Macromolecule Content

• Total Structure Weight: 10818.57 
• Atom Count: 717 
• Residue Count: 33 
• Unique nucleic acid chains: 1

1EHT

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

• DOI: 10.2210/pdb1EHT/pdb
• NDB: 1EHT

• Classification: RNA


• Deposited: 1997-03-20 Released: 1997-12-24 
• Deposition Author(s): Zimmermann, G.R., Pardi, A.

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Experimental Data Snapshot

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

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.Mol.Biol. 4: 644-649

• PubMed: 9253414 


• 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. 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.

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Related Citations: 

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




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
THEOPHYLLINE-BINDING RNA	A	33	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
TEP	A	THEOPHYLLINE C7 H8 N4 O2 ZFXYFBGIUFBOJW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-03-20 
• Released Date: 1997-12-24 
• Deposition Author(s): Zimmermann, G.R., Pardi, A.

Revision History 

• Version 1.0: 1997-12-24
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance