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) 
  • R-Value Work: 
    0.166 (Depositor) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6BI2

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 95.74 kDa 
  • Atom Count: 7,536 
  • Modeled Residue Count: 861 
  • Deposited Residue Count: 878 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Trastuzumab Anti-HER2 Fab Heavy ChainA [auth H],
C [auth I]
225Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Trastuzumab Anti-HER2 Fab Light ChainB [auth L],
D [auth M]
214Homo sapiensMutation(s): 0 

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]
E [auth H],
F [auth H],
H [auth L],
I [auth L],
J [auth I],
K [auth I],
L [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) 
  • R-Value Work:  0.166 (Depositor) 
  • 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

View Full Validation Report



Ligand Structure Quality Assessment 


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