1EHT

THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, 10 STRUCTURES

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 10 
  • Selection Criteria: LOWEST TOTAL ENERGY 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA.

Zimmermann, G.R., Jenison, R.D., Wick, C.L., Simorre, J.P., Pardi, A.

(1997) Nat Struct Biol 4: 644-649

  • DOI: 10.1038/nsb0897-644
  • Primary Citation of Related Structures:  
    1EHT

  • PubMed Abstract: 

    • To visualize the interplay of RNA structural interactions in a ligand binding site, we have determined the solution structure of a high affinity RNA-theophylline complex using NMR spectroscopy. The structure provides insight into the ability of this in vitro selected RNA to discriminate theophylline from the structurally similar molecule caffeine ...

    To visualize the interplay of RNA structural interactions in a ligand binding site, we have determined the solution structure of a high affinity RNA-theophylline complex using NMR spectroscopy. The structure provides insight into the ability of this in vitro selected RNA to discriminate theophylline from the structurally similar molecule caffeine. Numerous RNA structural motifs combine to form a well-ordered binding pocket where an intricate network of hydrogen bonds and stacking interactions lock the theophylline into the complex. Two internal loops interact to form the binding site which consists of a sandwich of three base triples. The complex also contains novel base-zipper and 1-3-2 stacking motifs, in addition to an adenosine platform and a reversed sugar. An important feature of the RNA is that many of the conserved core residues participate in multiple overlapping tertiary interactions. This complex illustrates how interlocking structural motifs can be assembled into a highly specific ligand-binding site that possesses high levels of affinity and molecular discrimination.

    Related Citations: 
    • High-Resolution Molecular Discrimination by RNA
      Jenison, R.D., Gill, S.C., Pardi, A., Polisky, B.
      (1994) Science 263: 1425
    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
THEOPHYLLINE-BINDING RNAA 33N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TEP
Query on TEP
Download Ideal Coordinates CCD File 
B [auth A]THEOPHYLLINE
C7 H8 N4 O2
ZFXYFBGIUFBOJW-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 10 
  • Selection Criteria: LOWEST TOTAL ENERGY 
  • OLDERADO: 1EHT Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-12-24
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-16
    Changes: Database references, Derived calculations, Other