SMTL ID : 5dto.1

Dengue virus full length NS5 complexed with viral Cap 0-RNA and SAH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x A- G- U- U: RNA (5'-R(P*AP*GP*UP*U)-3')(Non-covalent)

A-G-U-U.1: 18 residues within 4Å: Chain A: K.39, S.53, R.54, K.58, R.81, G.106, E.108, D.143, G.145, E.146, S.147, K.177, L.179, T.211, E.213 Ligands: SAH.4, M7G.7, MG.8 Protein-ligand interaction information (PLIP) not available

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: E.434, H.438, C.443, G.444, C.446 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.434, A:H.438, A:C.443, A:C.446 ZN.3: 4 residues within 4Å: Chain A: H.709, H.711, C.725, C.844 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.709, A:H.711, A:C.725, A:C.844

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.4: 19 residues within 4Å: Chain A: S.53, G.55, G.78, C.79, G.80, G.82, G.83, W.84, T.101, K.102, H.107, E.108, K.127, D.128, V.129, F.130, D.143 Ligands: A-G-U-U.1, A-G-U-U.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.53, A:C.79, A:G.82, A:G.83, A:W.84, A:T.101, A:K.102, A:E.108, A:D.128, A:V.129, A:D.143, A:D.143 Water bridges: A:R.81, A:S.85

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.5: 3 residues within 4Å: Chain A: D.530, D.661, P.704 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.661, H2O.2, H2O.2, H2O.3, H2O.8 MG.8: 2 residues within 4Å: Ligands: A-G-U-U.1, M7G.7 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 2 residues within 4Å: Chain A: R.496, K.653 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.496 Salt bridges: A:R.496

1 x M7G: 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE(Non-covalent)

M7G.7: 15 residues within 4Å: Chain A: K.11, L.14, N.15, Q.16, L.17, F.22, K.26, S.147, S.148, P.149, R.208, S.210, T.211 Ligands: A-G-U-U.1, MG.8 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.11, A:N.15, A:L.17, A:L.17, A:L.17, A:S.147, A:E.154, A:E.154, A:S.210, A:S.210 Water bridges: A:S.147, A:R.208 Salt bridges: A:K.26, A:K.26 pi-Stacking: A:F.22, A:F.22 pi-Cation interactions: A:F.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Molecular basis for specific viral RNA recognition and 2'-O-ribose methylation by the dengue virus nonstructural protein 5 (NS5). Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-11-25

Peptides

NS5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NS5