1BYJ

GENTAMICIN C1A A-SITE COMPLEX


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 38 
  • Conformers Submitted: 38 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural origins of gentamicin antibiotic action.

Yoshizawa, S.Fourmy, D.Puglisi, J.D.

(1998) EMBO J. 17: 6437-6448

  • DOI: 10.1093/emboj/17.22.6437

  • PubMed Abstract: 
  • Aminoglycoside antibiotics that bind to the ribosomal A site cause misreading of the genetic code and inhibit translocation. The clinically important aminoglycoside, gentamicin C, is a mixture of three components. Binding of each gentamicin component ...

    Aminoglycoside antibiotics that bind to the ribosomal A site cause misreading of the genetic code and inhibit translocation. The clinically important aminoglycoside, gentamicin C, is a mixture of three components. Binding of each gentamicin component to the ribosome and to a model RNA oligonucleotide was studied biochemically and the structure of the RNA complexed to gentamicin C1a was solved using magnetic resonance nuclear spectroscopy. Gentamicin C1a binds in the major groove of the RNA. Rings I and II of gentamicin direct specific RNA-drug interactions. Ring III of gentamicin, which distinguishes this subclass of aminoglycosides, also directs specific RNA interactions with conserved base pairs. The structure leads to a general model for specific ribosome recognition by aminoglycoside antibiotics and a possible mechanism for translational inhibition and miscoding. This study provides a structural rationale for chemical synthesis of novel aminoglycosides.


    Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5400, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (16S RNA)A27N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GE1
Query on GE1

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Download CCD File 
A
3,4-DIDEOXY-2,6-AMINO-ALPHA-D GALACTOPYRANOSE
C6 H14 N2 O2
FGFITZOBEYBNGG-JKUQZMGJSA-N
 Ligand Interaction
GE2
Query on GE2

Download SDF File 
Download CCD File 
A
3,5-DIAMINO-CYCLOHEXANOL
C6 H14 N2 O
ORKQZIAHTZABIG-FPFOFBBKSA-N
 Ligand Interaction
GE3
Query on GE3

Download SDF File 
Download CCD File 
A
5-METHYL-4-METHYLAMINO-TETRAHYDRO-PYRAN-2,3,5-TRIOL
C7 H15 N O4
VXWORWYFOFDZLY-JWXFUTCRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GE1Kd: 2000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 38 
  • Conformers Submitted: 38 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance