Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9172.53 
• Atom Count: 551 
• Residue Count: 24 
• Unique nucleic acid chains: 1

1O0K

Structure of the First Parallel DNA Quadruplex-drug Complex

• DOI: 10.2210/pdb1O0K/pdb
• NDB: DD0055

• Classification: DNA


• Deposited: 2003-02-22 Released: 2003-04-15 
• Deposition Author(s): Clark, G.R., Pytel, P.D., Squire, C.J., Neidle, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å

Literature

Structure of the First Parallel DNA Quadruplex-drug Complex

Clark, G.R., Pytel, P.D., Squire, C.J., Neidle, S.

(2003) J.Am.Chem.Soc. 125: 4066-4067

• PubMed: 12670225 
• DOI: 10.1021/ja0297988


• PubMed Abstract: 
  

The first crystal structure of a drug (daunomycin) bound to a parallel-stranded intermolecular telomeric G4 quadruplex (d(TGGGGT)4) has been determined to high resolution. A planar assemblage of three daunomycin molecules stacks onto the 5' end of the G4 column, with the daunosamine substituents occupying three of the four quadruplex grooves. The surface area of the terminal G-quartet in this parallel DNA quadruplex, presently occupied by three daunomycins, is sufficiently large that it could easily accommodate other potential telomerase inhibitors such as substituted porphyrins or telomestatin.

---

Organizational Affiliation: 

Department of Chemistry, University of Auckland, Auckland, New Zealand. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
5'-D(*TP*GP*GP*GP*GP*T)-3'	A,B,C,D	6	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
DM1	B, C, D	DAUNOMYCIN DAUNORUBICIN C27 H29 N O10 STQGQHZAVUOBTE-VGBVRHCVSA-N
NA	A, C	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 53.004	α = 90.00
b = 47.073	β = 119.80
c = 31.865	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
AMoRE	phasing
SHELXL-97	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-02-22 
• Released Date: 2003-04-15 
• Deposition Author(s): Clark, G.R., Pytel, P.D., Squire, C.J., Neidle, S.

Revision History 

• Version 1.0: 2003-04-15
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance