, 22603 Hamburg, Germany.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ulitsa Miklukho-Maklaya 16/10, 117997 Moscow V-437, Russian Federation.; Lomonosov Moscow State University, Moscow 119991, Russian Federation.,Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, U.K.,Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road MB-10, La Jolla, CA 92037, USA.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ulitsa Miklukho-Maklaya 16/10, 117997 Moscow V-437, Russian Federation.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FAB A.17
H
255N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FAB A.17
L
247N/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
DEP
Query on DEP

Download SDF File 
Download CCD File 
L
DIETHYL PHOSPHONATE
C4 H11 O3 P
MJUJXFBTEFXVKU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.661α = 90.00
b = 67.075β = 107.52
c = 66.698γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2018-03-07
    Type: Data collection, Source and taxonomy