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1pz5

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Structural basis of peptide-carbohydrate mimicry in an antibody combining site

Structural highlights

1pz5 is a 3 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A2NHM3_MOUSE

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Vyas NK, Vyas MN, Chervenak MC, Bundle DR, Pinto BM, Quiocho FA. Structural basis of peptide-carbohydrate mimicry in an antibody-combining site. Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):15023-8. Epub 2003 Nov 25. PMID:14645714 doi:10.1073/pnas.2431286100

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1pz5"

@@ Line 3: / Line 3: @@
 <StructureSection load='1pz5' size='340' side='right'caption='[[1pz5]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1pz5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PZ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PZ5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1pz5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PZ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PZ5 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1m71|1m71]], [[1m7d|1m7d]], [[1m7i|1m7i]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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://pdbe.org/1pz5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pz5 RCSB], [http://www.ebi.ac.uk/pdbsum/1pz5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pz5 ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pz5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pz5 OCA], [https://pdbe.org/1pz5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pz5 RCSB], [https://www.ebi.ac.uk/pdbsum/1pz5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pz5 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A2NHM3_MOUSE A2NHM3_MOUSE]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 29: / Line 31: @@
 ==See Also==
 *[[Antibody 3D structures|Antibody 3D structures]]
+*[[3D structures of non-human antibody|3D structures of non-human antibody]]
 == References ==
 <references/>
@@ Line 35: / Line 38: @@
 [[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Bundle, D R]]
+[[Category: Bundle DR]]
-[[Category: Chervenak, M C]]
+[[Category: Chervenak MC]]
-[[Category: Pinto, B M]]
+[[Category: Pinto BM]]
-[[Category: Quiocho, F A]]
+[[Category: Quiocho FA]]
-[[Category: Vyas, M N]]
+[[Category: Vyas MN]]
-[[Category: Vyas, N K]]
+[[Category: Vyas NK]]
-[[Category: Antibody-antigen structure]]
-[[Category: Immune system]]
-[[Category: Peptide-carbohydrate mimicry]]
-[[Category: Vaccine design]]

1pz5

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Current revision

Structural basis of peptide-carbohydrate mimicry in an antibody combining site

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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