2RRR image
Deposition Date 2011-03-24
Release Date 2011-06-08
Last Version Date 2024-05-01
Entry Detail
PDB ID:
2RRR
Keywords:
DNA
Title:
DNA oligomer containing ethylene cross-linked cyclic 2'-deoxyuridylate dimer
Biological Source:
Source Organism:
(Taxon ID: ) (Taxon ID: )
Method Details:
Experimental Method:
SOLUTION NMR
Conformers Calculated:
300
Conformers Submitted:
20
Selection Criteria:
structures with the lowest energy
2RRR validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*CP*TP*TP*CP*AP*TP*TP*AP*CP*AP*TP*CP*C)-3')
Chain IDs:A
Chain Length:14
Number of Molecules:1
Biological Source:
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*GP*AP*TP*GP*TP*AP*AP*TP*GP*AP*AP*GP*G)-3')
Chain IDs:B
Chain Length:14
Number of Molecules:1
Biological Source:
Ligand Molecules
NA
Primary Citation
Structural Feature of Bent DNA Recognized by HMGB1
J.Am.Chem.Soc. 133 5788 5790 (2011)
PMID: 21443191 DOI: 10.1021/ja2013399

Abstact

High Mobility Group Box 1 (HMGB1) protein, a potential therapeutic target, binds bent DNAs structure-specifically. Here we report on a crucial structural feature of the bent DNA required for strong binding to HMGB1. NMR structures of two bent DNA oligomers, only one of which binds strongly to HMGB1, revealed that the presence of a pocket structure on the minor groove is crucial for strong binding through penetration of a phenylalanine residue.

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Disease

Primary Citation of related structures
2RRQ