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

Crystal structure of the dengue virus methyltransferase bound to a 5'- capped octameric RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

1 x G3A- G- A- A- C- C- U- G- A: 5'-(*G3AP*GP*AP*AP*CP*CP*UP*GP*A)-3'(Non-covalent)

G3A-G-A-A-C-C-U-G-A.1: 12 residues within 4Å: Chain A: K.14, L.17, N.18, L.20, S.21, R.22, F.25, S.150, S.151, P.152, S.153, S.213 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.14, A:N.18, A:L.20, A:L.20, A:L.20, A:S.150 Water bridges: A:N.18, A:L.20, A:R.22, A:S.150, A:S.213, A:S.213, A:S.213 pi-Stacking: A:F.25, A:F.25

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

SO4.2: 5 residues within 4Å: Chain A: R.38, K.42, S.56, R.57, R.84 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.57 Water bridges: A:K.42, A:R.57 Salt bridges: A:R.38, A:K.42, A:R.57, A:R.84 SO4.3: 3 residues within 4Å: Chain A: R.76, E.99, R.101 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.76, A:R.101, A:K.125 SO4.4: 3 residues within 4Å: Chain A: S.229, N.232, R.236 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:K.15, A:R.236 Hydrogen bonds: A:N.232 Water bridges: A:S.229, A:S.229 SO4.5: 3 residues within 4Å: Chain A: K.29, K.30, R.211 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.29, A:K.30, A:R.211 SO4.8: 4 residues within 4Å: Chain B: G.109, H.110, E.111 Ligands: SAH.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.109, B:E.111, B:E.111 Salt bridges: B:H.110 SO4.9: 4 residues within 4Å: Chain B: R.38, K.42, R.57, R.84 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.57 Water bridges: B:R.57 Salt bridges: B:R.38, B:K.42, B:R.57, B:R.84

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

SAH.6: 16 residues within 4Å: Chain A: S.56, G.58, G.81, C.82, G.83, G.86, W.87, T.104, K.105, E.111, K.130, D.131, V.132, F.133, D.146, I.147 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.56, A:G.86, A:W.87, A:W.87, A:T.104, A:K.105, A:K.105, A:D.131, A:D.131, A:V.132, A:D.146 Water bridges: A:R.84, A:G.85, A:G.85 SAH.10: 17 residues within 4Å: Chain B: S.56, G.58, G.81, C.82, G.83, G.86, W.87, T.104, K.105, E.111, K.130, D.131, V.132, F.133, D.146, I.147 Ligands: SO4.8 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.56, B:G.86, B:W.87, B:W.87, B:K.105, B:K.105, B:D.131, B:V.132, B:D.146

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: K.61, L.209, S.210, R.211, E.216 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yap, L.J. et al., Crystal Structure of the Dengue Virus Methyltransferase Bound to a 5'-Capped Octameric RNA. Plos One (2010)

Release Date

2010-09-29

Peptides

NONSTRUCTURAL PROTEIN NS5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

NONSTRUCTURAL PROTEIN NS5

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