1kdd
From Proteopedia
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|PDB= 1kdd |SIZE=350|CAPTION= <scene name='initialview01'>1kdd</scene>, resolution 2.14Å | |PDB= 1kdd |SIZE=350|CAPTION= <scene name='initialview01'>1kdd</scene>, resolution 2.14Å | ||
|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]], [[1kd9|1KD9]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdd OCA], [http://www.ebi.ac.uk/pdbsum/1kdd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kdd RCSB]</span> | ||
}} | }} | ||
| Line 25: | Line 28: | ||
[[Category: Malashkevich, V N.]] | [[Category: Malashkevich, V N.]] | ||
[[Category: Tidor, B.]] | [[Category: Tidor, B.]] | ||
| - | [[Category: ACE]] | ||
[[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 21:46:57 2008'' |
Revision as of 18:46, 30 March 2008
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| , resolution 2.14Å | |||||||
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| Ligands: | |||||||
| Related: | 1KD8, 1KD9
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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-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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