SMTL ID : 7i2d.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 Z729352906 (DNV2_NS5A-x0258)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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: 6 residues within 4Å: Chain A: S.500, N.514, C.517, M.546, W.570, Y.619 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.514, A:M.546, A:M.546 pi-Cation interactions: A:Y.619 DMS.5: 5 residues within 4Å: Chain A: K.456, E.571, I.573, P.574, Y.575 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.456 Water bridges: A:Y.575 DMS.6: 5 residues within 4Å: Chain A: S.494, Y.495, M.498, W.540, M.541 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.495

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

PEG.7: 3 residues within 4Å: Chain A: H.538, E.539, M.541 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.539 PEG.10: 2 residues within 4Å: Chain A: P.559, W.560 No protein-ligand interaction detected (PLIP)

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

PO4.8: 7 residues within 4Å: Chain A: A.269, D.270, D.271, D.401, C.402, P.444, F.445 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.269, A:D.271, A:C.402, A:C.402 PO4.9: 5 residues within 4Å: Chain A: E.288, T.291, N.292, K.299, E.303 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.291, A:T.291, A:N.292 Salt bridges: A:K.299, A:K.307

1 x WHM: 2-[(3-fluorophenyl)methyl]-1lambda~6~,2-thiazolidine-1,1-dione(Non-covalent)

WHM.11: 5 residues within 4Å: Chain A: R.507, K.578, Q.582, I.588, G.589 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.578 Hydrogen bonds: A:Q.582

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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