SMTL ID : 4o4r.1 (2 other biounits)

Murine Norovirus RdRp in complex with PPNDS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

2 x 20V: 3-[(E)-{4-formyl-5-hydroxy-6-methyl-3-[(phosphonooxy)methyl]pyridin-2-yl}diazenyl]-7-nitronaphthalene-1,5-disulfonic acid(Non-covalent)

20V.1: 11 residues within 4Å: Chain A: M.219, M.221, Y.341, L.391, R.392, R.393, L.406, Q.414, K.419, Q.439 Ligands: 20V.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.391, A:Q.414 Hydrogen bonds: A:Y.341, A:R.392, A:K.419 Salt bridges: A:R.392, A:R.393, A:K.419 20V.2: 12 residues within 4Å: Chain A: M.28, F.29, K.166, L.169, Y.341, L.391, R.392, S.410, R.413, Q.414, K.419 Ligands: 20V.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.391, A:Q.414 Hydrogen bonds: A:Y.341, A:Y.341, A:R.392, A:R.413, A:Q.414 Water bridges: A:K.166 Salt bridges: A:K.166, A:R.392, A:K.419

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

SO4.3: 5 residues within 4Å: Chain A: T.25, G.48, S.49, S.58, L.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.49, A:L.59 Water bridges: A:K.50, A:Q.60 SO4.4: 2 residues within 4Å: Chain A: M.360, R.363 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.364 Salt bridges: A:R.363 SO4.5: 3 residues within 4Å: Chain A: T.117, K.127, M.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.117 Water bridges: A:D.114, A:G.301 Salt bridges: A:K.127 SO4.6: 2 residues within 4Å: Chain A: Q.61, R.64 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.64 SO4.7: 2 residues within 4Å: Chain A: K.68 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.68 Salt bridges: A:K.68 SO4.8: 5 residues within 4Å: Chain A: T.8, A.10, G.11, K.68 Ligands: SO4.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.10, A:G.11 Water bridges: A:T.8, A:K.68, A:K.68 Salt bridges: A:K.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Croci, R. et al., PPNDS inhibits murine Norovirus RNA-dependent RNA-polymerase mimicking two RNA stacking bases. Febs Lett. (2014)

Release Date

2014-11-05

Peptides

RNA-dependent-RNA-polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA-dependent-RNA-polymerase

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