SMTL ID : 4k6m.1 (1 other biounit)

Crystal Structure of the full-length Japanese encephalitis virus NS5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

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

SAH.1: 20 residues within 4Å: Chain A: S.56, G.58, G.81, C.82, G.83, R.84, G.85, G.86, W.87, T.104, K.105, H.110, E.111, V.130, D.131, V.132, F.133, D.146, I.147 Ligands: SO4.11 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.56, A:R.84, A:G.85, A:G.86, A:W.87, A:W.87, A:W.87, A:T.104, A:K.105, A:H.110, A:E.111, A:D.131, A:D.131, A:V.132 Water bridges: A:G.106, A:G.148

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

SO4.2: 3 residues within 4Å: Chain A: T.38, R.41, R.45 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.41 Salt bridges: A:R.41, A:R.45 SO4.3: 5 residues within 4Å: Chain A: R.28, E.34, R.41, R.57, R.213 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.34 Salt bridges: A:R.28, A:R.41, A:R.57, A:R.213 SO4.4: 5 residues within 4Å: Chain A: R.37, R.41, R.44, V.55, R.84 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.57 Salt bridges: A:R.37, A:R.41, A:R.44, A:R.84 SO4.5: 3 residues within 4Å: Chain A: A.31, R.243, R.246 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.243, A:R.246 SO4.6: 4 residues within 4Å: Chain A: R.28, R.213, S.215, N.216 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.215, A:N.216 Water bridges: A:R.213 Salt bridges: A:R.28 SO4.7: 3 residues within 4Å: Chain A: A.410, L.411, G.412 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.411, A:G.412 Water bridges: A:A.413, A:N.419 SO4.8: 5 residues within 4Å: Chain A: R.734, R.742, S.799, W.800, S.801 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.799, A:W.800, A:S.801 Water bridges: A:R.734 Salt bridges: A:R.734, A:R.742 SO4.9: 4 residues within 4Å: Chain A: K.360, R.474, G.539, K.694 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.539 Salt bridges: A:R.474, A:K.694 SO4.10: 2 residues within 4Å: Chain A: G.561, R.564 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.564 SO4.11: 4 residues within 4Å: Chain A: G.109, H.110, E.111 Ligands: SAH.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.111 Salt bridges: A:H.110

2 x ZN: ZINC ION(Non-covalent)

ZN.12: 4 residues within 4Å: Chain A: E.440, H.444, C.449, C.452 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.440, A:H.444, A:C.449, A:C.452 ZN.13: 4 residues within 4Å: Chain A: H.717, C.733, E.848, C.852 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.717, A:C.733, A:E.848, A:C.852

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, G. et al., Crystal Structure of the full-length Japanese encephalitis virus NS5 reveals a conserved methyltransferase-polymerase interface. Plos Pathog. (2013)

Release Date

2013-08-28

Peptides

Polyprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polyprotein

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