SMTL ID : 8gzr.1

Cryo-EM structure of the the NS5-NS3 RNA-elongation complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: D.541, T.542, D.671 Ligands: MN.2, CDP.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.541, A:T.542, A:D.671 MN.2: 6 residues within 4Å: Chain A: D.541, D.671, D.672 Chain C: U.40 Ligands: MN.1, CDP.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.541, A:D.671, A:D.672 MN.7: 3 residues within 4Å: Chain B: T.255, E.340 Ligands: CDP.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.255

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.720, H.722, C.736, C.855 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.720, A:H.722, A:C.736, A:C.855 ZN.4: 4 residues within 4Å: Chain A: E.445, H.449, C.454, C.457 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.445, A:H.449, A:C.454, A:C.457

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

SAH.5: 19 residues within 4Å: Chain A: S.64, G.66, G.89, C.90, G.91, R.92, G.93, G.94, W.95, T.112, K.113, H.118, E.119, K.138, D.139, V.140, F.141, D.154, I.155 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.64, A:G.66, A:C.90, A:R.92, A:G.93, A:G.94, A:W.95, A:W.95, A:K.113, A:E.119, A:E.119, A:D.139, A:V.140

2 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.6: 16 residues within 4Å: Chain A: K.464, R.479, D.541, T.542, G.544, W.545, D.546, S.608, T.613, N.617, D.671 Chain C: G.16, A.17, U.40 Ligands: MN.1, MN.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.479, A:G.544, A:W.545, A:D.546, A:S.608, A:N.617 Salt bridges: A:R.479, A:R.479 CDP.8: 12 residues within 4Å: Chain B: P.250, G.251, S.252, G.253, K.254, T.255, R.256, N.384, N.471, K.473, R.518 Ligands: MN.7 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:N.471 Hydrogen bonds: B:G.251, B:G.251, B:S.252, B:G.253, B:K.254, B:T.255, B:R.256, B:N.384, B:N.471, B:K.473, B:R.518 Salt bridges: B:K.254, B:R.518, B:R.518 pi-Cation interactions: B:R.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osawa, T. et al., Structures of dengue virus RNA replicase complexes. Mol.Cell (2023)

Release Date

2023-08-02

Peptides

Genome polyprotein: A
Genome polyprotein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Genome polyprotein

Genome polyprotein

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