1grm: Difference between revisions
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|PDB= 1grm |SIZE=350|CAPTION= <scene name='initialview01'>1grm</scene> | |PDB= 1grm |SIZE=350|CAPTION= <scene name='initialview01'>1grm</scene> | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=FOR:FORMYL GROUP'>FOR</scene> | |LIGAND= <scene name='pdbligand=ETA:ETHANOLAMINE'>ETA</scene>, <scene name='pdbligand=FOR:FORMYL+GROUP'>FOR</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1grm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1grm OCA], [http://www.ebi.ac.uk/pdbsum/1grm PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1grm RCSB]</span> | |||
}} | }} | ||
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[[Category: Lomize, A L.]] | [[Category: Lomize, A L.]] | ||
[[Category: Orekhov, V Y.]] | [[Category: Orekhov, V Y.]] | ||
[[Category: peptide antibiotic]] | [[Category: peptide antibiotic]] | ||
''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 20:49:53 2008'' | ||
Revision as of 20:49, 30 March 2008
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| Ligands: | , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN)
OverviewOverview
The spatial structure of the gramicidin A (GA) transmembrane ion-channel was refined on the base of cross-peak volumes measured in NOESY spectra (mixing time tau m = 100 and 200 ms). The refinement methods included the comparison of experimental cross-peak volumes with those calculated for low-energy GA conformations, dynamic averaging of the low-energy conformation set and restrained energy minimization. Accuracy of the spatial structure determination was estimated by the penalty function Fr defined as a root mean square deviation of interproton distances corresponding to the calculated and experimental cross-peak volumes. As the initial conformation we used the right-handed pi 6,3 LD pi 6,3 LD helix established on the base of NMR data regardless of the cross-peak volumes. The conformation is in a good agreement with NOE cross-peak volumes (Fr 0.2 to 0.5 A depending on NOESY spectrum). For a number of NOEs formed by the side chain protons, distances errors were found as much as 0.5-2.0 A. Restrained energy minimization procedure had little further success. However some of these errors were eliminated by the change in torsional angle chi 2 of D-Leu12 and dynamic averaging of the Val7 side chain conformations. Apparently, majority of deviations of the calculated and experimental cross-peak volumes are due to the intramolecular mobility of GA and cannot be eliminated within the framework of rigid globule model. In summary the spatial structure of GA ion-channel can be thought as a set of low-energy conformations, differing by the side chain torsion angles chi 1 Val7 and chi 2 D-Leu4 and D-Leu10 and the orientation of the C-terminal ethanolamine group. Root mean square differences between the atomic coordinates of conformations are in the range of 0.3-0.8 A.
About this StructureAbout this Structure
1GRM is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
[Refinement of the spatial structure of the gramicidin A ion channel], Lomize AL, Orekhov VIu, Arsen'ev AS, Bioorg Khim. 1992 Feb;18(2):182-200. PMID:1376600
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