SMTL ID : 7hkd.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 Z53825479 (DNV2_NS5A-x0172)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 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: 3 residues within 4Å: Chain A: G.60, R.63, L.64 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: 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: 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: 2 residues within 4Å: Chain A: H.538, M.541 No protein-ligand interaction detected (PLIP) PEG.10: 2 residues within 4Å: Chain A: P.559, W.560 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.560

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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.291, A:N.292, A:N.292 Salt bridges: A:K.299

1 x 8BT: N-cyclopentylmethanesulfonamide(Non-covalent)

8BT.11: 10 residues within 4Å: Chain A: F.136, K.139, L.146, R.219, E.222, F.223, G.339, Q.340, V.341, V.342 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.136, A:K.139, A:L.146 Hydrogen bonds: A:V.341, A:V.342 Water bridges: A:Q.340

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saini, M. 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

2024-10-30

Peptides

Genome polyprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Genome polyprotein

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