› 1y9h

Solution NMR

Methylation of cytosine at C5 in a CpG sequence context causes a conformational switch of a benzo[a]pyrene diol epoxide-N2-guanine adduct in DNA from a minor groove alignment to intercalation with base displacement

Released:
DOI: 10.2210/pdb1y9h/pdb
PDB entry 1y9h coloured by chain, ensemble of 9 models, front view.
PDB entry 1y9h coloured by chain, ensemble of 9 models, side view.
PDB entry 1y9h coloured by chain, ensemble of 9 models, top view.
Source organism: Synthetic construct
Primary publication:
Methylation of cytosine at C5 in a CpG sequence context causes a conformational switch of a benzo[a]pyrene diol epoxide-N2-guanine adduct in DNA from a minor groove alignment to intercalation with base displacement.
Zhang N, Lin C, Huang X, Kolbanovskiy A, Hingerty BE, Amin S, Broyde S, Geacintov NE, Patel DJ
J Mol Biol 346 951-65 (2005)
PMID: 15701509

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114849 (preferred)
Entry contents:
2 distinct DNA molecules
Macromolecules (2 distinct):
5'-D(*CP*CP*AP*TP*(5CM)P*(BPG)P*CP*TP*AP*CP*C)-3' Chain: A
Molecule details ›
Chain: A
Length: 11 nucleotides
Theoretical weight: 3.27 KDa
Source organism: Synthetic construct
Expression system: Not provided
5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.45 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand BAP 1 x BAP
1 modified residue:
Ligand 5CM 1 x 5CM

Experiments and Validation Details

Entry percentile scores
Refinement method: simulated annealing molecular dynamics matrix relaxation
Expression system: Not provided

Quick links

Citations

5 review citations

Environmental epigenetics of asthma: an update.
Ho SM. (2010)
4 more

1 mention without citation

Methylation of cytosine at C5 in a CpG sequence context causes a conformational switch of a benzo[a]pyrene diol epoxide-N2-guanine adduct in DNA from a minor groove alignment to intercalation with base displacement.
Zhang et al. (2005)