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2g5q

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|PDB= 2g5q |SIZE=350|CAPTION= <scene name='initialview01'>2g5q</scene>, resolution 2.700&Aring;
|PDB= 2g5q |SIZE=350|CAPTION= <scene name='initialview01'>2g5q</scene>, resolution 2.700&Aring;
|SITE=
|SITE=
-
|LIGAND= <scene name='pdbligand=AKN:(2R)-4-AMINO-N-{(1R,2S,3S,4R,5S)-5-AMINO-2-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-4-[(6-AMINO-6-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-3-HYDROXYCYCLOHEXYL}-2-HYDROXYBUTANAMIDE'>AKN</scene>
+
|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=AKN:(2R)-4-AMINO-N-{(1R,2S,3S,4R,5S)-5-AMINO-2-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-4-[(6-AMINO-6-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-3-HYDROXYCYCLOHEXYL}-2-HYDROXYBUTANAMIDE'>AKN</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
|ACTIVITY=
|ACTIVITY=
|GENE=
|GENE=
 +
|DOMAIN=
 +
|RELATEDENTRY=[[2g5k|2G5K]]
 +
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2g5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g5q OCA], [http://www.ebi.ac.uk/pdbsum/2g5q PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2g5q RCSB]</span>
}}
}}
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[[Category: Russell, R J.M.]]
[[Category: Russell, R J.M.]]
[[Category: Westhof, E.]]
[[Category: Westhof, E.]]
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[[Category: AKN]]
 
[[Category: amikacin]]
[[Category: amikacin]]
[[Category: aminoglycoside]]
[[Category: aminoglycoside]]
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[[Category: x-ray analysis]]
[[Category: x-ray analysis]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:00:44 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:12:11 2008''

Revision as of 00:12, 31 March 2008

Image:2g5q.gif


PDB ID 2g5q

Drag the structure with the mouse to rotate
, resolution 2.700Å
Ligands: , , , ,
Related: 2G5K


Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



Crystal structures of the bacterial ribosomal decoding site complexed with amikacin.


Overview

Amikacin is the 4,6-linked aminoglycoside modified at position N1 of the 2-deoxystreptamine ring (ring II) by the L-haba group. In the present study, the crystal structure of a complex between oligonucleotide containing the bacterial ribosomal A site and amikacin has been solved at 2.7 A resolution. Amikacin specifically binds to the A site in practically the same way as its parent compound kanamycin. In addition, the L-haba group interacts with the upper side of the A site through two direct contacts, O2*...H-N4(C1496) and N4*-H...O6(G1497). The present crystal structure shows how the introduction of the L-haba group on ring II of aminoglycoside is an effective mutation for obtaining a higher affinity to the bacterial A site.

About this Structure

2G5Q is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

Crystal structure of the bacterial ribosomal decoding site complexed with amikacin containing the gamma-amino-alpha-hydroxybutyryl (haba) group., Kondo J, Francois B, Russell RJ, Murray JB, Westhof E, Biochimie. 2006 Aug;88(8):1027-31. Epub 2006 Jun 13. PMID:16806634

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