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 2.0 of the entry. See complete history


Literature

Solution structure of the tobramycin-RNA aptamer complex.

Jiang, L.Patel, D.J.

(1998) Nat Struct Biol 5: 769-774

  • DOI: 10.1038/1804
  • Primary Citation of Related Structures:  
    2TOB

  • 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-Crick pair on complex formation ...

    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 nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(*AP*CP*UP*UP*GP*GP*UP*UP*UP*AP*GP*GP*UP*AP*AP*UP*GP*AP*GP*U)-3')A 20synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TOA
Query on TOA

Download Ideal Coordinates CCD File 
B [auth A]3-ammonio-3-deoxy-alpha-D-glucopyranose
C6 H14 N O5
BQCCAEOLPYCBAE-RXRWUWDJSA-O
 Ligand Interaction
2TB
Query on 2TB

Download Ideal Coordinates CCD File 
D [auth A]1,3-DIAMINO-4,5,6-TRIHYDROXY-CYCLOHEXANE
C6 H16 N2 O3
DTFAJAKTSMLKAT-JDCCYXBGSA-P
 Ligand Interaction
TOC
Query on TOC

Download Ideal Coordinates CCD File 
C [auth A]2,6-diammonio-2,3,6-trideoxy-alpha-D-glucopyranose
C6 H16 N2 O3
CEGXIUROHCNLCL-MOJAZDJTSA-P
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 13 
  • Selection Criteria: LOWEST NOE AND TOTAL ENERGY 
  • OLDERADO: 2TOB Olderado

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 1999-06-22
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-06-24
    Changes: Database references, Derived calculations, Other, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary