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 2.0 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: 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 ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
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'A 23N/A
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2,6-diamino-2,6-dideoxy-beta-L-idopyranose-(1-3)-beta-D-ribofuranoseB 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G38023GV
GlyCosmos:  G38023GV
Small Molecules
Ligands 2 Unique
IDChainsName / 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
 Ligand Interaction
NEB
Query on NEB

Download Ideal Coordinates CCD File 
D [auth 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 
  • OLDERADO: 1NEM Olderado

Structure Validation

View Full Validation Report




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