5ADO | pdb_00005ado

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

• PDB DOI: https://doi.org/10.2210/pdb5ADO/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Komagataella phaffii GS115
• Mutation(s): No 


• Deposited: 2015-08-21 Released: 2016-11-09 
• Deposition Author(s): Chatziefthimiou, S.D., Smirnov, I.V., Golovin, A.V., Stepanova, A.V., Peng, Y., Zolotareva, O.I., Belogurov, A.A., Ponomarenko, N.A., Blackburn, G.M., Gabibov, A.A., Lerner, R., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

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

• PubMed: 27774510 
• DOI: https://doi.org/10.1126/sciadv.1501695
• Primary Citation Related Structures: 
  5ADO, 5ADP


• 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 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.

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Organizational Affiliation: 
• 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.
European Molecular Biology Laboratory, Hamburg Unit, c/o German Synchrotron Research Center, Notkestrasse 85, 22603 Hamburg, Germany.
Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road MB-10, La Jolla, CA 92037, USA.
Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, U.K.
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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 54.22 kDa 
• Atom Count: 3,769 
• Modeled Residue Count: 424 
• Deposited Residue Count: 502 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB A.17	A [auth H]	255	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB A.17	B [auth L]	247	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DEP	C [auth L]	DIETHYL PHOSPHONATE C4 H11 O3 P MJUJXFBTEFXVKU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.661	α = 90
b = 67.075	β = 107.52
c = 66.698	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Chatziefthimiou, S.D., Smirnov, I.V., Golovin, A.V., Stepanova, A.V., Peng, Y., Zolotareva, O.I., Belogurov, A.A., Ponomarenko, N.A., Blackburn, G.M., Gabibov, A.A., Lerner, R., Wilmanns, M.

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2018-03-07
  Changes: Data collection, Source and taxonomy
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary