SMTL ID : 6xd0.1

Dengue serotype 3 RNA-dependent RNA polymerase bound to NITD-434

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 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.7: 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

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.457, K.458, W.558, M.559, E.560, D.561 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.458, A:K.458, A:E.560, A:D.561 GOL.4: 3 residues within 4Å: Chain A: E.163, K.167, D.170 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.163, A:E.163, A:K.167, A:D.170 Water bridges: A:R.130 GOL.6: 5 residues within 4Å: Chain A: P.98, N.417, D.418, Q.428, W.429 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.417, A:Q.428, A:Q.428 Water bridges: A:D.418, A:D.418

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

PEG.3: 2 residues within 4Å: Chain A: N.370, H.372 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.370 PEG.5: 3 residues within 4Å: Chain A: Y.238, V.387, K.391 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.391

1 x V0M: 2-[({2-[(2,6-dichlorophenyl)amino]phenyl}acetyl)amino]-2,3-dihydro-1H-indene-2-carboxylic acid(Non-covalent)

V0M.8: 14 residues within 4Å: Chain A: F.133, K.136, V.137, W.153, R.216, E.219, F.220, G.224, N.227, E.228, V.338, G.339, W.530, I.532 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.133, A:F.133, A:K.136, A:V.137, A:W.153, A:W.153, A:F.220, A:V.338, A:I.532, A:I.532, A:I.532 Hydrogen bonds: A:K.136, A:N.227, A:N.227 Salt bridges: A:K.136 pi-Stacking: A:F.220 pi-Cation interactions: A:K.136 Halogen bonds: A:N.227, A:E.228

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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