Framework 1CDR 1Framework 2CDR 2Framework 3aFramework 3bCDR 3Framework 4

The Complementarity Determining Region 2

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Residues 51-82

The gap correcting for the length variability in the CDR 2 region has been placed to be centered on position 63, resulting in an 8-residue gap in the VL domains (L59-L66, placed between L50 and L51 according to Kabat nomenclature) and a one- to four-residue gap in VH domains (between H52 and H53 according to Kabat).

In Va domains, a second gap has been placed in positions A74 and A75 to reflect the way in which the C-terminal branch of the CDR A2 loop is retracted from the dimer interface compared to the CDR 2 of other immunoglobulin variable domains. While in all other variable domains the descending branch of CDR 2 is part of the "inner" b-sheet (the one which forms the dimer interface), the descending branch of the Va CDR 2 (residues 67-73) is more closely associated with the "outer" b-sheet, although the hydrogen bonds to the strand formed by residues 78-82 are not very well conserved in the few Va -structures known. Again, like in the CDR 1, this splitting of the CDR 2 length variability into two insertion points necessitates more positions than allowed for in the IMGT nomenclature.

AAAAA Homepage Zürich University Dept. of Biochemistry Plückthun Group Annemarie Honegger

Last Modified by A.Honegger Friday, January 28, 2005