1oby

From Proteopedia

(Difference between revisions)

Revision as of 07:06, 7 February 2018

Crystal structure of the complex of PDZ2 of syntenin with a syndecan-4 peptide.

Structural highlights

1oby is a 4 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1nte, 1obx, 1obz, 1ejp, 1ejq
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SDC4_HUMAN] Cell surface proteoglycan that bears heparan sulfate.

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

Crystal structures of the PDZ2 domain of the scaffolding protein syntenin, both unbound and in complexes with peptides derived from C termini of IL5 receptor (alpha chain) and syndecan, reveal the molecular roots of syntenin's degenerate specificity. Three distinct binding sites (S(0), S(-1), and S(-2)), with affinities for hydrophobic side chains, function in a combinatorial way: S(-1) and S(-2) act together to bind syndecan, while S(0) and S(-1) are involved in the binding of IL5Ralpha. Neither mode of interaction is consistent with the prior classification scheme, which defined the IL5Ralpha interaction as class I (-S/T-X-phi) and the syndecan interaction as class II (-phi-X-phi). These results, in conjunction with other emerging structural data on PDZ domains, call for a revision of their classification and of the existing model of their mechanism.

Molecular roots of degenerate specificity in syntenin's PDZ2 domain: reassessment of the PDZ recognition paradigm.,Kang BS, Cooper DR, Devedjiev Y, Derewenda U, Derewenda ZS Structure. 2003 Jul;11(7):845-53. PMID:12842047^[1]

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

References

↑ Kang BS, Cooper DR, Devedjiev Y, Derewenda U, Derewenda ZS. Molecular roots of degenerate specificity in syntenin's PDZ2 domain: reassessment of the PDZ recognition paradigm. Structure. 2003 Jul;11(7):845-53. PMID:12842047

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
-==CRYSTAL STRUCTURE OF THE COMPLEX OF PDZ2 OF SYNTENIN WITH A SYNDECAN-4 PEPTIDE.==
+==Crystal structure of the complex of PDZ2 of syntenin with a syndecan-4 peptide.==
 <StructureSection load='1oby' size='340' side='right' caption='[[1oby]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1nte|1nte]], [[1obx|1obx]], [[1obz|1obz]], [[1ejp|1ejp]], [[1ejq|1ejq]]</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=1oby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oby OCA], [http://pdbe.org/1oby PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oby RCSB], [http://www.ebi.ac.uk/pdbsum/1oby PDBsum]</span></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=1oby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oby OCA], [http://pdbe.org/1oby PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oby RCSB], [http://www.ebi.ac.uk/pdbsum/1oby PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1oby ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 13: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ob/1oby_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ob/1oby_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1oby

From Proteopedia

Revision as of 07:06, 7 February 2018

Crystal structure of the complex of PDZ2 of syntenin with a syndecan-4 peptide.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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