SMTL ID : 6szv.1

Bat Influenza A polymerase elongation complex with incoming UTP analogue (core + endonuclease only)

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: 13 residues within 4Å: Chain A: T.34, Y.38, A.51, I.52, H.55, E.94, D.122, E.133, I.134, G.135, K.148 Ligands: MG.2, MG.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.34, A:A.51, A:I.52 Hydrogen bonds: A:Y.38, A:K.148 pi-Stacking: A:Y.38

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 4 residues within 4Å: Chain A: 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: 7 residues within 4Å: Chain A: H.55, D.122, E.133, I.134, K.148 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.5: 6 residues within 4Å: Chain B: D.314, N.315, D.454, K.490 Ligands: 2KH.4, MG.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.314, B:N.315, B:D.454 MG.6: 6 residues within 4Å: Chain B: D.314, D.454, D.455 Chain F: G.26 Ligands: 2KH.4, MG.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.314, B:D.454, B:D.455 MG.7: 2 residues within 4Å: Chain D: A.1, G.2 No protein-ligand interaction detected (PLIP)

1 x 2KH: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine(Non-covalent)

2KH.4: 17 residues within 4Å: Chain B: K.238, R.248, D.314, N.315, T.316, K.317, W.318, N.319, M.418, G.419, S.453, D.454, K.490 Chain E: A.4 Chain F: G.26 Ligands: MG.5, MG.6 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:R.248, B:R.248, B:K.317, B:W.318, B:N.319, B:N.319, B:G.419, B:S.453, B:D.454 Water bridges: B:K.238 Salt bridges: B:K.244, 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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