SMTL ID : 5ikm.1

1.9 Angstrom Crystal Structure of NS5 Methyl Transferase from Dengue Virus 1 in Complex with S-Adenosylmethionine and Beta-D-Fructopyranose.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 2 residues within 4Å: Chain A: G.228, N.229 Ligand excluded by PLIP

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

SO4.2: 2 residues within 4Å: Chain A: K.202 Ligands: BDF.12 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.202 SO4.3: 6 residues within 4Å: Chain A: R.41, K.45, V.58, S.59, R.60, R.87 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.60 Water bridges: A:R.87 Salt bridges: A:R.41, A:K.45, A:R.87 SO4.4: 3 residues within 4Å: Chain A: H.249, R.250, K.251 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.249, A:K.251 Water bridges: A:R.250 Salt bridges: A:H.249 SO4.5: 3 residues within 4Å: Chain A: M.240, R.244, M.247 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.35, A:R.244 Salt bridges: A:R.244 SO4.6: 3 residues within 4Å: Chain A: R.163, R.166 Ligands: MLT.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.166 Water bridges: A:E.152, A:R.163, A:R.163 Salt bridges: A:R.163 SO4.7: 2 residues within 4Å: Chain A: R.18, Q.22 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.22 Water bridges: A:R.18, A:R.18 Salt bridges: A:R.18 SO4.8: 3 residues within 4Å: Chain A: G.96, L.97, K.98 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.96, A:K.98 SO4.9: 3 residues within 4Å: Chain A: K.98, Y.122, R.265 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.122 Water bridges: A:R.265, A:R.265 Salt bridges: A:R.265 SO4.10: 2 residues within 4Å: Chain A: E.141, K.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.142 Salt bridges: A:K.79

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.11: 18 residues within 4Å: Chain A: S.59, G.61, G.84, C.85, G.86, G.88, G.89, W.90, T.107, K.108, H.113, K.133, D.134, V.135, F.136, D.149, I.150 Ligands: MLT.13 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:S.59, A:G.88, A:G.89, A:W.90, A:W.90, A:T.107, A:K.108, A:K.108, A:H.113, A:D.134, A:D.134, A:V.135, A:D.149 Water bridges: A:D.82, A:G.84, A:C.85, A:R.87, A:R.87, A:E.114, A:E.114 Salt bridges: A:D.149

1 x BDF: beta-D-fructopyranose(Non-covalent)

BDF.12: 6 residues within 4Å: Chain A: K.169, E.172, P.173, K.202, H.203 Ligands: SO4.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.169, A:K.169, A:K.202, A:H.203 Water bridges: A:E.172, A:P.173

1 x MLT: D-MALATE(Non-covalent)

MLT.13: 7 residues within 4Å: Chain A: K.108, D.134, F.136, F.137, R.166 Ligands: SO4.6, SAM.11 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.137 Hydrogen bonds: A:D.134 Water bridges: A:K.108, A:K.108 Salt bridges: A:K.108, A:R.166, A:R.166

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 4 residues within 4Å: Chain A: R.176, G.177, K.202, H.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.202, A:H.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., 1.9 Angstrom Crystal Structure of NS5 Methyl Transferase from Dengue Virus 1 in Complex with S-Adenosylmethionine and Beta-D-Fructopyranose. To Be Published

Release Date

2016-03-16

Peptides

NS5 Methyl Transferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NS5 Methyl Transferase