1AW4

STRUCTURAL BASIS OF DNA FOLDING AND RECOGNITION IN AMP-DNA APTAMER COMPLEX, NMR, 7 STRUCTURES

• PDB DOI: https://doi.org/10.2210/pdb1AW4/pdb
• NAKB: 1AW4

• Classification: DNA
• Mutation(s): No 


• Deposited: 1997-10-09 Released: 1998-04-15 
• Deposition Author(s): Lin, C.H., Patel, D.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 21 
• Conformers Submitted: 7 
• Selection Criteria: LEAST TOTAL ENERGY, NOE VIOLATION, VDW 

Literature

Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP.

Lin, C.H., Patel, D.J.

(1997) Chem Biol 4: 817-832

• PubMed: 9384529 
• DOI: https://doi.org/10.1016/s1074-5521(97)90115-0
• Primary Citation of Related Structures:  
  1AW4


• PubMed Abstract: 
  

  Structural studies by nuclear magnetic resonance (NMR) of RNA and DNA aptamer complexes identified through in vitro selection and amplification have provided a wealth of information on RNA and DNA tertiary structure and molecular recognition in solution. The RNA and DNA aptamers that target ATP (and AMP) with micromolar affinity exhibit distinct binding site sequences and secondary structures. We report below on the tertiary structure of the AMP-DNA aptamer complex in solution and compare it with the previously reported tertiary structure of the AMP-RNA aptamer complex in solution.

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Organizational Affiliation: 

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

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.2 kDa 
• Atom Count: 612 
• Modelled Residue Count: 27 
• Deposited Residue Count: 27 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
ATP-BINDING DNA APTAMER	A	27	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	B [auth A], C [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 21 
• Conformers Submitted: 7 
• Selection Criteria: LEAST TOTAL ENERGY, NOE VIOLATION, VDW 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-04-15 
Deposition Author(s): Lin, C.H., Patel, D.J.

Revision History  

• Version 1.0: 1998-04-15
  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