View source for 6wn7


==Homo sapiens S100A5==
<StructureSection load='6wn7' size='340' side='right'caption='[[6wn7]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6wn7]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WN7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WN7 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.25&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=6wn7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wn7 OCA], [https://pdbe.org/6wn7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wn7 RCSB], [https://www.ebi.ac.uk/pdbsum/6wn7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wn7 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/S10A5_HUMAN S10A5_HUMAN] Binds calcium, zinc and copper. One subunit can simultaneously bind 2 calcium ions or 2 copper ions plus 1 zinc ion. Calcium and copper ions compete for the same binding sites.<ref>PMID:10882717</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Many proteins interact with short linear regions of target proteins. For some proteins, however, it is difficult to identify a well-defined sequence motif that defines its target peptides. To overcome this difficulty, we used supervised machine learning to train a model that treats each peptide as a collection of easily-calculated biochemical features rather than as an amino acid sequence. As a test case, we dissected the peptide-recognition rules for human S100A5 (hA5), a low-specificity calcium binding protein. We trained a Random Forest model against a recently released, high-throughput phage display dataset collected for hA5. The model identifies hydrophobicity and shape complementarity, rather than polar contacts, as the primary determinants of peptide binding specificity in hA5. We tested this hypothesis by solving a crystal structure of hA5 and through computational docking studies of diverse peptides onto hA5. These structural studies revealed that peptides exhibit multiple binding modes at the hA5 peptide interface-all of which have few polar contacts with hA5. Finally, we used our trained model to predict new, plausible binding targets in the human proteome. This revealed a fragment of the protein alpha-1-syntrophin that binds to hA5. Our work helps better understand the biochemistry and biology of hA5, as well as demonstrating how high-throughput experiments coupled with machine learning of biochemical features can reveal the determinants of binding specificity in low-specificity proteins.

Learning peptide recognition rules for a low-specificity protein.,Wheeler LC, Perkins A, Wong CE, Harms MJ Protein Sci. 2020 Sep 26. doi: 10.1002/pro.3958. PMID:32979254<ref>PMID:32979254</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6wn7" style="background-color:#fffaf0;"></div>

==See Also==
*[[S100 proteins 3D structures|S100 proteins 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Harms MJ]]
[[Category: Perkins A]]
[[Category: Wheeler LC]]
[[Category: Wong CE]]