2ARG

FORMATION OF AN AMINO ACID BINDING POCKET THROUGH ADAPTIVE ZIPPERING-UP OF A LARGE DNA HAIRPIN LOOP, NMR, 9 STRUCTURES

• PDB DOI: https://doi.org/10.2210/pdb2ARG/pdb
• NAKB: 2ARG

• Classification: DNA
• Mutation(s): No 


• Deposited: 1998-08-19 Released: 1999-03-23 
• Deposition Author(s): Lin, C.H., Wang, W., Jones, R.A., Patel, D.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 9 
• Selection Criteria: LEAST NOE, VDW, AND BOND ANGLE VIOLATION, LEAST TOTAL ENERGY 

Literature

Formation of an amino-acid-binding pocket through adaptive zippering-up of a large DNA hairpin loop.

Lin, C.H., Wang, W., Jones, R.A., Patel, D.J.

(1998) Chem Biol 5: 555-572

• PubMed: 9818148 
• DOI: https://doi.org/10.1016/s1074-5521(98)90114-4
• Primary Citation of Related Structures:  
  2ARG


• PubMed Abstract: 
  

  In vitro selection has identified DNA aptamers that target cofactors, amino acids, peptides and proteins. Structure determination of such ligand-DNA aptamer complexes should elucidate the details of adaptive DNA structural transitions, binding-pocket architectures and ligand recognition. We have determined the solution structure of the complex of a DNA aptamer containing a guanine-rich 18-residue hairpin loop that binds L-argininamide with approximately 100 microM affinity.

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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: 9.55 kDa 
• Atom Count: 636 
• Modelled Residue Count: 30 
• Deposited Residue Count: 30 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA APTAMER [5'-D (*TP*GP*AP*CP*CP*AP*GP*GP*GP*CP*AP*AP*AP*CP*GP*GP*TP*AP* GP*GP*TP*GP*AP*GP*TP*GP*GP*TP*CP*A)-3']	A	30	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AAR	B [auth A]	ARGININEAMIDE C6 H16 N5 O ULEBESPCVWBNIF-BYPYZUCNSA-O

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 9 
• Selection Criteria: LEAST NOE, VDW, AND BOND ANGLE VIOLATION, LEAST TOTAL ENERGY 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-03-23 
Deposition Author(s): Lin, C.H., Wang, W., Jones, R.A., Patel, D.J.

Revision History  

• Version 1.0: 1999-03-23
  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: 2022-03-09
  Changes: Database references, Derived calculations, Other
• Version 2.0: 2022-07-06
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary