SMTL ID : 4y34.1

Crystal Structure of Coxsackievirus B3 3D polymerase in complex with GPC-N143

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x 45Z: 2,2'-[(4-fluorobenzene-1,2-diyl)bis(oxy)]bis(5-nitrobenzonitrile)(Non-covalent)

45Z.1: 16 residues within 4Å: Chain A: L.107, L.110, D.111, T.114, R.188, Y.195, H.199, V.210, G.290, C.291, S.292, G.293, T.294, S.295, I.296, Y.327 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.107, A:Y.195, A:V.210 Hydrogen bonds: A:R.188, A:G.290

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

SO4.2: 3 residues within 4Å: Chain A: R.174, S.235, G.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.236 Water bridges: A:Y.237 Salt bridges: A:R.174 SO4.3: 4 residues within 4Å: Chain A: R.416, L.448, P.449, T.453 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.416, A:K.457 SO4.4: 3 residues within 4Å: Chain A: Q.384, Y.385, R.455 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.455 SO4.6: 6 residues within 4Å: Chain A: K.38, L.162, K.376, D.397, E.400 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.397 Salt bridges: A:K.38, A:K.376 SO4.10: 4 residues within 4Å: Chain A: G.426, E.427, H.428, E.429 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.427, A:H.428, A:E.429

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: K.38, R.163, S.164, K.167, R.174, K.376 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.38, A:K.38, A:R.163, A:S.164, A:S.164, A:R.174, A:R.174, A:K.376, A:K.376 GOL.7: 6 residues within 4Å: Chain A: W.404, T.405, K.406, D.407, N.410, H.414 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.404, A:K.406, A:D.407, A:N.410 GOL.8: 5 residues within 4Å: Chain A: M.393, D.397, S.401, L.418 Ligands: SO4.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.401 GOL.9: 4 residues within 4Å: Chain A: Y.385, L.388, L.459, H.463 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.385, A:Y.385

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van der Linden, L. et al., The RNA Template Channel of the RNA-Dependent RNA Polymerase as a Target for Development of Antiviral Therapy of Multiple Genera within a Virus Family. Plos Pathog. (2015)

Release Date

2015-04-01

Peptides

3D polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

3D polymerase