SMTL ID : 9f37.1

Replication-like initiation state of influenza polymerase with GTP and CTP at respectively the -1 and +1 positions (strain A/little yellow-shouldered bat/Guatemala/060/2010/H17N10)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

hetero-1-1-1-mer

Ligands

5 x GOL: GLYCEROL

GOL.1: 5 residues within 4Å: Chain A: I.279, R.280, L.692, K.693, Y.696 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.280, A:R.280 Water bridges: A:R.280 GOL.2: 8 residues within 4Å: Chain A: S.236, F.237, Y.246, K.259 Chain B: D.79, Q.93, T.94, D.95 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:K.259 Hydrogen bonds: B:D.95, B:D.95 GOL.3: 7 residues within 4Å: Chain A: E.589, R.592 Chain B: F.521, G.522, L.559, F.560, D.563 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.589, A:R.592 Water bridges: A:R.591, B:F.560 GOL.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.9: 3 residues within 4Å: Chain C: A.287, S.288, L.544 1 PLIP interactions: 1 interactions with chain C Water bridges: C:S.291

1 x CTP: CYTIDINE-5'-TRIPHOSPHATE

CTP.5: 18 residues within 4Å: Chain B: R.248, D.314, N.315, T.316, K.317, W.318, N.319, M.416, M.418, G.419, S.453, D.454, K.490 Chain D: G.16, C.17 Ligands: GTP.6, MG.7, MG.8 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:K.317, B:W.318, B:N.319, B:N.319, B:G.419, B:S.453 Water bridges: B:R.248, B:R.248, B:R.248, B:R.248, B:R.248, B:K.317, B:K.317, B:K.490 Salt bridges: B:R.248, B:R.248, B:K.317, B:K.317, B:K.490, B:K.490, B:K.490

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE

GTP.6: 17 residues within 4Å: Chain A: K.673 Chain B: K.244, D.314, N.422, D.454, D.455, E.500, T.502, S.503, H.658, G.659, P.660 Chain D: G.16, C.17, U.18 Ligands: CTP.5, MG.7 24 PLIP interactions: 20 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.422, B:N.422, B:S.453, B:D.454, B:S.503, B:S.503, B:G.659, A:R.672 Water bridges: B:Y.33, B:K.244, B:K.244, B:K.244, B:D.455, B:K.490, B:K.490, B:E.500, B:E.500, B:E.500, A:K.673, A:K.673 Salt bridges: B:K.244, B:H.658, B:H.658, A:K.673

2 x MG: MAGNESIUM ION

MG.7: 6 residues within 4Å: Chain B: D.314, D.454, D.455 Ligands: CTP.5, GTP.6, MG.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.314, B:D.454, B:D.455, H2O.11 MG.8: 6 residues within 4Å: Chain B: D.314, N.315, D.454, K.490 Ligands: CTP.5, MG.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.314, B:N.315, B:D.454

1 x MGT: 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE

MGT.10: 14 residues within 4Å: Chain C: R.273, Q.315, F.332, S.333, F.334, R.348, F.366, E.370, F.372, K.385, F.413, N.438, S.528, A.530 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Q.315, C:R.348, C:K.385, C:N.438, C:S.528 Salt bridges: C:R.273, C:R.273, C:E.370 pi-Stacking: C:F.366 pi-Cation interactions: C:F.366

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cusack, S. et al., High-resolution structure of a replication-initiation like configuration of influenza polymerase active site visualises the essential role of a conserved dibasic motif in the PA subunit. Biorxiv (2024)

Release Date

2024-09-18

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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