407D

STRUCTURAL BASIS FOR RECOGNITION OF A-T AND T-A BASE PAIRS IN THE MINOR GROOVE OF B-DNA

• PDB DOI: https://doi.org/10.2210/pdb407D/pdb
• NAKB: 407D

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 1998-06-24 Released: 1998-10-19 
• Deposition Author(s): Rees, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.236 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Literature

A structural basis for recognition of A.T and T.A base pairs in the minor groove of B-DNA.

Kielkopf, C.L., White, S., Szewczyk, J.W., Turner, J.M., Baird, E.E., Dervan, P.B., Rees, D.C.

(1998) Science 282: 111-115

• PubMed: 9756473 
• DOI: https://doi.org/10.1126/science.282.5386.111
• Primary Citation of Related Structures:  
  407D, 408D


• PubMed Abstract: 
  

  Polyamide dimers containing three types of aromatic rings-pyrrole, imidazole, and hydroxypyrrole-afford a small-molecule recognition code that discriminates among all four Watson-Crick base pairs in the minor groove. The crystal structure of a specific polyamide dimer-DNA complex establishes the structural basis for distinguishing T.A from A.T base pairs. Specificity for the T.A base pair is achieved by means of distinct hydrogen bonds between pairs of substituted pyrroles on the ligand and the O2 of thymine and N3 of adenine. In addition, shape-selective recognition of an asymmetric cleft between the thymine-O2 and the adenine-C2 was observed. Although hitherto similarities among the base pairs in the minor groove have been emphasized, the structure illustrates differences that allow specific minor groove recognition.

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Organizational Affiliation: 

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.54 kDa 
• Atom Count: 593 
• Modelled 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*TP*AP*CP*TP*GP*G)-3')	A, B	10	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HP1	C [auth A], E [auth B]	~{N}-[5-[[5-[[5-[[3-[3-(dimethylamino)propylamino]-3-oxidanylidene-propyl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-4-oxidanyl-pyrrol-3-yl]-1-methyl-imidazole-2-carboxamide C31 H41 N11 O6 LNQWOHIRWNQTSI-UHFFFAOYSA-N
TRS	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Binding Affinity Annotations
ID	Source	Binding Affinity
HP1	PDBBind:  407D	Kd: 344 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.236 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.44	α = 90
b = 30.51	β = 120.47
c = 42.76	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-19 
Deposition Author(s): Rees, D.C.

Revision History  

• Version 1.0: 1998-10-19
  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: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2017-05-03
  Changes: Source and taxonomy, Structure summary
• Version 2.0: 2018-09-26
  Changes: Advisory, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations