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2g5q
From Proteopedia
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|PDB= 2g5q |SIZE=350|CAPTION= <scene name='initialview01'>2g5q</scene>, resolution 2.700Å | |PDB= 2g5q |SIZE=350|CAPTION= <scene name='initialview01'>2g5q</scene>, resolution 2.700Å | ||
|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'-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'-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=[[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.]] | ||
| - | [[Category: AKN]] | ||
[[Category: amikacin]] | [[Category: amikacin]] | ||
[[Category: aminoglycoside]] | [[Category: aminoglycoside]] | ||
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[[Category: x-ray analysis]] | [[Category: x-ray analysis]] | ||
| - | ''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 03:12:11 2008'' |
Revision as of 00:12, 31 March 2008
| |||||||
| , 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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