SMTL ID : 7kbc.1

The crystal structure of the 2009/H1N1/California PA endonuclease mutant E119D (construct with truncated loop 51-72) in complex with baloxavir acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

4 x E4Z: Baloxavir acid(Non-covalent)

E4Z.1: 19 residues within 4Å: Chain A: A.40, M.41, Y.44, E.46, K.54, A.57, I.58, H.61, E.81, L.107, D.109, I.121, Y.131, K.135 Ligands: GOL.5, GOL.6, MN.8, MN.9, SO4.10 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.44, A:I.58, A:I.58, A:H.61 Hydrogen bonds: A:K.135 Water bridges: A:V.123 pi-Stacking: A:H.61 Halogen bonds: A:M.41, A:E.46 E4Z.11: 19 residues within 4Å: Chain B: A.40, M.41, Y.44, E.46, K.54, A.57, I.58, H.61, E.81, L.107, D.109, I.121, Y.131, K.135 Ligands: GOL.15, GOL.16, MN.18, MN.19, SO4.20 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.44, B:I.58, B:I.58, B:H.61 Hydrogen bonds: B:K.135 Water bridges: B:V.123 pi-Stacking: B:H.61 Halogen bonds: B:M.41, B:E.46 E4Z.21: 19 residues within 4Å: Chain C: A.40, M.41, Y.44, E.46, K.54, A.57, I.58, H.61, E.81, L.107, D.109, I.121, Y.131, K.135 Ligands: GOL.25, GOL.26, MN.28, MN.29, SO4.30 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:Y.44, C:I.58, C:I.58, C:H.61 Hydrogen bonds: C:K.135 Water bridges: C:V.123 pi-Stacking: C:H.61 Halogen bonds: C:M.41, C:E.46 E4Z.31: 19 residues within 4Å: Chain D: A.40, M.41, Y.44, E.46, K.54, A.57, I.58, H.61, E.81, L.107, D.109, I.121, Y.131, K.135 Ligands: GOL.35, GOL.36, MN.38, MN.39, SO4.40 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.44, D:I.58, D:I.58, D:H.61 Hydrogen bonds: D:K.135 Water bridges: D:V.123 pi-Stacking: D:H.61 Halogen bonds: D:M.41, D:E.46

4 x QQ4: Hexa Vinylpyrrolidone K15(Non-covalent)

QQ4.2: 5 residues within 4Å: Chain A: M.32, F.66, I.79, G.82, R.83 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.66, A:I.79 QQ4.12: 5 residues within 4Å: Chain B: M.32, F.66, I.79, G.82, R.83 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.66, B:I.79 QQ4.22: 5 residues within 4Å: Chain C: M.32, F.66, I.79, G.82, R.83 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.66, C:I.79 QQ4.32: 5 residues within 4Å: Chain D: M.32, F.66, I.79, G.82, R.83 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.66, D:I.79

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: G.72, S.73, R.76, K.114 Ligand excluded by PLIP GOL.4: 2 residues within 4Å: Chain A: W.89, K.103 Ligand excluded by PLIP GOL.5: 2 residues within 4Å: Chain A: K.135 Ligands: E4Z.1 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: I.80, E.81, G.82, R.83, A.88 Ligands: E4Z.1 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain B: G.72, S.73, R.76, K.114 Ligand excluded by PLIP GOL.14: 2 residues within 4Å: Chain B: W.89, K.103 Ligand excluded by PLIP GOL.15: 2 residues within 4Å: Chain B: K.135 Ligands: E4Z.11 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain B: I.80, E.81, G.82, R.83, A.88 Ligands: E4Z.11 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain C: G.72, S.73, R.76, K.114 Ligand excluded by PLIP GOL.24: 2 residues within 4Å: Chain C: W.89, K.103 Ligand excluded by PLIP GOL.25: 2 residues within 4Å: Chain C: K.135 Ligands: E4Z.21 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain C: I.80, E.81, G.82, R.83, A.88 Ligands: E4Z.21 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain C: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain D: G.72, S.73, R.76, K.114 Ligand excluded by PLIP GOL.34: 2 residues within 4Å: Chain D: W.89, K.103 Ligand excluded by PLIP GOL.35: 2 residues within 4Å: Chain D: K.135 Ligands: E4Z.31 Ligand excluded by PLIP GOL.36: 6 residues within 4Å: Chain D: I.80, E.81, G.82, R.83, A.88 Ligands: E4Z.31 Ligand excluded by PLIP GOL.37: 6 residues within 4Å: Chain D: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP

8 x MN: MANGANESE (II) ION(Non-covalent)

MN.8: 6 residues within 4Å: Chain A: H.61, D.109, D.120, I.121 Ligands: E4Z.1, MN.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.61, A:D.109, A:I.121 MN.9: 5 residues within 4Å: Chain A: H.61, E.81, D.109 Ligands: E4Z.1, MN.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.81, A:D.109, H2O.1, H2O.1 MN.18: 6 residues within 4Å: Chain B: H.61, D.109, D.120, I.121 Ligands: E4Z.11, MN.19 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.61, B:D.109, B:I.121 MN.19: 5 residues within 4Å: Chain B: H.61, E.81, D.109 Ligands: E4Z.11, MN.18 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.81, B:D.109, H2O.2, H2O.3 MN.28: 6 residues within 4Å: Chain C: H.61, D.109, D.120, I.121 Ligands: E4Z.21, MN.29 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.61, C:D.109, C:I.121 MN.29: 5 residues within 4Å: Chain C: H.61, E.81, D.109 Ligands: E4Z.21, MN.28 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.81, C:D.109, H2O.4, H2O.4 MN.38: 6 residues within 4Å: Chain D: H.61, D.109, D.120, I.121 Ligands: E4Z.31, MN.39 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.61, D:D.109, D:I.121 MN.39: 5 residues within 4Å: Chain D: H.61, E.81, D.109 Ligands: E4Z.31, MN.38 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.81, D:D.109, H2O.6, H2O.6

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 4 residues within 4Å: Chain A: Y.44, R.85, W.89 Ligands: E4Z.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.89 Salt bridges: A:R.85 SO4.20: 4 residues within 4Å: Chain B: Y.44, R.85, W.89 Ligands: E4Z.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.89 Salt bridges: B:R.85 SO4.30: 4 residues within 4Å: Chain C: Y.44, R.85, W.89 Ligands: E4Z.21 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.89 Salt bridges: C:R.85 SO4.40: 4 residues within 4Å: Chain D: Y.44, R.85, W.89 Ligands: E4Z.31 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.89 Salt bridges: D:R.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, G. et al., Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism. Nucleic Acids Res. (2021)

Release Date

2021-02-03

Peptides

Protein PA-X: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Protein PA-X

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