› 4da3

X-ray diffraction
2.4Å resolution

Crystal structure of an intramolecular human telomeric DNA G-quadruplex 21-mer bound by the naphthalene diimide compound MM41.

Released:
DOI: 10.2210/pdb4da3/pdb
PDB entry 4da3 coloured by chain, front view.
PDB entry 4da3 coloured by chain, side view.
PDB entry 4da3 coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
Structure-based design and evaluation of naphthalene diimide G-quadruplex ligands as telomere targeting agents in pancreatic cancer cells.
Micco M, Collie GW, Dale AG, Ohnmacht SA, Pazitna I, Gunaratnam M, Reszka AP, Neidle S
J Med Chem 56 2959-74 (2013)
PMID: 23514618

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117308 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3') Chain: A
Molecule details ›
Chain: A
Length: 21 nucleotides
Theoretical weight: 6.67 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand K 3 x K
Ligand 0DX 1 x 0DX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P3121
Unit cell:
a: 51.31Å b: 51.31Å c: 51.94Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.244 0.242 0.282
Expression system: Not provided

Quick links

Citations

16 review citations

The Structure and Function of DNA G-Quadruplexes.
Spiegel et al. (2020)
15 more

10 mentions without citation

Major Achievements in the Design of Quadruplex-Interactive Small Molecules.
Mendes et al. (2022)
9 more