SMTL ID : 5kqs.1

Structure of NS5 methyltransferase from Zika virus bound to S-adenosylmethionine and 7-methyl-guanosine-5'-diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x M7G: 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE(Non-covalent)

M7G.1: 12 residues within 4Å: Chain A: K.15, L.18, N.19, M.21, F.26, K.30, S.152, S.153, S.154, R.215, S.217 Ligands: GOL.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:K.15, A:K.15, A:M.21, A:M.21, A:M.21, A:S.152, A:S.152, A:R.215, A:R.215, A:S.217 Water bridges: A:S.152, A:S.152 Salt bridges: A:K.30, A:R.215 pi-Stacking: A:F.26, A:F.26

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.39, R.43, S.58, R.59, R.86 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.43, A:R.59, A:R.59, A:R.86, A:R.86 GOL.3: 4 residues within 4Å: Chain A: N.19, S.154 Ligands: M7G.1, ACT.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.19 Water bridges: A:M.21 GOL.4: 4 residues within 4Å: Chain A: D.133, F.135, R.165 Ligands: SAM.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.133, A:R.165, A:R.165 GOL.5: 2 residues within 4Å: Chain A: Y.121, S.263 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.121

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 3 residues within 4Å: Chain A: S.153, S.154 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.153, A:S.154

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

SAM.7: 19 residues within 4Å: Chain A: S.58, G.60, G.83, C.84, G.85, G.87, G.88, W.89, T.106, K.107, H.112, V.132, D.133, V.134, F.135, D.148, I.149 Ligands: GOL.4, PO4.8 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.58, A:G.87, A:G.88, A:W.89, A:W.89, A:T.106, A:K.107, A:H.112, A:D.133, A:D.133, A:V.134 Water bridges: A:D.81, A:G.83, A:R.86, A:S.90, A:Y.222 Salt bridges: A:D.148

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 4 residues within 4Å: Chain A: G.111, H.112, E.113 Ligands: SAM.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.113 Salt bridges: A:H.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Coloma, J. et al., Structures of NS5 Methyltransferase from Zika Virus. Cell Rep (2016)

Release Date

2016-09-14

Peptides

Methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methyltransferase

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