5L2H

Crystal Structure of W26A mutant of anti-EGFR Centyrin P54AR4-83v2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Engineering a targeted delivery platform using Centyrins.

Goldberg, S.D.Cardoso, R.M.Lin, T.Spinka-Doms, T.Klein, D.Jacobs, S.A.Dudkin, V.Gilliland, G.O'Neil, K.T.

(2016) Protein Eng Des Sel 29: 563-572

  • DOI: https://doi.org/10.1093/protein/gzw054
  • Primary Citation of Related Structures:  
    5L2H

  • PubMed Abstract: 

    Targeted delivery of therapeutic payloads to specific tissues and cell types is an important component of modern pharmaceutical development. Antibodies or other scaffold proteins can provide the cellular address for delivering a covalently linked therapeutic via specific binding to cell-surface receptors. Optimization of the conjugation site on the targeting protein, linker chemistry and intracellular trafficking pathways can all influence the efficiency of delivery and potency of the drug candidate. In this study, we describe a comprehensive engineering experiment for an EGFR binding Centyrin, a highly stable fibronectin type III (FN3) domain, wherein all possible single-cysteine replacements were evaluated for expression, purification, conjugation efficiency, retention of target binding, biophysical properties and delivery of a cytotoxic small molecule payload. Overall, 26 of the 94 positions were identified as ideal for cysteine modification, conjugation and drug delivery. Conjugation-tolerant positions were mapped onto a crystal structure of the Centyrin, providing a structural context for interpretation of the mutagenesis experiment and providing a foundation for a Centyrin-targeted delivery platform.


  • Organizational Affiliation

    Janssen Research and Development, L.L.C., 1400 McKean Road, Spring House, PA 19477, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Centyrin
A, B, C, D
103synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.35α = 90
b = 61.709β = 100.41
c = 59.515γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Database references
  • Version 1.2: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references