SMTL ID : 7i2n.1

Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z1685106505 (DNV2_NS5A-x0571)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.449, H.451, C.465, C.584 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.449, A:H.451, A:C.465, A:C.584 ZN.2: 4 residues within 4Å: Chain A: E.175, H.179, C.184, C.187 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.175, A:H.179, A:C.184, A:C.187

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 4 residues within 4Å: Chain A: G.60, R.63, L.64, L.485 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.63

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 5 residues within 4Å: Chain A: S.500, N.514, C.517, M.546, W.570 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.545, A:L.547 DMS.5: 4 residues within 4Å: Chain A: K.456, E.571, I.573, Y.575 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.456 DMS.6: 4 residues within 4Å: Chain A: S.494, Y.495, M.498, W.540 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.495

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 8 residues within 4Å: Chain A: A.269, D.270, D.271, D.401, C.402, V.403, P.444, F.445 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.271, A:C.402, A:C.402, A:C.402 PO4.8: 5 residues within 4Å: Chain A: E.288, T.291, N.292, K.299, E.303 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.291, A:T.291, A:N.292 Salt bridges: A:K.299

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

PEG.9: 2 residues within 4Å: Chain A: P.559, W.560 No protein-ligand interaction detected (PLIP)

1 x TQC: (3M)-5-cyclobutyl-3-(1-methyl-1H-imidazol-2-yl)-1,2,4-oxadiazole(Non-covalent)

TQC.10: 10 residues within 4Å: Chain A: M.57, V.58, N.59, S.478, Q.479, G.480, W.483, E.487, T.488, L.491 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:M.57, A:N.59, A:W.483, A:T.488 Hydrogen bonds: A:S.478 pi-Stacking: A:W.483, A:W.483

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aschenbrenner, J.C. et al., Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2. To Be Published

Release Date

2025-04-02

Peptides

NS5 RNA-dependent RNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NS5 RNA-dependent RNA polymerase

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