1kd9: Difference between revisions
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|PDB= 1kd9 |SIZE=350|CAPTION= <scene name='initialview01'>1kd9</scene>, resolution 2.1Å | |PDB= 1kd9 |SIZE=350|CAPTION= <scene name='initialview01'>1kd9</scene>, resolution 2.1Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=ACE:ACETYL GROUP'>ACE</scene> | |LIGAND= <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1kd8|1KD8]], [[1kdd|1KDD]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kd9 OCA], [http://www.ebi.ac.uk/pdbsum/1kd9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kd9 RCSB]</span> | |||
}} | }} | ||
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[[Category: Malashkevich, V N.]] | [[Category: Malashkevich, V N.]] | ||
[[Category: Tidor, B.]] | [[Category: Tidor, B.]] | ||
[[Category: coiled coil heterodimer]] | [[Category: coiled coil heterodimer]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:46:54 2008'' | ||
Revision as of 21:46, 30 March 2008
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| , resolution 2.1Å | |||||||
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| Related: | 1KD8, 1KDD
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12La16L BASE-d12La16L
OverviewOverview
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 <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.
About this StructureAbout this Structure
1KD9 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
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
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