SMTL ID : 2p3l.1 (1 other biounit)

Crystal Structure of Dengue Methyltransferase in Complex with GpppA and S-Adenosyl-L-Homocysteine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: K.38, R.66, R.221, T.224 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.66, A:R.66, A:R.66, A:R.221 Salt bridges: A:K.38, A:R.66, A:R.221 SO4.2: 6 residues within 4Å: Chain A: R.47, K.51, V.64, S.65, R.66, R.93 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.66, A:R.66 Salt bridges: A:R.47, A:K.51, A:R.93 SO4.3: 2 residues within 4Å: Chain A: K.114, H.119 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.114, A:H.119 SO4.4: 2 residues within 4Å: Chain A: P.117, G.118 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.118 SO4.5: 4 residues within 4Å: Chain A: G.118, H.119, E.120 Ligands: SAH.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.120 Salt bridges: A:H.119

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

SAH.6: 18 residues within 4Å: Chain A: S.65, G.67, G.90, C.91, G.92, G.95, W.96, T.113, K.114, H.119, V.139, D.140, V.141, F.142, D.155, I.156 Ligands: SO4.5, CIT.8 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.65, A:C.91, A:G.95, A:W.96, A:W.96, A:T.113, A:K.114, A:H.119, A:D.140, A:D.140, A:V.141, A:D.155 Water bridges: A:G.67, A:G.94, A:S.97

1 x G3A: GUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE(Non-covalent)

G3A.7: 11 residues within 4Å: Chain A: K.23, L.26, N.27, L.29, K.31, F.34, K.38, S.159, S.160, P.161, S.223 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:K.23, A:N.27, A:N.27, A:N.27, A:L.29, A:L.29, A:S.159, A:S.159, A:S.223 Water bridges: A:K.31, A:K.31, A:K.31, A:K.31, A:S.159, A:S.159, A:S.159, A:S.223 Salt bridges: A:K.38 pi-Stacking: A:F.34, A:F.34

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.8: 5 residues within 4Å: Chain A: K.114, D.140, F.142, F.143 Ligands: SAH.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.142, A:F.142 Hydrogen bonds: A:D.140 Salt bridges: A:K.114

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: K.39, R.66, R.221 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.38, A:K.39, A:K.39, A:R.66, A:R.221, A:R.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Egloff, M.P. et al., Structural and functional analysis of methylation and 5'-RNA sequence requirements of short capped RNAs by the methyltransferase domain of dengue virus NS5. J.Mol.Biol. (2007)

Release Date

2007-08-28

Peptides

type II methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

type II methyltransferase

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