386D

THREE-DIMENSIONAL STRUCTURE AND REACTIVITY OF A PHOTOCHEMICAL CLEAVAGE AGENT BOUND TO DNA

• PDB DOI: https://doi.org/10.2210/pdb386D/pdb
• NAKB: 386D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1998-03-11 Released: 1998-03-12 
• Deposition Author(s): Gasper, S.M., Armitage, B., Shui, X., Hu, G.G., Yu, C., Schuster, G., Williams, L.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.268 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

Literature

Three-Dimensional Structure and Reactivity of a Photochemical Cleavage Agent Bound to DNA

Gasper, S.M., Armitage, B., Shui, X., Hu, G.G., Yu, C., Schuster, G., Williams, L.D.

(1998) J Am Chem Soc 120: 12402-12409

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2.21 kDa 
• Atom Count: 170 
• Modelled Residue Count: 6 
• Deposited Residue Count: 6 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')	A	6	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AQS	B [auth A]	N,N-BIS(3-AMINOPROPYL)-2-ANTHRAQUINONESULFONAMIDE C20 H25 N3 O4 S HUHBNNVFLMYFIE-UHFFFAOYSA-P

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.268 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.02	α = 90
b = 31.02	β = 90
c = 64.91	γ = 120

Software Package:

Software Name	Purpose
MAD	model building
X-PLOR	refinement
ADSC	data collection
MAD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-03-12 
Deposition Author(s): Gasper, S.M., Armitage, B., Shui, X., Hu, G.G., Yu, C., Schuster, G., Williams, L.D.

Revision History  

• Version 1.0: 1998-03-12
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2024-02-21
  Changes: Atomic model, Data collection, Database references, Derived calculations