8E5D: Crystal structure of double-stranded DNA deaminase toxin DddA in complex with DNA with the target cytosine parked in the major groove

PDB ID: 8E5DDownload
MMDB ID: 230536
PDB Deposition Date: 2022/8/21
Updated in MMDB: 2023/10
Experimental Method:
x-ray diffraction
Resolution: 2.39  Å
Source Organism:
Burkholderia cenocepacia▼
Similar Structures:
Biological Unit for 8E5D: trimeric; determined by author and by software (PISA)
Molecular Components in 8E5D
Label Count Molecule
Protein (1 molecule)
1
Double-stranded DNA Deaminase Toxin a
Molecule annotation
Nucleotides(2 molecules)
1
DNA (5'-d(*gp*tp*ap*cp*cp*gp*gp*ap*cp*gp*tp*tp*gp*c)-3')
Molecule annotation
1
DNA (5'-d(*gp*tp*ap*cp*cp*gp*gp*ap*cp*gp*tp*tp*gp*c)-3')
Molecule annotation
Chemicals and Non-standard biopolymers (3 molecules)
1
1
ZINC IONZINC ION
2
1
MAGNESIUM IONMAGNESIUM ION
3
1
PHOSPHATE IONPHOSPHATE ION
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303