SMTL ID : 7hkz.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 POB0029 (DNV2_NS5A-x0851)

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: 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, Y.619 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.514, A:M.546, A:Y.619 pi-Cation interactions: A:Y.619 DMS.5: 4 residues within 4Å: Chain A: K.456, E.571, I.573, 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, S.528, W.540 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.528 pi-Cation interactions: A:Y.495

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

PO4.7: 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:N.292 Water bridges: A:N.292, A:N.292 Salt bridges: A:K.299

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

PEG.8: 0 residues within 4Å: (No contacts) 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 01: [(2S,6R)-1-(methanesulfonyl)-6-methylpiperidin-2-yl]methanol

01.11: 10 residues within 4Å: Chain A: V.244, E.245, G.246, E.247, G.248, L.249, L.252, Y.344, S.398, T.537 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.249, A:L.252, A:L.252 Hydrogen bonds: A:G.246, A:Y.344 01.12: 3 residues within 4Å: Chain A: K.125, K.126, D.232 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.126

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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