Introduction Numbering Sequences Structures Modelling Macros Publications Links
PDB Files Redundancy Structural Variability Accessibility Antigen Contacts Dimer Contacts Torsion Angles Hydrogen Bonds
Redundancy of Variable Domain PDB Files
For many of the antibodies in the PDB multible structures exist, e.g. crystals formed under different conditions were solved, because unliganded structures were compared to structures of antibodies complexed with different ligands, individual antibodies and antibody-anti-idotype antibody complexes or different constructs containing the same variable domains.
To identify these clusters of related variable domains, the GCG Pileup module was used to arrange the variable domain sequences according to sequence similarity. In the sequence lists linked to this page, variable domains with identical sequence are listed in the same row, sorted according to the resolution of the structure.
Comparison of these "redundant" structures can be valuable to get an idea of the conformational flexibility of the structure, and in particular of the conformational changes observed upon ligand binding or imposed by different crystal packing in different crystal forms
Vk - Domains
Alignment (620 K gif image)
Vl - Domains
Alignment (108 K gif image)
VH - Domains
Alignment (700 K gif image)
AAAAA Homepage Zürich University Dept. of Biochemistry Plückthun Group Annemarie Honegger

Last Modified by A.Honegger Wednesday, March 26, 2008