SMTL ID : 7xd9.1 (5 other biounits)

Crystal Structure of Dengue Virus serotype 2 (DENV2) Polymerase Elongation Complex (CTP Form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

monomer

Ligands

1 x G- G- A- U- A- U- A- A- U: RNA (9-mer)(Non-covalent)

G-G-A-U-A-U-A-A-U.1: 31 residues within 4Å: Chain A: R.138, R.141, S.142, K.197, Y.344, S.398, G.399, D.400, D.401, C.446, S.447, H.448, R.466, L.491, S.494, Y.495, M.498, T.527, S.528, R.529 Chain B: A.22, U.23, U.24, A.25, U.26, A.27, U.28, C.29, C.30 Ligands: MG.2, CTP.8 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.271, D.401, S.447 Ligands: G-G-A-U-A-U-A-A-U.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.401, H2O.3, H2O.4 MG.3: 4 residues within 4Å: Chain A: D.271, T.272, D.400 Ligands: CTP.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.271, A:T.272, A:D.400

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 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.5: 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

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: R.133, T.137, V.163, W.169 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.133, A:T.137 GOL.7: 4 residues within 4Å: Chain A: E.245, G.246, E.247, K.251 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.247, A:K.251, A:K.251 Water bridges: A:E.247, A:E.247

1 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.8: 17 residues within 4Å: Chain A: K.95, K.194, R.209, D.271, T.272, G.274, W.275, D.276, S.338, T.343, N.347, D.400, K.426 Chain B: G.21, A.22 Ligands: G-G-A-U-A-U-A-A-U.1, MG.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.194, A:K.194, A:G.274, A:W.275, A:D.276, A:D.276, A:N.347 Water bridges: A:D.271 Salt bridges: A:K.95, A:K.95, A:R.209, A:R.209, A:K.426

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, J. et al., Structural basis of transition from initiation to elongation in de novo viral RNA-dependent RNA polymerases. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2022-12-21

Peptides

NS5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NS5

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