4DFP: Crystal structure of the large fragment of DNA Polymerase I from Thermus aqauticus in a ternary complex with 7-(aminopentinyl)-7-deaza-dGTP

PDB ID: 4DFPDownload
MMDB ID: 99721
PDB Deposition Date: 2012/1/24
Updated in MMDB: 2023/09
Experimental Method:
x-ray diffraction
Resolution: 2  Å
Source Organism:
synthetic construct▼
Similar Structures:
Biological Unit for 4DFP: trimeric; determined by author and by software (PISA)
Molecular Components in 4DFP
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
5'-d(aaacggcgccgtggtc)-3'
Molecule annotation
Chemicals and Non-standard biopolymers (18 molecules)
1
5
MAGNESIUM IONMAGNESIUM ION
2
5
1,2-ETHANEDIOL1,2-ETHANEDIOL
3
7
FORMIC ACIDFORMIC ACID
4
1
2-amino-5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one2-amino-5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
* 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