5NKL: Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with the artificial base pair dDs-dPxTP

PDB ID: 5NKLDownload
MMDB ID: 152181
PDB Deposition Date: 2017/3/31
Updated in MMDB: 2017/10
Experimental Method:
x-ray diffraction
Resolution: 1.7  Å
Source Organism:
synthetic construct▼
Similar Structures:
Biological Unit for 5NKL: trimeric; determined by author and by software (PISA)
Molecular Components in 5NKL
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*(dnu)p*gp*gp*cp*gp*cp*cp*gp*tp*gp*gp*tp*c)-3')
Molecule annotation
Chemicals and Non-standard biopolymers (7 molecules)
1
2
MAGNESIUM IONMAGNESIUM ION
2
1
ACETATE IONACETATE ION
3
1
[[(2~{R},3~{S},5~{R})-5-[4-[(4~{R})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate[[(2~{R},3~{S},5~{R})-5-[4-[(4~{R})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
4
1
[[(2~{R},3~{S},5~{R})-5-[4-[(4~{S})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate[[(2~{R},3~{S},5~{R})-5-[4-[(4~{S})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
5
2
GLYCEROLGLYCEROL
* 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