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1kd9

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[[Image:1kd9.jpg|left|200px]]
 
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==X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12La16L BASE-d12La16L==
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The line below this paragraph, containing "STRUCTURE_1kd9", creates the "Structure Box" on the page.
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<StructureSection load='1kd9' size='340' side='right'caption='[[1kd9]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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</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>
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<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>
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{{STRUCTURE_1kd9| PDB=1kd9 | SCENE= }}
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<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>
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</table>
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'''X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12La16L BASE-d12La16L'''
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==See Also==
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*[[Gcn4 3D Structures|Gcn4 3D Structures]]
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*[[Gnc4 3D Structures|Gnc4 3D Structures]]
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==Overview==
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__TOC__
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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.
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</StructureSection>
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[[Category: Large Structures]]
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==About this Structure==
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[[Category: Keating AE]]
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KD9 OCA].
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[[Category: Kim PS]]
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[[Category: Malashkevich VN]]
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==Reference==
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[[Category: Tidor B]]
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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]
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[[Category: Keating, A E.]]
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[[Category: Kim, P S.]]
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[[Category: Malashkevich, V N.]]
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[[Category: Tidor, B.]]
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[[Category: Coiled coil heterodimer]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 22:36:00 2008''
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Current revision

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

PDB ID 1kd9

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