2ogn
From Proteopedia
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|PDB= 2ogn |SIZE=350|CAPTION= <scene name='initialview01'>2ogn</scene>, resolution 3.56Å | |PDB= 2ogn |SIZE=350|CAPTION= <scene name='initialview01'>2ogn</scene>, resolution 3.56Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=G80:(3AS,4R,5S,6S,8R,9R,9AR,10R)-5-HYDROXY-4,6,9,10-TETRAMETHYL-1-OXO-6-VINYLDECAHYDRO-3A,9-PROPANOCYCLOPENTA[8]ANNULEN-8-YL (PIPERIDIN-4-YLTHIO)ACETATE'>G80</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=G80:(3AS,4R,5S,6S,8R,9R,9AR,10R)-5-HYDROXY-4,6,9,10-TETRAMETHYL-1-OXO-6-VINYLDECAHYDRO-3A,9-PROPANOCYCLOPENTA[8]ANNULEN-8-YL+(PIPERIDIN-4-YLTHIO)ACETATE'>G80</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ogn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ogn OCA], [http://www.ebi.ac.uk/pdbsum/2ogn PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2ogn RCSB]</span> | ||
}} | }} | ||
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[[Category: Davidovich, C.]] | [[Category: Davidovich, C.]] | ||
[[Category: Yonath, A.]] | [[Category: Yonath, A.]] | ||
| - | [[Category: G80]] | ||
[[Category: antibiotic]] | [[Category: antibiotic]] | ||
[[Category: peptidyl transferase center]] | [[Category: peptidyl transferase center]] | ||
| Line 34: | Line 36: | ||
[[Category: sb-280080]] | [[Category: sb-280080]] | ||
| - | ''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 04:17:36 2008'' |
Revision as of 01:17, 31 March 2008
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| , resolution 3.56Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-280080
Overview
New insights into functional flexibility at the peptidyl transferase center (PTC) and its vicinity were obtained by analysis of pleuromutilins binding modes to the ribosome. The crystal structures of Deinococcus radiodurans large ribosomal subunit complexed with each of three pleuromutilin derivatives: retapamulin (SB-275833), SB-280080, and SB-571519, show that all bind to the PTC with their core oriented similarly at the A-site and their C14 extensions pointing toward the P-site. Except for an H-bond network with a single nucleotide, G2061, which involves the essential keto group of all three compounds, only minor hydrophobic contacts are formed between the pleuromutilin C14 extensions and any ribosomal component, consistent with the PTC tolerance to amino acid diversity. Efficient drug binding mode is attained by a mechanism based on induced-fit motions exploiting the ribosomal intrinsic functional flexibility and resulting in conformational rearrangements that seal the pleuromutilin-binding pocket and tightens it up. Comparative studies identified a network of remote interactions around the PTC, indicating that pleuromutilins selectivity is acquired by nonconserved nucleotides residing in the PTC vicinity, in a fashion resembling allosterism. Likewise, pleuromutilin resistant mechanisms involve nucleotides residing in the environs of the binding pocket, consistent with their slow resistance-development rates.
About this Structure
2OGN is a Single protein structure of sequence from Deinococcus radiodurans. Full crystallographic information is available from OCA.
Reference
Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity., Davidovich C, Bashan A, Auerbach-Nevo T, Yaggie RD, Gontarek RR, Yonath A, Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4291-6. Epub 2007 Mar 8. PMID:17360517
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