SMTL ID : 1r6a.1 (1 other biounit)

Structure of the dengue virus 2'O methyltransferase in complex with s-adenosyl homocysteine and ribavirin 5' triphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: G.108, H.109, E.110 Ligands: SAH.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.110 Salt bridges: A:H.109 SO4.2: 2 residues within 4Å: Chain A: K.104, H.109 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.104, A:H.109 SO4.3: 6 residues within 4Å: Chain A: R.37, K.41, V.54, S.55, R.56, R.83 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.54, A:R.56 Salt bridges: A:R.37, A:K.41, A:R.56, A:R.83 SO4.4: 3 residues within 4Å: Chain A: R.56, K.60, R.211 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.60, A:K.60, A:R.211 Salt bridges: A:R.56, A:K.60, A:R.211 SO4.5: 3 residues within 4Å: Chain A: K.29, R.56, R.211 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:K.28, A:K.29, A:R.56, A:R.211 SO4.6: 2 residues within 4Å: Chain A: V.155, R.159 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.162 Salt bridges: A:R.159 SO4.7: 3 residues within 4Å: Chain A: Q.33, E.66, R.67 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.33, A:E.66 Salt bridges: A:R.67

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.8: 18 residues within 4Å: Chain A: S.55, G.57, G.80, C.81, G.82, G.84, G.85, W.86, T.103, K.104, E.110, V.129, D.130, V.131, F.132, D.145, I.146 Ligands: SO4.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.55, A:C.81, A:G.84, A:G.85, A:W.86, A:W.86, A:K.104, A:H.109, A:D.130, A:V.131

1 x RVP: RIBAVIRIN MONOPHOSPHATE(Non-covalent)

RVP.9: 12 residues within 4Å: Chain A: K.13, L.16, N.17, L.19, G.20, K.21, F.24, K.28, S.149, S.150, P.151, S.213 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.13, A:L.19, A:K.21, A:S.149, A:S.213 Water bridges: A:K.28, A:K.28, A:S.149 Salt bridges: A:K.28 pi-Stacking: A:F.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benarroch, D. et al., A structural basis for the inhibition of the NS5 dengue virus mRNA 2'-O-methyltransferase domain by ribavirin 5'-triphosphate. J.Biol.Chem. (2004)

Release Date

2004-09-21

Peptides

Genome polyprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Genome polyprotein

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