SMTL ID : 5m3h.1

Bat influenza A/H17N10 polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-2-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: D.425 Chain B: K.562, H.571 No protein-ligand interaction detected (PLIP)

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

PO4.2: 2 residues within 4Å: Chain A: D.528, N.531 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.528, A:D.528, A:N.531 PO4.3: 6 residues within 4Å: Chain A: C.280, T.281, R.283, R.400, N.695, P.697 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.281, A:T.281 PO4.4: 4 residues within 4Å: Chain A: G.333, V.334, N.335, T.336 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.333, A:N.335, A:N.335 Salt bridges: A:K.329 PO4.5: 6 residues within 4Å: Chain B: D.314, N.315, T.316, K.317, K.490 Ligands: PO4.10 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.316, B:T.316, B:K.317 Water bridges: B:R.248, B:D.314, 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: 6 residues within 4Å: Chain B: G.283, G.284, N.285, E.286 Chain C: 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: 8 residues within 4Å: Chain A: E.579, R.581, R.582 Chain B: F.521, G.522, L.559, F.560, D.563 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:F.521, B:D.563 Water bridges: B:F.560, A:E.579, A:R.581 Salt bridges: A:R.582 PO4.9: 7 residues within 4Å: Chain B: W.318, N.319, Q.322, F.421, N.422, S.425, S.453 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.319, B:Q.322, B:F.421, B:F.421, B:S.425, B:S.425 Water bridges: B:S.425, B:S.425, B:S.425 PO4.10: 6 residues within 4Å: Chain A: E.660, K.663 Chain B: K.244, D.314, K.490 Ligands: PO4.5 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:D.454 Salt bridges: B:K.244, B:K.490, A:K.663 PO4.11: 5 residues within 4Å: Chain B: K.540, I.544 Chain C: R.225, L.227, V.238 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Salt bridges: B:K.540 Hydrogen bonds: C:R.225, C:V.238 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: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.283, C:F.226 Salt bridges: C:R.153 PO4.13: 5 residues within 4Å: Chain C: R.273, E.314, Q.315, Q.347, S.528 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.314, C:E.314, C:Q.315, C:Q.315, C:Q.347, C:E.526, C:S.528 Salt bridges: C:R.273 PO4.14: 4 residues within 4Å: Chain B: K.678 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 PO4.15: 6 residues within 4Å: Chain B: N.25, R.507 Chain C: E.671, I.675, G.678, S.680 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.25, B:N.25, C:G.678 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: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:F.177, C:N.179, C:E.180 Salt bridges: B:R.730

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lukarska, M. et al., Structural basis of an essential interaction between influenza polymerase and Pol II CTD. Nature (2017)

Release Date

2016-12-21

Peptides

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

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