SMTL ID : 2p1d.1 (1 other biounit)

Crystal structure of dengue methyltransferase in complex with GTP and S-Adenosyl-L-homocysteine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: G.118, H.119, E.120 Ligands: SAH.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.120 Salt bridges: A:H.119 SO4.2: 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 SO4.3: 3 residues within 4Å: Chain A: R.66, K.70, R.221 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.70, A:R.221 Salt bridges: A:R.66, A:K.70, A:R.221 SO4.4: 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 Salt bridges: A:R.47, A:K.51, A:R.66, A:R.93 SO4.5: 4 residues within 4Å: Chain A: V.238, S.239, N.242, R.246 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.238, A:N.242 Salt bridges: A:R.246 SO4.6: 2 residues within 4Å: Chain A: K.21, I.249 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.21 SO4.7: 4 residues within 4Å: Chain A: K.38, K.39, R.66, R.221 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.39, A:R.66, A:R.221 SO4.8: 2 residues within 4Å: Chain A: H.61, G.268 No protein-ligand interaction detected (PLIP) SO4.9: 5 residues within 4Å: Chain A: K.114, D.140, F.142, R.172 Ligands: SAH.11 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.114, A:R.172 SO4.10: 1 residues within 4Å: Chain A: H.61 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.61

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

SAH.11: 21 residues within 4Å: Chain A: S.65, G.67, G.90, C.91, G.92, R.93, G.94, G.95, W.96, T.113, K.114, H.119, E.120, V.139, D.140, V.141, F.142, D.155, I.156 Ligands: SO4.1, SO4.9 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.65, A:G.67, A:R.93, A:G.94, A:G.95, A:W.96, A:W.96, A:K.114, A:G.115, A:H.119, A:D.140, A:V.141 pi-Cation interactions: A:K.114

1 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.12: 10 residues within 4Å: Chain A: K.23, L.26, N.27, L.29, F.34, K.38, S.159, S.160, P.161, S.223 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.23, A:N.27, A:L.29, A:L.29, A:L.29, A:S.159, A:S.159, A:S.223 Salt bridges: A:K.38 pi-Stacking: A:F.34, A:F.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Egloff, M.P. et al., An RNA cap (nucleoside-2'-O)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization. EMBO J. (2002)

Release Date

2007-03-20

Peptides

type II methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

type II methyltransferase

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