SMTL ID : 6xd1.1

Dengue serotype 3 RNA-dependent RNA polymerase bound to NITD-640

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.447, A:H.449, A:C.463 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

1 x V0J: (2R)-4-(butyl{[2'-(1H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]methyl}carbamoyl)-1-(2,2-diphenylpropanoyl)piperazine-2-carboxylic acid(Non-covalent)

V0J.3: 20 residues within 4Å: Chain A: V.45, K.46, T.48, D.154, S.155, A.156, M.189, G.190, K.191, R.192, E.193, F.199, G.200, S.205, R.206, I.208, W.209, W.212, K.313, M.324 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.45, A:T.48, A:A.156, A:F.199, A:I.208, A:W.209, A:W.212 Hydrogen bonds: A:R.192, A:R.192, A:E.193, A:K.313 Water bridges: A:Y.43, A:Y.43, A:N.187, A:N.187, A:K.191, A:G.200 Salt bridges: A:R.192 pi-Stacking: A:F.199 pi-Cation interactions: A:R.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arora, R. et al., Two RNA Tunnel Inhibitors Bind in Highly Conserved Sites in Dengue Virus NS5 Polymerase: Structural and Functional Studies. J.Virol. (2020)

Release Date

2020-09-23

Peptides

RNA-dependent RNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA-dependent RNA polymerase

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