7Y0G

Crystal structure of anti-mPEG h15-2b Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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This is version 1.2 of the entry. See complete history


Literature

Structural determination of an antibody that specifically recognizes polyethylene glycol with a terminal methoxy group.

Nguyen, M.T.Shih, Y.C.Lin, M.H.Roffler, S.R.Hsiao, C.Y.Cheng, T.L.Lin, W.W.Lin, E.C.Jong, Y.J.Chang, C.Y.Su, Y.C.

(2022) Commun Chem 5: 88-88

  • DOI: https://doi.org/10.1038/s42004-022-00709-0
  • Primary Citation of Related Structures:  
    7Y0G

  • PubMed Abstract: 

    Covalent attachment of methoxy poly(ethylene) glycol (mPEG) to therapeutic molecules is widely employed to improve their systemic circulation time and therapeutic efficacy. mPEG, however, can induce anti-PEG antibodies that negatively impact drug therapeutic effects. However, the underlying mechanism for specific binding of antibodies to mPEG remains unclear. Here, we determined the first co-crystal structure of the humanized 15-2b anti-mPEG antibody in complex with mPEG, which possesses a deep pocket in the antigen-binding site to accommodate the mPEG polymer. Structural and mutational analyses revealed that mPEG binds to h15-2b via Van der Waals and hydrogen bond interactions, whereas the methoxy group of mPEG is stabilized in a hydrophobic environment between the V H :V L interface. Replacement of the heavy chain hydrophobic V37 residue with a neutral polar serine or threonine residue offers additional hydrogen bond interactions with methoxyl and hydroxyl groups, resulting in cross-reactivity to mPEG and OH-PEG. Our findings provide insights into understanding mPEG-binding specificity and antigenicity of anti-mPEG antibodies.


  • Organizational Affiliation

    Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS²B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
15-2b light chainA,
C [auth D],
E [auth G],
G [auth J]
214Homo sapiensMutation(s): 0 
Entity Groups  
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
15-2b heavy chainB,
D [auth E],
F [auth H],
H [auth K]
229Homo 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: 2.08 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.994α = 90
b = 112.285β = 90.58
c = 158.73γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)TaiwanMOST109-2636-B-009-003
Ministry of Science and Technology (MoST, Taiwan)Taiwan110-2113-M-A49-026-MY3

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-05-08
    Changes: Database references