1kd8: Difference between revisions

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-[[Image:1kd8.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1kd8", creates the "Structure Box" on the page.
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-{{STRUCTURE_1kd8|  PDB=1kd8  |  SCENE=  }}
-'''X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12Ia16V BASE-d12La16L'''
+==X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12Ia16V BASE-d12La16L==
+<StructureSection load='1kd8' size='340' side='right'caption='[[1kd8]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== 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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#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=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>
+<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.
-==Overview==
+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>
-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.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KD8 OCA].
+</div>
+<div class="pdbe-citations 1kd8" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/11752430 11752430]
+*[[Gcn4 3D Structures|Gcn4 3D Structures]]
-[[Category: Keating, A E.]]
+*[[Gnc4 3D Structures|Gnc4 3D Structures]]
-[[Category: Kim, P S.]]
+== References ==
-[[Category: Malashkevich, V N.]]
+<references/>
-[[Category: Tidor, B.]]
+__TOC__
-[[Category: Coiled coil heterodimer]]
+</StructureSection>
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 22:35:56 2008''
+[[Category: Large Structures]]
+[[Category: Keating AE]]
+[[Category: Kim PS]]
+[[Category: Malashkevich VN]]
+[[Category: Tidor B]]