SMTL ID : 4y2a.1

Crystal Structure of Coxsackie Virus B3 3D polymerase in complex with GPC-N114 inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

1 x 1FS: 2,2'-[(4-chlorobenzene-1,2-diyl)bis(oxy)]bis(5-nitrobenzonitrile)(Non-covalent)

1FS.1: 18 residues within 4Å: Chain A: L.107, E.108, L.110, D.111, K.127, S.184, R.188, Y.195, H.199, V.210, G.290, C.291, S.292, G.293, T.294, S.295, I.296, Y.327 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.107, A:R.188, A:V.210 Hydrogen bonds: A:K.127, A:S.295, A:I.296

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

SO4.2: 4 residues within 4Å: Chain A: K.61, R.174, S.235, G.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.236 Salt bridges: A:K.61, A:R.174 SO4.3: 5 residues within 4Å: Chain A: R.416, T.447, L.448, P.449, T.453 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.448 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 SO4.5: 5 residues within 4Å: Chain A: K.38, K.376, D.397, E.400, S.401 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.397 Salt bridges: A:K.38, A:K.376 SO4.6: 3 residues within 4Å: Chain A: G.426, E.427, H.428 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.427, A:H.428

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: T.405, K.406, N.410, H.414 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.406, A:D.407 GOL.8: 4 residues within 4Å: Chain A: Y.385, L.388, L.459, H.463 No protein-ligand interaction detected (PLIP) GOL.9: 3 residues within 4Å: Chain A: R.44, S.45, G.46 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.44, A:S.45, A:S.45, A:G.46 GOL.10: 5 residues within 4Å: Chain A: K.38, R.163, S.164, K.167, R.174 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.38, A:K.38, A:R.163, A:S.164, A:S.164, A:R.174

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