3GDX: Dna polymerase beta with a gapped DND substrate and dTMP(CF2)PP

PDB ID: 3GDXDownload
MMDB ID: 72482
PDB Deposition Date: 2009/2/24
Updated in MMDB: 2023/09
Experimental Method:
x-ray diffraction
Resolution: 2.2  Å
Source Organism:
synthetic construct▼
Similar Structures:
Biological Unit for 3GDX: tetrameric; determined by author and by software (PISA)
Molecular Components in 3GDX
Label Count Molecule
Protein (1 molecule)
1
DNA Polymerase Beta
Molecule annotation
Nucleotides(3 molecules)
1
5'-d(*cp*cp*gp*ap*cp*ap*gp*cp*gp*cp*ap*tp*cp*ap*gp*c)-3'
Molecule annotation
1
5'-d(*gp*cp*tp*gp*ap*tp*gp*cp*gp*c)-3'
Molecule annotation
1
5'-d(p*gp*tp*cp*gp*g)-3'
Molecule annotation
Chemicals and Non-standard biopolymers (7 molecules)
1
1
5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]thymidine5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]thymidine
2
2
MAGNESIUM IONMAGNESIUM ION
3
2
SODIUM IONSODIUM ION
4
2
CHLORIDE IONCHLORIDE 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