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1kd8

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(New page: 200px<br /><applet load="1kd8" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kd8, resolution 1.90&Aring;" /> '''X-RAY STRUCTURE OF T...)
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[[Image:1kd8.jpg|left|200px]]<br /><applet load="1kd8" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1kd8, resolution 1.90&Aring;" />
 
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'''X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12Ia16V BASE-d12La16L'''<br />
 
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==Overview==
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==X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12Ia16V BASE-d12La16L==
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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 load='1kd8' size='340' side='right'caption='[[1kd8]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<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>
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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]] 1.9&#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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<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>
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</table>
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==About this Structure==
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==See Also==
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1KD8 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with ACE as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KD8 OCA].
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*[[Gcn4 3D Structures|Gcn4 3D Structures]]
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*[[Gnc4 3D Structures|Gnc4 3D Structures]]
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==Reference==
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__TOC__
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=11752430 11752430]
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</StructureSection>
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Keating, A.E.]]
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[[Category: Keating AE]]
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[[Category: Kim, P.S.]]
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[[Category: Kim PS]]
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[[Category: Malashkevich, V.N.]]
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[[Category: Malashkevich VN]]
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[[Category: Tidor, B.]]
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[[Category: Tidor B]]
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[[Category: ACE]]
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[[Category: coiled coil heterodimer]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 01:10:05 2007''
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Current revision

X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12Ia16V BASE-d12La16L

PDB ID 1kd8

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