PDBe 5f3z

X-ray diffraction
2Å resolution

Dengue serotype 3 RNA-dependent RNA polymerase bound to PC-79-SH52

Released:

Function and Biology Details

Reactions catalysed:
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(purine-ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-purine-ribonucleotide)-[mRNA]
ATP + H(2)O = ADP + phosphate
NTP + H(2)O = NDP + phosphate
Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala.
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
S-adenosyl-L-methionine + G(5')pppR-RNA = S-adenosyl-L-homocysteine + m(7)G(5')pppR-RNA
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
RNA-directed RNA polymerase NS5 Chain: A
Molecule details ›
Chain: A
Length: 635 amino acids
Theoretical weight: 73.62 KDa
Source organism: Dengue virus 3
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6YMS4 (Residues: 2762-3390; Coverage: 19%)
Gene name: pol
Structure domains: Alpha-Beta Plaits

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: C2221
Unit cell:
a: 161.3Å b: 176.22Å c: 57.84Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.184 0.219
Expression system: Escherichia coli BL21(DE3)