SMTL ID : 4lq3.1

Crystal structure of human norovirus RNA-dependent RNA-polymerase bound to the inhibitor PPNDS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x G- G: 5'-R(P*GP*G)-3'(Non-covalent)

G-G.1: 8 residues within 4Å: Chain A: K.28, T.117, R.127, N.129, R.420, G.421, P.422, N.423 Protein-ligand interaction information (PLIP) not available

4 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.2: 8 residues within 4Å: Chain A: E.324, V.325, T.326, N.327, K.353, D.355, K.358 Ligands: 20V.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.355 Salt bridges: A:K.353 20V.3: 2 residues within 4Å: Chain A: K.358 Ligands: 20V.2 No protein-ligand interaction detected (PLIP) 20V.4: 15 residues within 4Å: Chain A: K.167, D.168, E.169, R.393, L.407, S.411, I.412, R.414, Q.415, R.420, Q.440, L.444, V.505, D.508, E.511 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Q.415, A:E.511 Hydrogen bonds: A:D.168, A:R.393, A:S.411, A:R.414, A:Q.440, A:E.511 Salt bridges: A:R.393, A:R.393 20V.5: 4 residues within 4Å: Chain A: K.461, I.464, A.465, K.468 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.464 Hydrogen bonds: A:K.461 Water bridges: A:K.468 Salt bridges: A:K.468

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: D.241, D.345, E.346, T.390 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.241, A:D.345, A:E.346, A:T.390

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tarantino, D. et al., Naphthalene-sulfonate inhibitors of human norovirus RNA-dependent RNA-polymerase. Antiviral Res. (2014)

Release Date

2014-02-12

Peptides

RNA-dependent RNA-polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA-dependent RNA-polymerase

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