2f4s
From Proteopedia
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|PDB= 2f4s |SIZE=350|CAPTION= <scene name='initialview01'>2f4s</scene>, resolution 2.800Å | |PDB= 2f4s |SIZE=350|CAPTION= <scene name='initialview01'>2f4s</scene>, resolution 2.800Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=XXX:(2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-3,4-DIOL'>XXX</scene> | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>, <scene name='pdbligand=XXX:(2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-3,4-DIOL'>XXX</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2f4t|2F4T]], [[2f4u|2F4U]], [[2f4v|2F4V]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2f4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f4s OCA], [http://www.ebi.ac.uk/pdbsum/2f4s PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2f4s RCSB]</span> | ||
}} | }} | ||
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[[Category: Murray, J B.]] | [[Category: Murray, J B.]] | ||
[[Category: Russell, R J.]] | [[Category: Russell, R J.]] | ||
| - | [[Category: XXX]] | ||
[[Category: a-site rna]] | [[Category: a-site rna]] | ||
[[Category: neamine]] | [[Category: neamine]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:57:56 2008'' |
Revision as of 23:57, 30 March 2008
| |||||||
| , resolution 2.800Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Related: | 2F4T, 2F4U, 2F4V
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
A-site RNA in complex with neamine
Overview
The X-ray crystal structures for the complexes of three designer antibiotics, compounds 1, 2, and 3, bound to two models for the ribosomal aminoacyl-tRNA site (A site) at 2.5-3.0 Angstroms resolution and that of neamine at 2.8 Angstroms resolution are described. Furthermore, the complex of antibiotic 1 bound to the A site in the entire 30S ribosomal subunit of Thermus thermophilus is reported at 3.8 Angstroms resolution. Molecular dynamics simulations revealed that the designer compounds provide additional stability to bases A1492 and A1493 in their extrahelical forms. Snapshots from the simulations were used for free energy calculations, which revealed that van der Waals and hydrophobic effects were the driving forces behind the binding of designer antibiotic 3 when compared to the parental neamine.
About this Structure
2F4S is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site., Murray JB, Meroueh SO, Russell RJ, Lentzen G, Haddad J, Mobashery S, Chem Biol. 2006 Feb;13(2):129-38. PMID:16492561
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