1PRP

CRYSTAL STRUCTURE OF D(CGCGAATTCGCG) COMPLEXED WITH PROPAMIDINE, A SHORT-CHAIN HOMOLOGUE OF THE DRUG PENTAMIDIN

• PDB DOI: https://doi.org/10.2210/pdb1PRP/pdb
• NAKB: 1PRP

• Classification: DNA
• Mutation(s): No 


• Deposited: 1993-07-23 Released: 1994-01-15 
• Deposition Author(s): Nunn, C.M., Jenkins, T.C., Neidle, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work: 0.174 
• R-Value Observed: 0.174 

Literature

Crystal structure of d(CGCGAATTCGCG) complexed with propamidine, a short-chain homologue of the drug pentamidine.

Nunn, C.M., Jenkins, T.C., Neidle, S.

(1993) Biochemistry 32: 13838-13843

• PubMed: 8268158 
• DOI: https://doi.org/10.1021/bi00213a012
• Primary Citation of Related Structures:  
  1PRP


• PubMed Abstract: 
  

  The crystal structure of the complex between propamidine and the self-complementary DNA dodecamer d(CGCGAATTCGCG) duplex has been determined to a resolution of 2.1 A and a R-factor of 17.4%. The propamidine binds to the DNA within the minor groove, with specific hydrogen-bonding interactions from the amidinium groups to the bases and sugar groups of the DNA, via a 4-base-pair binding site. A network of water molecules lies over the mouth of the minor groove. The structure provides a rationale for the superior DNA-binding properties of propamidine as compared to pentamidine [cf. Edwards, K. J., Jenkins, T. C. & Neidle, S. (1992) Biochemistry 31, 7104-7109]. This is seen to result from (i) decreased minor groove width at the binding site and (ii) reduced mobility of the bound propamidine molecule.

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Organizational Affiliation: 

Cancer Research Campaign Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey, U.K.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.64 kDa 
• Atom Count: 578 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')	A, B	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TNT	C [auth A]	1,3-BIS(AMIDINOPHENOXY)PROPANE C17 H20 N4 O2 WTFXJFJYEJZMFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work: 0.174 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25	α = 90
b = 40.88	β = 90
c = 67.28	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-15 
Deposition Author(s): Nunn, C.M., Jenkins, T.C., Neidle, S.

Revision History  

• Version 1.0: 1994-01-15
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations