SMTL ID : 6tw1.1

Bat Influenza A polymerase termination complex with pyrophosphate using 44-mer vRNA template with mutated oligo(U) sequence

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x M4H: 5-oxidanyl-4-oxidanylidene-1-[(1-pyrrolo[2,3-b]pyridin-1-ylcyclopentyl)methyl]pyridine-3-carboxylic acid(Non-covalent)

M4H.1: 14 residues within 4Å: Chain A: T.34, Y.38, A.51, I.52, H.55, E.94, L.120, D.122, E.133, I.134, G.135, Y.144 Ligands: MG.2, MG.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.34, A:A.51, A:I.52, A:H.55 Hydrogen bonds: A:Y.144 pi-Stacking: A:Y.38, A:Y.38 pi-Cation interactions: A:K.48, A:H.55

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: H.55, E.94, D.122 Ligands: M4H.1, MG.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.94, A:D.122 MG.3: 6 residues within 4Å: Chain A: H.55, D.122, E.133, I.134 Ligands: M4H.1, MG.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.55, A:D.122, A:E.133, A:I.134 MG.4: 6 residues within 4Å: Chain B: D.314, D.454, D.455 Chain E: A.9, U.10 Ligands: MG.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.314, B:D.454, B:D.455 MG.5: 6 residues within 4Å: Chain B: D.314, N.315, D.454 Chain E: U.10 Ligands: MG.4, POP.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.314, B:N.315, B:D.454

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.6: 10 residues within 4Å: Chain B: R.248, N.315, T.316, K.317, W.318, N.319, D.454, K.490 Chain E: U.10 Ligands: MG.5 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.315, B:K.317, B:W.318, B:N.319 Water bridges: B:R.248, B:R.248, B:R.248, B:K.317 Salt bridges: B:R.248, B:K.317, B:K.490

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wandzik, J.M. et al., A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase. Cell (2020)

Release Date

2020-04-15

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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