2f4t: Difference between revisions
No edit summary |
No edit summary |
||
| Line 4: | Line 4: | ||
|PDB= 2f4t |SIZE=350|CAPTION= <scene name='initialview01'>2f4t</scene>, resolution 3.000Å | |PDB= 2f4t |SIZE=350|CAPTION= <scene name='initialview01'>2f4t</scene>, resolution 3.000Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=AB9:(2R)-4-AMINO-N-{(1R,2S,3R,4R,5S)-5-AMINO-2-{2-[(2-AMINOETHYL)AMINO]ETHOXY}-4-[(2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-3-HYDROXYCYCLOHEXYL}-2-HYDROXYBUTANAMIDE'>AB9</scene> | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=AB9:(2R)-4-AMINO-N-{(1R,2S,3R,4R,5S)-5-AMINO-2-{2-[(2-AMINOETHYL)AMINO]ETHOXY}-4-[(2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-3-HYDROXYCYCLOHEXYL}-2-HYDROXYBUTANAMIDE'>AB9</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> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY=[[2f4s|2F4S]], [[2f4u|2F4U]], [[2f4v|2F4V]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2f4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f4t OCA], [http://www.ebi.ac.uk/pdbsum/2f4t PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2f4t RCSB]</span> | |||
}} | }} | ||
| Line 27: | Line 30: | ||
[[Category: Murray, J B.]] | [[Category: Murray, J B.]] | ||
[[Category: Russell, R J.]] | [[Category: Russell, R J.]] | ||
[[Category: asite rna]] | [[Category: asite rna]] | ||
[[Category: designer antibiotic]] | [[Category: designer antibiotic]] | ||
''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 02:57:54 2008'' | ||
Revision as of 02:57, 31 March 2008
| |||||||
| , resolution 3.000Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Related: | 2F4S, 2F4U, 2F4V
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Asite RNA + designer antibiotic
OverviewOverview
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 StructureAbout this Structure
2F4T is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
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
Page seeded by OCA on Mon Mar 31 02:57:54 2008