7TUS | pdb_00007tus

Sculpting a uniquely reactive cysteine residue for site-specific antibody conjugation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.257 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Sculpting a Uniquely Reactive Cysteine Residue for Site-Specific Antibody Conjugation.

Hwang, D.Nilchan, N.Park, H.Roy, R.N.Roush, W.R.Rader, C.

(2022) Bioconjug Chem 33: 1192-1200

  • DOI: https://doi.org/10.1021/acs.bioconjchem.2c00146
  • Primary Citation Related Structures: 
    7TUS

  • PubMed Abstract: 

    Catalytic antibody 38C2 and its humanized version h38C2 harbor a uniquely reactive lysine at the bottom of a 11 Å deep pocket that permits site-specific conjugation of β-diketone-, β-lactam-, and heteroaryl methylsulfonyl-functionalized small and large molecules. Various dual variable domain formats pair a tumor-targeting antibody with h38C2 to enable precise, fast, and stable assembly of antibody-drug conjugates (ADCs). Here, we expand the scope of this ADC assembly strategy by mutating h38C2's reactive lysine to a cysteine. X-ray crystallography of this point mutant, h38C2_K99C, confirmed a deeply buried unpaired cysteine. Probing h38C2_K99C with maleimide, monobromomaleimide, and dibromomaleimide derivatives of a fluorophore revealed highly disparate conjugation efficiencies and stabilities. Dibromomaleimide emerged as a suitable electrophile for the precise, fast, efficient, and stable assembly of ADCs with the h38C2_K99C module. Mass spectrometry indicated the presence of a thio-monobromomaleimide linkage which was further supported by in silico docking studies. Using a dibromomaleimide derivative of the highly potent tubulin polymerization inhibitor monomethyl auristatin F, h38C2_K99C-based ADCs were found to be as potent as h38C2-based ADCs and afford a new assembly route for ADCs with single and dual payloads.


  • Organizational Affiliation
    • Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, United States.

Macromolecule Content 

  • Total Structure Weight: 192.96 kDa 
  • Atom Count: 13,140 
  • Modeled Residue Count: 1,722 
  • Deposited Residue Count: 1,760 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody Heavy Chain
A, C, E, G
221Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody Light Chain
B, D, F, H
219Homo sapiensMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG



Download:Ideal Coordinates CCD File
I [auth A]
N [auth C]
P [auth D]
Q [auth E]
S [auth G]
I [auth A],
N [auth C],
P [auth D],
Q [auth E],
S [auth G],
T [auth G]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
J [auth A]
K [auth A]
L [auth A]
O [auth C]
R [auth E]
J [auth A],
K [auth A],
L [auth A],
O [auth C],
R [auth E],
U [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG

Query on MG



Download:Ideal Coordinates CCD File
M [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.257 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.469α = 90
b = 73.57β = 110.06
c = 127.58γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary