1NEM

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

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 9 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

wwPDB Validation   3D Report Full Report


This is version 2.1 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 7: 817-827

  • DOI: https://doi.org/10.1016/s0969-2126(99)80105-1
  • Primary Citation of Related Structures:  
    1NEM

  • 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 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 nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
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)-3'23N/A
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2,6-diamino-2,6-dideoxy-beta-L-idopyranose-(1-3)-beta-D-ribofuranose
B
2N/A
Glycosylation Resources
GlyTouCan:  G38023GV
GlyCosmos:  G38023GV
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BDG
Query on BDG
Download Ideal Coordinates CCD File 
C [auth A]2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose
C6 H14 N2 O4
SQTHUUHOUPJYLK-UKFBFLRUSA-N
NEB
Query on NEB
Download Ideal Coordinates CCD File 
D [auth A]2-DEOXY-D-STREPTAMINE
C6 H15 N2 O3
DTFAJAKTSMLKAT-JDCCYXBGSA-O
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 9 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-08-31
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-12-27
    Changes: Data collection, Database references, Structure summary