4WO3 | pdb_00004wo3

THE SECOND C-KIT DNA QUADRUPLEX CRYSTAL STRUCTURE

• PDB DOI: https://doi.org/10.2210/pdb4WO3/pdb
• NAKB: 4WO3

• Classification: DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2014-10-15 Released: 2014-10-29 
• Deposition Author(s): Wei, D., Neidle, S.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 
  0.243 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

THE SECOND C-KIT1 DNA QUADRUPLEX CRYSTAL STRUCTURE

Wei, D., Neidle, S.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.25 kDa 
• Atom Count: 946 
• Modeled Residue Count: 44 
• Deposited Residue Count: 44 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*CP*TP*GP*GP*GP*AP*GP*GP*AP*GP*GP*G)-3')	A [auth B], B [auth A]	22	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	C [auth B], D [auth B], E [auth B], F [auth A], G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free:  0.243 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.85	α = 90
b = 94.85	β = 90
c = 30.363	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PHASES	phasing
XIA	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-10-29 
Deposition Author(s): Wei, D., Neidle, S.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C129/A4489
Cancer Research UK	United Kingdom	a China Fellowship

Revision History  

• Version 1.0: 2014-10-29
  Type: Initial release
  
• Version 1.1: 2014-11-26
  Changes: Derived calculations, Non-polymer description, Other, Refinement description, Structure summary
• Version 1.2: 2019-06-12
  Changes: Data collection, Database references
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description