4WO2 | pdb_00004wo2

CRYSTAL STRUCTURE OF HUMAN NATIVE CKIT PROTO-ONCOGENE PROMOTER QUADRUPLEX DNA

• PDB DOI: https://doi.org/10.2210/pdb4WO2/pdb
• NAKB: 4WO2

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


• Deposited: 2014-10-15 Released: 2014-10-22 
• Deposition Author(s): wei, D., parkinson, g.n., neidle, s.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.223 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF HUMAN NATIVE CKIT-1 PROTO-ONCOGENE PROMOTER QUADRUPLEX DNA

Wei, D., Parkinson, G.N., Neidle, S.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.29 kDa 
• Atom Count: 1,108 
• 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, B	22	Homo sapiens

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.223 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.44	α = 90
b = 31.44	β = 90
c = 186.81	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASES	phasing
REFMAC	refinement
xia2	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-10-22 
Deposition Author(s): wei, D., parkinson, g.n., 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: 2014-10-22
  Type: Initial release
  
• Version 1.1: 2019-06-12
  Changes: Data collection, Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2025-12-10
  Changes: Atomic model, Data collection, Derived calculations, Structure summary