1kdd: Difference between revisions
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[[Image:1kdd.jpg|left|200px]] | [[Image:1kdd.jpg|left|200px]] | ||
'''X-ray structure of the coiled coil GCN4 ACID BASE HETERODIMER ACID-d12La16I BASE-d12La16L''' | {{Structure | ||
|PDB= 1kdd |SIZE=350|CAPTION= <scene name='initialview01'>1kdd</scene>, resolution 2.14Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=ACE:ACETYL GROUP'>ACE</scene> | |||
|ACTIVITY= | |||
|GENE= | |||
}} | |||
'''X-ray structure of the coiled coil GCN4 ACID BASE HETERODIMER ACID-d12La16I BASE-d12La16L''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1KDD is a [ | 1KDD is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KDD OCA]. | ||
==Reference== | ==Reference== | ||
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:// | 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] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Keating, A E.]] | [[Category: Keating, A E.]] | ||
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[[Category: coiled coil heterodimer]] | [[Category: coiled coil heterodimer]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:15:51 2008'' | ||
Revision as of 10:15, 20 March 2008
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| 1kdd, resolution 2.14Å | |||||||||||||
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| Ligands: | ACE | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
X-ray structure of the coiled coil GCN4 ACID BASE HETERODIMER ACID-d12La16I BASE-d12La16L
Overview
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 Structure
1KDD is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
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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