4S1D

Structure of IgG1 Fab fragment in complex with Biotincytidinamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Hapten-directed spontaneous disulfide shuffling: a universal technology for site-directed covalent coupling of payloads to antibodies.

Dengl, S.Hoffmann, E.Grote, M.Wagner, C.Mundigl, O.Georges, G.Thorey, I.Stubenrauch, K.G.Bujotzek, A.Josel, H.P.Dziadek, S.Benz, J.Brinkmann, U.

(2015) Faseb J. 29: 1763-1779

  • DOI: 10.1096/fj.14-263665

  • PubMed Abstract: 
  • Humanized hapten-binding IgGs were designed with an accessible cysteine close to their binding pockets, for specific covalent payload attachment. Individual analyses of known structures of digoxigenin (Dig)- and fluorescein (Fluo) binding antibodies ...

    Humanized hapten-binding IgGs were designed with an accessible cysteine close to their binding pockets, for specific covalent payload attachment. Individual analyses of known structures of digoxigenin (Dig)- and fluorescein (Fluo) binding antibodies and a new structure of a biotin (Biot)-binder, revealed a "universal" coupling position (52(+2)) in proximity to binding pockets but without contributing to hapten interactions. Payloads that carry a free thiol are positioned on the antibody and covalently linked to it via disulfides. Covalent coupling is achieved and driven toward complete (95-100%) payload occupancy by spontaneous redox shuffling between antibody and payload. Attachment at the universal position works with different haptens, antibodies, and payloads. Examples are the haptens Fluo, Dig, and Biot combined with various fluorescent or peptidic payloads. Disulfide-bonded covalent antibody-payload complexes do not dissociate in vitro and in vivo. Coupling requires the designed cysteine and matching payload thiol because payload or antibody without the Cys/thiol are not linked (<5% nonspecific coupling). Hapten-mediated positioning is necessary as hapten-thiol-payload is only coupled to antibodies that bind matching haptens. Covalent complexes are more stable in vivo than noncovalent counterparts because digoxigeninylated or biotinylated fluorescent payloads without disulfide-linkage are cleared more rapidly in mice (approximately 50% reduced 48 hour serum levels) compared with their covalently linked counterparts. The coupling technology is applicable to many haptens and hapten binding antibodies (confirmed by automated analyses of the structures of 140 additional hapten binding antibodies) and can be applied to modulate the pharmacokinetics of small compounds or peptides. It is also suitable to link payloads in a reduction-releasable manner to tumor- or tissue-targeting delivery vehicles.


    Organizational Affiliation

    *Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany; Roche Diagnostics GmbH, Penzberg, Germany; and Roche Discovery Technologies, Roche Innovation Center Basel, Basel, Switzerland ulrich.brinkmann@roche.com stefan.dengl@roche.com eike.hoffmann@roche.com.,*Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany; Roche Diagnostics GmbH, Penzberg, Germany; and Roche Discovery Technologies, Roche Innovation Center Basel, Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MAB M33 FAB FRAGMENT, heavy chain
H, C, E, O
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MAB M33 FAB FRAGMENT, light chain
L, D, F, P
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
O
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
41M
Query on 41M

Download SDF File 
Download CCD File 
D, E, H, P
N~6~-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}-L-lysinamide
N-epsilon-Biotinyl-lysine-amid
C16 H29 N5 O3 S
BFTIPPVTTJTHLM-MNXVOIDGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 89.094α = 90.00
b = 119.620β = 117.15
c = 96.181γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
DA+data collection
XDSdata reduction
SADABSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-05-13
    Type: Database references