1pz5: Difference between revisions
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|RELATEDENTRY=[[1m71|1M71]], [[1m7d|1M7D]], [[1m7i|1M7I]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pz5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pz5 OCA], [http://www.ebi.ac.uk/pdbsum/1pz5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1pz5 RCSB]</span> | |||
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[[Category: vaccine design]] | [[Category: vaccine design]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:06:34 2008'' | ||
Revision as of 20:06, 30 March 2008
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| 1pz5, resolution 1.80Å | |||||||||||||
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| Related: | 1M71, 1M7D, 1M7I
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
Structural basis of peptide-carbohydrate mimicry in an antibody combining site
Overview
The structure of a complex between the Fab fragment of the antibody (SYA/J6) specific for the cell surface O-antigen polysaccharide of the pathogen Shigella flexneri Y and an octapeptide (Met-Asp-Trp-Asn-Met-His-Ala-Ala), a functional mimic of the O-antigen, has been determined at 1.8-A resolution. Comparison of the structure with that of the complex with the pentasaccharide antigen [-->2)-alpha-L-Rha-(1-->2)-alpha-L-Rha-(1-->3)-alpha-L-Rha-(1-->3)-beta-D- GlcNAc-(1-->2)-alpha-L-Rha-(1-->] reveals the molecular recognition process by which a peptide mimics a carbohydrate in binding to an antibody. The binding modes of the two ligands differ considerably. Octapeptide binding complements the shape of the combining site groove much better than pentasaccharide binding. Moreover, the peptide makes a much greater number of contacts (126), which are mostly van der Waals interactions, with the Fab than the saccharide (74). An unusual feature is also the involvement of 12 water molecules in mediating hydrogen bonds between residues within the peptide or of the peptide and Fab. Despite better shape complementarity and greater number of contacts, the octapeptide binds with an affinity (KA = 2.5 x 10(5) M-1, measured by calorimetry) only approximately 2-fold tighter than the pentasaccharide. The structural results are relevant to the design of peptide mimetics with improved affinity for use as vaccines.
About this Structure
1PZ5 is a Protein complex structure of sequences from Mus musculus. Full crystallographic information is available from OCA.
Reference
Structural basis of peptide-carbohydrate mimicry in an antibody-combining site., Vyas NK, Vyas MN, Chervenak MC, Bundle DR, Pinto BM, Quiocho FA, Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):15023-8. Epub 2003 Nov 25. PMID:14645714
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