1D64 | pdb_00001d64

CRYSTAL STRUCTURE OF A PENTAMIDINE-OLIGONUCLEOTIDE COMPLEX: IMPLICATIONS FOR DNA-BINDING PROPERTIES

• PDB DOI: https://doi.org/10.2210/pdb1D64/pdb
• NAKB: 1D64

• Classification: DNA
• Mutation(s): No 


• Deposited: 1992-03-02 Released: 1993-01-15 
• Deposition Author(s): Edwards, K.J., Jenkins, T.C., Neidle, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work: 
  0.184 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal structure of a pentamidine-oligonucleotide complex: implications for DNA-binding properties.

Edwards, K.J., Jenkins, T.C., Neidle, S.

(1992) Biochemistry 31: 7104-7109

• PubMed: 1643044 
• DOI: https://doi.org/10.1021/bi00146a011
• Primary Citation Related Structures: 
  1D64


• PubMed Abstract: 
  

  The crystal structure of the complex formed between the dodecanucleotide d(CGCGAATTCGCG)2 and the drug pentamidine, which is active against the Pneumocystis carinii pathogen in AIDS patients, has been determined to a resolution of 2.1 A and an R-factor of 19.4%. Analysis of the structure has shown the drug to be bound in the 5'-AATT minor groove region of the duplex, with the amidinium groups H-bonded to adenine N3 atoms in an interstrand manner. The drug molecule adopts an extended conformation, and the immediate binding site spans four base pairs. Structural details of the drug-DNA interactions are discussed, and comparison is made with the dodecamer complex of the structurally similar berenil ligand.

---

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: 7.67 kDa 
• Atom Count: 588 
• Modeled 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
PNT	C [auth B]	1,5-BIS(4-AMIDINOPHENOXY)PENTANE C19 H24 N4 O2 XDRYMKDFEDOLFX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work:  0.184 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.37	α = 90
b = 40	β = 90
c = 66.07	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-01-15 
Deposition Author(s): Edwards, K.J., Jenkins, T.C., Neidle, S.

Revision History  

• Version 1.0: 1993-01-15
  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: 2024-02-07
  Changes: Data collection, Database references, Derived calculations