1NEM

Saccharide-RNA recognition in the neomycin B / RNA aptamer complex


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer

Jiang, L.Majumdar, A.Hu, W.Jaishree, T.J.Xu, W.Patel, D.J.

(1999) Structure Fold.Des. 7: 817-827


  • PubMed Abstract: 
  • Aminoglycoside antibiotics can target RNA folds with micromolar affinity and inhibit biological processes ranging from protein biosynthesis to ribozyme action and viral replication. Specific features of aminoglycoside antibiotic-RNA recognition have ...

    Aminoglycoside antibiotics can target RNA folds with micromolar affinity and inhibit biological processes ranging from protein biosynthesis to ribozyme action and viral replication. Specific features of aminoglycoside antibiotic-RNA recognition have been probed using chemical, biochemical, spectroscopic and computational approaches on both natural RNA targets and RNA aptamers identified through in vitro selection. Our previous studies on tobramycin-RNA aptamer complexes are extended to neomycin B bound to its selected RNA aptamer with 100 nM affinity.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*GP*GP*AP*CP*UP*GP*GP*GP*CP*GP*AP*GP*AP*AP*GP*UP*UP*UP*AP*GP*UP*CP*C)-3'A23N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BDG
Query on BDG

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Download CCD File 
A
O-2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE
C6 H14 N2 O4
SQTHUUHOUPJYLK-UKFBFLRUSA-N
 Ligand Interaction
IDG
Query on IDG

Download SDF File 
Download CCD File 
A
O-2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPYRANOSE
C6 H14 N2 O4
SQTHUUHOUPJYLK-BSQWINAVSA-N
 Ligand Interaction
BDR
Query on BDR

Download SDF File 
Download CCD File 
A
BETA-D-RIBOFURANOSYL
C5 H10 O5
HMFHBZSHGGEWLO-TXICZTDVSA-N
 Ligand Interaction
NEB
Query on NEB

Download SDF File 
Download CCD File 
A
2-DEOXY-D-STREPTAMINE
C6 H15 N2 O3
DTFAJAKTSMLKAT-JDCCYXBGSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-08-31
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance