5hmy

X-ray diffraction
2.1Å resolution

Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 15

Released:

Function and Biology Details

Reactions catalysed:
S-adenosyl-L-methionine + a 5'-(5'-triphosphoguanosine)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA]
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleotide)-[mRNA]
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
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.
NTP + H(2)O = NDP + phosphate
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
PDBe Complex ID:
PDB-CPX-180557 (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
UniProt:
  • Canonical: Q6YMS4 (Residues: 2762-3390; Coverage: 19%)
Gene name: pol
Sequence domains:
Structure domains: Flavivirus RNA-directed RNA polymerase, thumb domain

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: 160.88Å b: 177.11Å c: 58.07Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.184 0.213
Expression system: Escherichia coli