SMTL ID : 7xd8.1 (5 other biounits)

Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Native Form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 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: 30 residues within 4Å: Chain A: R.138, R.141, S.142, N.143, Y.344, S.398, G.399, D.400, D.401, C.446, S.447, R.466, L.491, S.494, Y.495, M.498, T.527, S.528, R.529 Chain B: G.21, A.22, U.23, U.24, A.25, U.26, A.27, U.28, C.29, C.30 Ligands: GOL.4 Protein-ligand interaction information (PLIP) not available

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.3: 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 GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: P.526 Chain B: A.27, U.28 Ligands: G-G-A-U-A-U-A-A-U.1, G-G-A-U-A-U-A-A-U.1, G-G-A-U-A-U-A-A-U.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.526

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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