6BI2 | pdb_00006bi2

Trastuzumab Fab D185A (Light Chain) Mutant Biotin Conjugation.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.202 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BTNClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Tuning a Protein-Labeling Reaction to Achieve Highly Site Selective Lysine Conjugation.

Pham, G.H.Ou, W.Bursulaya, B.DiDonato, M.Herath, A.Jin, Y.Hao, X.Loren, J.Spraggon, G.Brock, A.Uno, T.Geierstanger, B.H.Cellitti, S.E.

(2018) Chembiochem 19: 799-804

  • DOI: https://doi.org/10.1002/cbic.201700611
  • Primary Citation of Related Structures:  
    6BHZ, 6BI0, 6BI2

  • PubMed Abstract: 

    Activated esters are widely used to label proteins at lysine side chains and N termini. These reagents are useful for labeling virtually any protein, but robust reactivity toward primary amines generally precludes site-selective modification. In a unique case, fluorophenyl esters are shown to preferentially label human kappa antibodies at a single lysine (Lys188) within the light-chain constant domain. Neighboring residues His189 and Asp151 contribute to the accelerated rate of labeling at Lys188 relative to the ≈40 other lysine sites. Enriched Lys188 labeling can be enhanced from 50-70 % to >95 % by any of these approaches: lowering reaction temperature, applying flow chemistry, or mutagenesis of specific residues in the surrounding protein environment. Our results demonstrated that activated esters with fluoro-substituted aromatic leaving groups, including a fluoronaphthyl ester, can be generally useful reagents for site-selective lysine labeling of antibodies and other immunoglobulin-type proteins.


  • Organizational Affiliation

    Genomics Institute of the Novartis Research Foundation (GNF), Biotherapeutics & Biotechnology, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trastuzumab Anti-HER2 Fab Heavy ChainA [auth H],
C [auth I]
225Homo 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
Trastuzumab Anti-HER2 Fab Light ChainB [auth L],
D [auth M]
214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BTN (Subject of Investigation/LOI)
Query on BTN

Download Ideal Coordinates CCD File 
G [auth L],
M
BIOTIN
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-ZKWXMUAHSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth H]
F [auth H]
H [auth L]
I [auth L]
J [auth I]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.202 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.646α = 109.8
b = 69.139β = 100.29
c = 91.471γ = 90.08
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BTNClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.2: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Structure summary