SMTL ID : 6evk.1

Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter and cap analogue m7GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: D.435 Chain B: H.571 No protein-ligand interaction detected (PLIP)

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

PO4.2: 5 residues within 4Å: Chain A: S.424, E.425, L.426, K.644, R.647 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.426 Salt bridges: A:K.644, A:R.647 PO4.3: 6 residues within 4Å: Chain A: K.303, T.427, N.428, S.429, R.463, E.466 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.303, A:R.463 PO4.4: 2 residues within 4Å: Chain A: D.538, N.541 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.538, A:D.538, A:N.541 PO4.5: 5 residues within 4Å: Chain A: C.290, T.291, R.293, N.705, P.707 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.291, A:N.705 PO4.6: 4 residues within 4Å: Chain B: D.314, T.316, K.317, K.490 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.316, B:T.316, B:K.317 Water bridges: B:D.314, B:D.314 Salt bridges: B:K.317, B:K.490 PO4.7: 3 residues within 4Å: Chain B: R.569, T.579, R.580 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.580 Salt bridges: B:R.569, B:R.580 PO4.8: 5 residues within 4Å: Chain B: G.283, G.284, N.285 Chain C: R.225, F.226 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:F.226, B:G.283, B:N.285, B:N.285, B:E.286 Water bridges: B:E.286 PO4.9: 8 residues within 4Å: Chain A: E.589, R.591, R.592 Chain B: F.521, G.522, L.559, F.560, D.563 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.521, B:D.563, B:D.563 Salt bridges: A:R.592 PO4.10: 7 residues within 4Å: Chain B: W.318, N.319, Q.322, F.421, N.422, S.425, S.453 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.319, B:Q.322, B:F.421, B:N.422, B:N.422, B:S.425, B:S.425, B:S.453 PO4.11: 6 residues within 4Å: Chain B: R.611, N.612, L.620 Chain C: L.131, L.134, T.135 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.612 Salt bridges: B:R.611 PO4.13: 3 residues within 4Å: Chain C: M.62, K.63, Y.64 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Salt bridges: B:K.678 Hydrogen bonds: C:K.63, C:Y.64 PO4.14: 5 residues within 4Å: Chain B: N.25, R.507 Chain C: E.671, I.675, G.678 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.25, B:R.507

1 x MGP: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

MGP.12: 14 residues within 4Å: Chain C: F.332, S.333, R.341, R.348, T.364, F.366, E.370, F.372, K.385, F.413, Q.415, N.438, M.440, Y.441 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:R.341, C:T.364, C:T.364, C:K.385, C:N.438, C:N.438 Salt bridges: C:R.348, C:E.370 pi-Stacking: C:F.366, C:F.366, C:F.413

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pflug, A. et al., Capped RNA primer binding to influenza polymerase and implications for the mechanism of cap-binding inhibitors. Nucleic Acids Res. (2018)

Release Date

2017-12-13

Peptides

Polymerase acidic protein: A
RNA-directed RNA polymerase catalytic subunit: B
Polymerase basic protein 2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Polymerase acidic protein

RNA-directed RNA polymerase catalytic subunit

Polymerase basic protein 2

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