2LG3 | pdb_00002lg3

Structure of the duplex containing HNE derived (6S,8R,11S) gamma-HO-PdG when placed opposite dT

• PDB DOI: https://doi.org/10.2210/pdb2LG3/pdb
• NAKB: 2LG3
• BMRB: 17791

• Classification: DNA
• Mutation(s): No 


• Deposited: 2011-07-19 Released: 2012-08-01 
• Deposition Author(s): Huang, H., Wang, H., Kozekova, A., Lloyd, R.S., Rizzo, C.J., Stone, M.P.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 1 
• Selection Criteria: back calculated data agree with experimental NOESY spectrum 

Literature

Ring-chain tautomerization of trans-4-hydroxynonenal derived (6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct when placed opposite 2'-deoxythymidine in duplex

Huang, H., Wang, H., Kozekova, A., Lloyd, R.S., Rizzo, C.J., Stone, M.P.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.5 kDa 
• Atom Count: 498 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3')	A	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3')	B	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HND	C [auth A]	(4S)-nonane-1,4-diol C9 H20 O2 BBKPDHOKNRMWQN-VIFPVBQESA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 1 
• Selection Criteria: back calculated data agree with experimental NOESY spectrum 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-01 
Deposition Author(s): Huang, H., Wang, H., Kozekova, A., Lloyd, R.S., Rizzo, C.J., Stone, M.P.

Revision History  

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references