View source for 1kdd


==X-ray structure of the coiled coil GCN4 ACID BASE HETERODIMER ACID-d12La16I BASE-d12La16L==
<StructureSection load='1kdd' size='340' side='right'caption='[[1kdd]], [[Resolution|resolution]] 2.14&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1kdd]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KDD 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]] 2.14&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</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=1kdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdd OCA], [https://pdbe.org/1kdd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kdd RCSB], [https://www.ebi.ac.uk/pdbsum/1kdd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kdd ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
An important goal in biology is to predict from sequence data the high-resolution structures of proteins and the interactions that occur between them. In this paper, we describe a computational approach that can make these types of predictions for a series of coiled-coil dimers. Our method comprises a dual strategy that augments extensive conformational sampling with molecular mechanics minimization. To test the performance of the method, we designed six heterodimeric coiled coils with a range of stabilities and solved x-ray crystal structures for three of them. The stabilities and structures predicted by the calculations agree very well with experimental data: the average error in unfolding free energies is &lt;1 kcal/mol, and nonhydrogen atoms in the predicted structures superimpose onto the experimental structures with rms deviations &lt;0.7 A. We have also tested the method on a series of homodimers derived from vitellogenin-binding protein. The predicted relative stabilities of the homodimers show excellent agreement with previously published experimental measurements. A critical step in our procedure is to use energy minimization to relax side-chain geometries initially selected from a rotamer library. Our results show that computational methods can predict interaction specificities that are in good agreement with experimental data.

Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils.,Keating AE, Malashkevich VN, Tidor B, Kim PS Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):14825-30. PMID:11752430<ref>PMID:11752430</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1kdd" style="background-color:#fffaf0;"></div>

==See Also==
*[[Gcn4 3D Structures|Gcn4 3D Structures]]
*[[Gnc4 3D Structures|Gnc4 3D Structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Keating AE]]
[[Category: Kim PS]]
[[Category: Malashkevich VN]]
[[Category: Tidor B]]