9PZ5 | pdb_00009pz5

Native anti-NANP Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 
    0.256 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Single-residue engineering of lambda ( lambda ) antibody light chains reduces conformational flexibility and enhances thermal stability.

Jewel, Y.Young, T.Park, M.Ly, K.Gonzalez, A.Mallett, T.C.Williams, J.C.

(2025) Comput Struct Biotechnol J 27: 4730-4739

  • DOI: https://doi.org/10.1016/j.csbj.2025.10.045
  • Primary Citation of Related Structures:  
    9PZ5, 9PZ6, 9Q0P

  • PubMed Abstract: 

    Monoclonal antibodies with lambda (λ) light chains are less commonly used in therapeutics due to their lower biophysical stability compared to kappa (κ) variants. Here, we identify a conserved glycine residue (Gly111) in the λ light chain hinge as a driver of large-scale Fab elbow-angle transitions. Using microsecond-scale molecular dynamics simulations of the EBV-neutralizing Fab AMMO1, we show that substituting Gly111 with threonine (G111T) increases the free energy barrier between conformational states, effectively arresting these transitions. Structural and biophysical analyses-including crystallography, differential scanning fluorimetry, and surface plasmon resonance-confirm that the mutation maintains Fab architecture and antigen binding while increasing thermal stability by up to 2.5 °C. The same mutation applied to a second λ-Fab yielded similar stabilization, and simulations of three clinical λ-Fabs revealed consistent reductions in elbow-angle flexibility. These results demonstrate a generalizable, single-residue engineering strategy to enhance the stability of λ-based Fabs without compromising function, with direct implications for therapeutic antibody development and manufacturability.


  • Organizational Affiliation
    • Department of Cancer Biology and Molecular Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IgG heavy chainA [auth H]230Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IgG lambda light chainB [auth L]217Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free:  0.256 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.657α = 90
b = 72.785β = 90
c = 138.74γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2025-12-03 
  • Deposition Author(s): Young, T.

Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release