121D | pdb_0000121d

MOLECULAR STRUCTURE OF THE A-TRACT DNA DODECAMER D(CGCAAATTTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN

• PDB DOI: https://doi.org/10.2210/pdb121D/pdb
• NAKB: 121D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1993-04-14 Released: 1994-01-15 
• Deposition Author(s): Tabernero, L., Verdaguer, N., Coll, M., Fita, I., Van Der Marel, G.A., Van Boom, J.H., Rich, A., Aymami, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 
  0.198 (Depositor) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Molecular structure of the A-tract DNA dodecamer d(CGCAAATTTGCG) complexed with the minor groove binding drug netropsin.

Tabernero, L., Verdaguer, N., Coll, M., Fita, I., van der Marel, G.A., van Boom, J.H., Rich, A., Aymami, J.

(1993) Biochemistry 32: 8403-8410

• PubMed: 8395202 
• DOI: https://doi.org/10.1021/bi00084a004
• Primary Citation Related Structures: 
  121D


• PubMed Abstract: 
  

  The molecular structure of the complex between the minor groove binding drug netropsin and the dodecamer d(CGCAAATTTGCG) has been solved and refined by X-ray diffraction analysis to an R-factor of 19.8% and 2.2-A resolution. The drug lies in the narrow minor groove of the B-DNA fragment, covering five of the six A.T base pairs (from A5.T20 to T9.A16). The long six A.T base pair tract allows the drug to bind in a position that optimizes its contacts with the DNA, establishing hydrogen bonds with O2 of thymines and N3 of adenines. The DNA molecule shows a high propeller twist only at the A6.T19 step of the A-tract. Two three-centered hydrogen bonds are observed in the major groove at half of the A-tract.

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Organizational Affiliation: 
• Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.76 kDa 
• Atom Count: 564 
• 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*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')	A, B	12	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work:  0.198 (Depositor) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.65	α = 90
b = 42.03	β = 90
c = 65.33	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-15 
Deposition Author(s): Tabernero, L., Verdaguer, N., Coll, M., Fita, I., Van Der Marel, G.A., Van Boom, J.H., Rich, A., Aymami, J.

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: 2018-04-18
  Changes: Advisory, Data collection
• Version 1.4: 2024-02-07
  Changes: Advisory, Data collection, Database references, Derived calculations