SMTL ID : 6fhh.1

Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter bound to a 22-mer modified Pol II CTD peptide with serine 5 thiophosphorylated.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-2-mer

Ligands

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

PO4.1: 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 PO4.2: 6 residues within 4Å: Chain A: C.290, T.291, R.293, R.410, N.705, P.707 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.291, A:T.291 Water bridges: A:K.548 PO4.3: 4 residues within 4Å: Chain A: K.339, G.343, N.345, T.346 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.343, A:N.345, A:N.345, A:T.346 Salt bridges: A:K.339 PO4.5: 5 residues within 4Å: Chain B: D.314, N.315, 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:R.248, B:N.315 Salt bridges: B:K.317, B:K.490 PO4.6: 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 PO4.7: 7 residues within 4Å: Chain B: G.283, G.284, N.285, E.286 Chain C: R.225, F.226 Ligands: PO4.12 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.284, B:N.285, B:N.285, B:E.286, C:F.226 PO4.8: 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 PO4.9: 8 residues within 4Å: Chain A: E.589, R.591, R.592 Chain B: F.521, G.522, L.559, F.560, D.563 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:F.521, B:L.559, B:D.563, B:D.563 Water bridges: B:F.560, A:R.591, A:R.591 PO4.10: 7 residues within 4Å: Chain B: W.318, N.319, Q.322, F.421, N.422, S.425, S.453 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.319, B:Q.322, B:F.421, B:S.425, B:S.425, B:S.453 PO4.11: 5 residues within 4Å: Chain B: K.540, I.544 Chain C: L.227, V.238, E.239 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:V.238 Salt bridges: B:K.540 PO4.12: 6 residues within 4Å: Chain B: G.283, E.286 Chain C: R.153, R.225, F.226 Ligands: PO4.7 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:F.226, B:G.283 Salt bridges: C:R.153 PO4.13: 6 residues within 4Å: Chain C: R.273, E.314, Q.315, Q.347, V.527, S.528 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.314, C:E.314, C:E.314, C:Q.315, C:Q.315, C:Q.347, C:S.528 Salt bridges: C:R.273 PO4.14: 3 residues within 4Å: Chain C: M.62, K.63, Y.64 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.63, C:Y.64 Salt bridges: B:K.678 PO4.15: 7 residues within 4Å: Chain B: P.22, N.25, R.507 Chain C: E.671, I.675, G.678, S.680 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.25 Salt bridges: B:R.507 PO4.16: 6 residues within 4Å: Chain B: P.710, R.730 Chain C: F.177, P.178, N.179, E.180 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Salt bridges: B:R.730 Hydrogen bonds: C:N.179, C:E.180, C:E.180

1 x ZN: ZINC ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Claron, M. et al., Towards New Anti-Influenza Therapeutics: Structure-Activity Relationships in the Interaction between Heterotrimeric Influenza Polymerase and Pol II C-terminal domain. To Be Published

Release Date

2019-01-30

Peptides

Polymerase acidic protein: A
RNA-directed RNA polymerase catalytic subunit: B
Polymerase basic protein 2: C
TYR-SER-PRO-THR-TPS-PRO-SER: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

F
X

G
Y

Polymerase acidic protein

RNA-directed RNA polymerase catalytic subunit

Polymerase basic protein 2

TYR-SER-PRO-THR-TPS-PRO-SER

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