SMTL ID : 3vws.1

Dengue serotype 3 RNA-dependent RNA polymerase bound to NITD-107

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.447, H.449, C.463, C.582 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.447, A:H.449, A:C.463, A:C.582 ZN.2: 4 residues within 4Å: Chain A: E.172, H.176, C.181, C.184 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.172, A:H.176, A:C.181, A:C.184

2 x VWS: 5-{[(4-chlorophenyl)sulfonyl]amino}-2-methyl-1-benzofuran-3-carboxylic acid(Non-covalent)

VWS.3: 11 residues within 4Å: Chain A: N.140, V.146, F.147, T.148, W.212, F.220, S.335, G.336, R.527, W.530 Ligands: VWS.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.146, A:F.147, A:F.147 Hydrogen bonds: A:N.140, A:V.146, A:T.148, A:R.527 Water bridges: A:T.148, A:G.336 VWS.4: 13 residues within 4Å: Chain A: K.136, F.147, R.216, N.227, G.336, Q.337, V.338, G.339, T.340, Y.341, W.530, I.532 Ligands: VWS.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.338, A:I.532, A:I.532 Hydrogen bonds: A:N.227, A:G.339, A:T.340, A:Y.341 Water bridges: A:K.136 Salt bridges: A:K.136

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 2 residues within 4Å: Chain A: P.557, W.558 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noble, C.G. et al., Conformational flexibility of the Dengue virus RNA-dependent RNA polymerase revealed by a complex with an inhibitor. J.Virol. (2013)

Release Date

2013-02-27

Peptides

Non-structural protein 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Non-structural protein 5

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