› 1g5k

Solution NMR

NMR Structrure of d(CCAAAGXACTGGG), X is a 3'-phosphoglycolate, 5'-phosphate gapped lesion, 10 structures

Released:
DOI: 10.2210/pdb1g5k/pdb
PDB entry 1g5k coloured by chain, ensemble of 10 models, front view.
PDB entry 1g5k coloured by chain, ensemble of 10 models, side view.
PDB entry 1g5k coloured by chain, ensemble of 10 models, top view.
Source organism: Synthetic construct
Primary publication:
Synthesis, characterization and solution structure of tethered oligonucleotides containing an internal 3'-phosphoglycolate, 5'-phosphate gapped lesion.
Junker HD, Hoehn ST, Bunt RC, Marathius V, Chen J, Turner CJ, Stubbe J
Nucleic Acids Res 30 5497-508 (2002)
PMID: 12490718

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113849 (preferred)
Entry contents:
3 distinct DNA molecules
Macromolecules (3 distinct):
5'-D(*CP*CP*AP*AP*AP*G)-3' Chain: A
Molecule details ›
Chain: A
Length: 6 nucleotides
Theoretical weight: 1.8 KDa
Source organism: Synthetic construct
Expression system: Not provided
5'-D(P*AP*CP*TP*GP*GP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 6 nucleotides
Theoretical weight: 1.85 KDa
Source organism: Synthetic construct
Expression system: Not provided
5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.94 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand PGA 1 x PGA
No modified residues

Experiments and Validation Details

Entry percentile scores
Refinement method: CONJUGATE GRADIENT MINIMIZATION
Expression system: Not provided

Quick links

Citations

3 citation in other articles

DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics.
Chen et al. (2008)
2 more

1 mention without citation

Synthesis, characterization and solution structure of tethered oligonucleotides containing an internal 3'-phosphoglycolate, 5'-phosphate gapped lesion.
Junker et al. (2002)