365D | pdb_0000365d

STRUCTURAL BASIS FOR G C RECOGNITION IN THE DNA MINOR GROOVE

• PDB DOI: https://doi.org/10.2210/pdb365D/pdb
• NAKB: 365D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1997-12-17 Released: 1998-02-05 
• Deposition Author(s): Kielkopf, C.L., Baird, E.E., Dervan, P.B., Rees, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.260 (Depositor) 
• R-Value Work: 
  0.222 (Depositor) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Structural basis for G.C recognition in the DNA minor groove.

Kielkopf, C.L., Baird, E.E., Dervan, P.B., Rees, D.C.

(1998) Nat Struct Biol 5: 104-109

• PubMed: 9461074 
• DOI: https://doi.org/10.1038/nsb0298-104
• Primary Citation Related Structures: 
  365D


• PubMed Abstract: 
  

  Small molecules that target specific DNA sequences offer a potentially general approach for the regulation of gene expression. Pyrrole-imidazole polyamides represent the only class of synthetic small molecules that can bind predetermined DNA sequences with affinities and specificities comparable to DNA binding proteins. Antiparallel side-by-side pairings of two aromatic amino acids, imidazole (Im) and pyrrole (Py), distinguish G.C from C.G, and both from A.T/T.A base pairs. A high resolution X-ray crystal structure of a four-ring pyrrole-imidazole polyamide specifically bound as a dimer to a six-base pair predetermined DNA site reveals a structural framework of hydrogen bonds and interactions with the walls of the minor groove that underlies the pairing rules for DNA recognition.

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Organizational Affiliation: 
• Division of Biology, California Institute of Technology, Pasadena 91125, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.55 kDa 
• Atom Count: 573 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IIP	C [auth A], D [auth B]	IMIDAZOLE-PYRROLE POLYAMIDE C30 H41 N12 O5 IILSDRPSIOPDCJ-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.260 (Depositor) 
• R-Value Work:  0.222 (Depositor) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.396	α = 90
b = 38.959	β = 90
c = 44.421	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-02-05 
Deposition Author(s): Kielkopf, C.L., Baird, E.E., Dervan, P.B., Rees, D.C.

Revision History  

• Version 1.0: 1998-02-05
  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: 2024-02-21
  Changes: Data collection, Database references, Derived calculations