261D | pdb_0000261d

CRYSTAL STRUCTURE OF THE DNA DECAMER D(CGCAATTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN

• PDB DOI: https://doi.org/10.2210/pdb261D/pdb
• NAKB: 261D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1996-11-08 Released: 1997-04-22 
• Deposition Author(s): Nunn, C.M., Garman, E., Neidle, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 
  0.201 (Depositor) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Crystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin.

Nunn, C.M., Garman, E., Neidle, S.

(1997) Biochemistry 36: 4792-4799

• PubMed: 9125500 
• DOI: https://doi.org/10.1021/bi9628228
• Primary Citation Related Structures: 
  261D


• PubMed Abstract: 
  

  The crystal structure of netropsin bound to the decamer d(CGCAATTGCG) has been determined at 2.4 A resolution. This is the first example of a crystal structure of netropsin bound to decamer DNA. The central eight bases of each DNA single-strand base pair with a self-complementary strand to form an octamer B-DNA duplex. These duplexes lie end to end within the unit cell. The terminal 5'-C and G-3' bases are unpaired and interact with the neighboring duplexes via interactions within both the major and minor groove to form base triplet interactions of the type C(+)-G x C and G*(G x C), respectively. The triplet interaction of the type C(+)-G x C is known to exist within triplex DNA with the C+ base oriented parallel with the Watson-Crick guanine base to which it hydrogen bonds. The netropsin molecule lies within the minor groove of the octamer duplex and assumes a class I type position, with bifurcated hydrogen-bonding interactions from the amide groups of the netropsin to the A x T base pairs of the minor groove. The netropsin molecule fits within a five base pair long minor groove site by bending of the flexible amidinium group at one end of the drug.

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Organizational Affiliation: 
• The CRC Biomolecular Structure Unit, The Institute of Cancer Research, Sutton, Surrey, U.K. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.52 kDa 
• Atom Count: 501 
• Modeled Residue Count: 19 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*AP*AP*TP*TP*GP*CP*G)-3')	A, B	10	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NT	C [auth B]	NETROPSIN C18 H26 N10 O3 IDBIFFKSXLYUOT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work:  0.201 (Depositor) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.84	α = 90
b = 39.8	β = 90
c = 54.08	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
X-PLOR	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-04-22 
Deposition Author(s): Nunn, C.M., Garman, E., Neidle, S.

Revision History  

• Version 1.0: 1997-04-22
  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: 2018-04-04
  Changes: Data collection
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations