4DF8: Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with aminopentinyl-7-deaza-2-dATP

PDB ID: 4DF8Download
MMDB ID: 99717
PDB Deposition Date: 2012/1/23
Updated in MMDB: 2023/09
Experimental Method:
x-ray diffraction
Resolution: 2  Å
Source Organism:
synthetic construct▼
Similar Structures:
Biological Unit for 4DF8: trimeric; determined by author and by software (PISA)
Molecular Components in 4DF8
Label Count Molecule
Protein (1 molecule)
1
DNA Polymerase I, Thermostable
Molecule annotation
Nucleotides(2 molecules)
1
DNA (5'-d(*gp*ap*cp*cp*ap*cp*gp*gp*cp*gp*cp*(doc))-3')
Molecule annotation
1
DNA (5'-d(*ap*ap*ap*tp*gp*gp*cp*gp*cp*cp*gp*tp*gp*gp*tp*c)-3')
Molecule annotation
Chemicals and Non-standard biopolymers (14 molecules)
1
1
5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine
2
3
MAGNESIUM IONMAGNESIUM ION
3
4
1,2-ETHANEDIOL1,2-ETHANEDIOL
4
4
FORMIC ACIDFORMIC ACID
5
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