Catalytic Antibodies

Ever since the discovery of catalytic activity in antibodies, researchers have tried to elicit specific catalysts by immunizing animals with transition-state analogs of the reaction to be catalyzed. A number of Fab fragments derived from monoclonal antibodies generated by this procedures, as well as a few engineered Fv fragments, have been successfully crystallized

PDB Files of Catalytic Antibodies:

15C8 1A0Q 1A3L 1A4J 1A4K 1AJ7 1AXS 1C1E 1C5B

1C5C 1CF8 1CT8 1D5B 1D5I 1D6V 1EAP 1F3D

1FIG 1GAF 1HKL 1HYX 1HYY 1KEL 1KEM 1KNO

1MIG 1YEC 1YED 1YEE 1YEF 1YEG 1YEH 1YEI

1YEJ 1YEK 25C8 2RCS 35C8 3FCT 43C9 43CA

(Follow these links to the structures in the PDB database)

Annotated sequence alignments of the VL and the VH domains of these antibodies shows which of the Fabs are related:

VL Sequences

VH Sequences

Antigen contact analysis reveals which residues are actually involved in Antigen contacts

VLAntigen Contacts

VH Antigen Contacts

Binding Modes of Different Antigens

Hapten Binders

Oligomer Binders

Protein Binders

Comparison of the different antibody-antigen complexes in the PDB database shows that the smaller the antigen molecule is, the deeper it has to bury in the antigen combining site to obtain a sufficient ly large interface area: Haptens usually insert into a deep binding pocket, while proteins show a relatively flat binding surface:

Superposition of Catalytic Antibody Structures

As this superposition of the catalytic antibody structures in the PDB shows, they are typical hapten complexes. The envelope of the superimposed ligands gives an idea of the maximal possible size of the binding pocket: A funnel-shaped cavity of about 20 Å diameter and a depth of about 20 Å, inserted along the axis of the VL/VH heterodimer.

Last Modified by A.Honegger Thursday, November 8, 2001