1kd9: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1kd9]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KD9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KD9 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1kd9]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KD9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KD9 FirstGlance]. <br>
</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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#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=1kd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kd9 OCA], [https://pdbe.org/1kd9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kd9 RCSB], [https://www.ebi.ac.uk/pdbsum/1kd9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kd9 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=1kd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kd9 OCA], [https://pdbe.org/1kd9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kd9 RCSB], [https://www.ebi.ac.uk/pdbsum/1kd9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kd9 ProSAT]</span></td></tr>
</table>
</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 1kd9" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Gcn4 3D Structures|Gcn4 3D Structures]]
*[[Gnc4 3D Structures|Gnc4 3D Structures]]
*[[Gnc4 3D Structures|Gnc4 3D Structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>

Revision as of 09:05, 3 April 2024

X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12La16L BASE-d12La16LX-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12La16L BASE-d12La16L

Structural highlights

1kd9 is a 6 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

1kd9, resolution 2.10Å

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