8PPU: Pyrococcus abyssi DNA polymerase D (PolD) in its editing mode bound to a primer/template substrate containing three consecutive mismatches

PDB ID: 8PPUDownload
MMDB ID: 240253
PDB Deposition Date: 2023/7/10
Updated in MMDB: 2023/12
Experimental Method:
electron microscopy
Resolution: 3.02  Å
Source Organism:
Similar Structures:
Biological Unit for 8PPU: heptameric; determined by author
Molecular Components in 8PPU
Label Count Molecule
Proteins (5 molecules)
1
DNA Polymerase II Small Subunit
Molecule annotation
3
DNA Polymerase Sliding Clamp
Molecule annotation
1
DP2
Molecule annotation
Nucleotides(2 molecules)
1
DNA (5'-d(p*cp*cp*gp*gp*gp*cp*cp*gp*ap*gp*cp*cp*gp*tp*(gs)p*(c7r)p*(pst)p*(pst)p*(pst))-3')
Molecule annotation
1
DNA (5'-d(p*ap*gp*cp*ap*cp*gp*gp*cp*tp*cp*gp*gp*cp*cp*cp*gp*g)-3')
Molecule annotation
Chemicals and Non-standard biopolymers (6 molecules)
1
3
MAGNESIUM IONMAGNESIUM ION
2
3
ZINC IONZINC 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