3UKB | pdb_00003ukb

(R)-cEt-BNA decamer structure

• PDB DOI: https://doi.org/10.2210/pdb3UKB/pdb
• NAKB: 3UKB

• Classification: DNA
• Mutation(s): No 


• Deposited: 2011-11-09 Released: 2012-06-20 
• Deposition Author(s): Pallan, P.S., Egli, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 
  0.208 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.146 (Depositor) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Structure and nuclease resistance of 2',4'-constrained 2'-O-methoxyethyl (cMOE) and 2'-O-ethyl (cEt) modified DNAs.

Pallan, P.S., Allerson, C.R., Berdeja, A., Seth, P.P., Swayze, E.E., Prakash, T.P., Egli, M.

(2012) Chem Commun (Camb) 48: 8195-8197

• PubMed: 22614180 
• DOI: https://doi.org/10.1039/c2cc32286b
• Primary Citation Related Structures: 
  3UKB, 3UKC, 3UKE


• PubMed Abstract: 
  

  Combining the structural elements of the second generation 2'-O-methoxyethyl (MOE) and locked nucleic acid (LNA) antisense oligonucleotide (AON) modifications yielded the highly nuclease resistant 2',4'-constrained MOE and ethyl bicyclic nucleic acids (cMOE and cEt BNA, respectively). Crystal structures of DNAs with cMOE or cEt BNA residues reveal their conformational preferences. Comparisons with MOE and LNA structures allow insights into their favourable properties for AON applications.

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Organizational Affiliation: 
• Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 6.15 kDa 
• Atom Count: 492 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free:  0.208 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.146 (Depositor) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.022	α = 90
b = 44.897	β = 90
c = 44.911	γ = 90

Software Package:

Software Name	Purpose
MD2	data collection
CCP4	model building
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-20 
Deposition Author(s): Pallan, P.S., Egli, M.

Revision History  

• Version 1.0: 2012-06-20
  Type: Initial release
  
• Version 1.1: 2012-08-08
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description