1CVY | pdb_00001cvy

CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO CCAGATCTGG

• PDB DOI: https://doi.org/10.2210/pdb1CVY/pdb
• NAKB: 1CVY

• Classification: DNA
• Mutation(s): No 


• Deposited: 1999-08-24 Released: 2000-01-15 
• Deposition Author(s): Kielkopf, C.L., Bremer, R.E., White, S., Baird, E.E., Dervan, P.B., Rees, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.229 (Depositor) 
• R-Value Work: 
  0.229 (Depositor) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove.

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

(2000) J Mol Biology 295: 557-567

• PubMed: 10623546 
• DOI: https://doi.org/10.1006/jmbi.1999.3364
• Primary Citation Related Structures: 
  1CVX, 1CVY


• PubMed Abstract: 
  

  Synthetic polyamides composed of three types of aromatic amino acids, N-methylimidazole (Im), N-methylpyrrole (Py) and N-methyl-3-hydroxypyrrole (Hp) bind specific DNA sequences as antiparallel dimers in the minor groove. The side-by-side pairings of aromatic rings in the dimer afford a general recognition code that allows all four base-pairs to be distinguished. To examine the structural consequences of changing the DNA sequence context on T.A recognition by Hp/Py pairs in the minor groove, crystal structures of polyamide dimers (ImPyHpPy)(2) and the pyrrole counterpart (ImPyPyPy)(2) bound to the six base-pair target site 5'-AGATCT-3' in a ten base-pair oligonucleotide have been determined to a resolution of 2.27 and 2.15 A, respectively. The structures demonstrate that the principles of Hp/Py recognition of T.A are consistent between different sequence contexts. However, a general structural explanation for the non-additive reduction in binding affinity due to introduction of the hydroxyl group is less clear. Comparison with other polyamide-DNA cocrystal structures reveals structural themes and differences that may relate to sequence preference.

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

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.39 kDa 
• Atom Count: 550 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPY	C [auth A], D [auth B]	IMIDAZOLE-PYRROLE POLYAMIDE C31 H42 N11 O5 NCFLEKZHRQALKT-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.229 (Depositor) 
• R-Value Work:  0.229 (Depositor) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.493	α = 90
b = 38.593	β = 90
c = 47.112	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-01-15 
Deposition Author(s): Kielkopf, C.L., Bremer, R.E., White, S., Baird, E.E., Dervan, P.B., Rees, D.C.

Revision History  

• Version 1.0: 2000-01-15
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-02-01
  Changes: Structure summary
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations