1kd8: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1kd8]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KD8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KD8 FirstGlance]. <br> | <table><tr><td colspan='2'>[[1kd8]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KD8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KD8 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> | ||
<tr id=' | <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=1kd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kd8 OCA], [https://pdbe.org/1kd8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kd8 RCSB], [https://www.ebi.ac.uk/pdbsum/1kd8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kd8 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=1kd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kd8 OCA], [https://pdbe.org/1kd8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kd8 RCSB], [https://www.ebi.ac.uk/pdbsum/1kd8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kd8 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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==See Also== | ==See Also== | ||
*[[Gcn4 3D Structures|Gcn4 3D Structures]] | |||
*[[Gnc4 3D Structures|Gnc4 3D Structures]] | *[[Gnc4 3D Structures|Gnc4 3D Structures]] | ||
== References == | == References == | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Keating | [[Category: Keating AE]] | ||
[[Category: Kim | [[Category: Kim PS]] | ||
[[Category: Malashkevich | [[Category: Malashkevich VN]] | ||
[[Category: Tidor | [[Category: Tidor B]] | ||
Latest revision as of 09:53, 30 October 2024
X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12Ia16V BASE-d12La16LX-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12Ia16V BASE-d12La16L
Structural highlights
Publication Abstract from PubMedAn 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 <1 kcal/mol, and nonhydrogen atoms in the predicted structures superimpose onto the experimental structures with rms deviations <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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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