2TOB

SOLUTION STRUCTURE OF THE TOBRAMYCIN-RNA APTAMER COMPLEX, NMR, 13 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 13 
  • Selection Criteria: LOWEST NOE AND TOTAL ENERGY 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of the tobramycin-RNA aptamer complex.

Jiang, L.Patel, D.J.

(1998) Nat.Struct.Mol.Biol. 5: 769-774

  • DOI: 10.1038/1804

  • PubMed Abstract: 
  • We have solved the solution structure of the aminoglycoside antibiotic tobramycin complexed with a stem-loop RNA aptamer. The 14 base loop of the RNA aptamer 'zippers up' alongside the attached stem through alignment of four mismatches and one Watson ...

    We have solved the solution structure of the aminoglycoside antibiotic tobramycin complexed with a stem-loop RNA aptamer. The 14 base loop of the RNA aptamer 'zippers up' alongside the attached stem through alignment of four mismatches and one Watson-Crick pair on complex formation. The tobramycin inserts into the deep groove centered about the mismatch pairs and is partially encapsulated between its floor and a looped out guanine base that flaps over the bound antibiotic. Several potential intermolecular hydrogen bonds between the charged NH3 groups of tobramycin and acceptor atoms on base pair edges and backbone phosphates anchor the aminoglycoside antibiotic within its sequence/structure specific RNA binding pocket.


    Organizational Affiliation

    Cellular Biochemistry & Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*CP*UP*UP*GP*GP*UP*UP*UP*AP*GP*GP*UP*AP*AP*UP*GP*AP*GP*U)-3')A20N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TOC
Query on TOC

Download SDF File 
Download CCD File 
A
2,3,6-TRIDEOXY-2,6-DIAMINO GLUCOSE
C6 H16 N2 O3
CEGXIUROHCNLCL-MOJAZDJTSA-P
 Ligand Interaction
2TB
Query on 2TB

Download SDF File 
Download CCD File 
A
1,3-DIAMINO-4,5,6-TRIHYDROXY-CYCLOHEXANE
C6 H16 N2 O3
DTFAJAKTSMLKAT-JDCCYXBGSA-P
 Ligand Interaction
TOA
Query on TOA

Download SDF File 
Download CCD File 
A
3-DEOXY-3-AMINO GLUCOSE
C6 H14 N O5
BQCCAEOLPYCBAE-RXRWUWDJSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 13 
  • Selection Criteria: LOWEST NOE AND TOTAL ENERGY 
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1998-06-17 
  • Released Date: 1999-06-22 
  • Deposition Author(s): Jiang, L., Patel, D.J.

Revision History 

  • Version 1.0: 1999-06-22
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance