SMTL ID : 7kaf.1

The crystal structure of the 2009/H1N1/California PA endonuclease I38T (construct with truncated loop 51-72) in complex with baloxavir acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-octamer

Ligands

8 x E4Z: Baloxavir acid(Non-covalent)

E4Z.1: 17 residues within 4Å: Chain A: A.40, M.41, Y.44, E.46, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.3, MN.4, SO4.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.44, A:A.57, A:T.58, A:H.61 Hydrogen bonds: A:K.135 Water bridges: A:Y.131 Halogen bonds: A:M.41 E4Z.7: 17 residues within 4Å: Chain B: A.40, M.41, Y.44, E.46, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.9, MN.10, SO4.11 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.44, B:A.57, B:T.58, B:H.61 Hydrogen bonds: B:K.135 Water bridges: B:Y.131 Halogen bonds: B:M.41 E4Z.13: 17 residues within 4Å: Chain C: A.40, M.41, Y.44, E.46, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.15, MN.16, SO4.17 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.44, C:A.57, C:T.58, C:H.61 Hydrogen bonds: C:K.135 Water bridges: C:Y.131 Halogen bonds: C:M.41 E4Z.19: 17 residues within 4Å: Chain D: A.40, M.41, Y.44, E.46, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.21, MN.22, SO4.23 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.44, D:A.57, D:T.58, D:H.61 Hydrogen bonds: D:E.81, D:K.135 Water bridges: D:Y.131 Halogen bonds: D:M.41 E4Z.25: 17 residues within 4Å: Chain E: A.40, M.41, Y.44, E.46, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.27, MN.28, SO4.29 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:Y.44, E:A.57, E:T.58, E:H.61 Hydrogen bonds: E:K.135 Halogen bonds: E:M.41 E4Z.31: 17 residues within 4Å: Chain F: A.40, M.41, Y.44, E.46, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.33, MN.34, SO4.35 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:Y.44, F:A.57, F:T.58, F:H.61 Hydrogen bonds: F:K.135 Halogen bonds: F:M.41 E4Z.37: 17 residues within 4Å: Chain G: A.40, M.41, Y.44, E.46, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.39, MN.40, SO4.41 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:Y.44, G:A.57, G:T.58, G:H.61 Hydrogen bonds: G:K.135 Halogen bonds: G:M.41 E4Z.43: 17 residues within 4Å: Chain H: A.40, M.41, Y.44, E.46, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.45, MN.46, SO4.47 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:Y.44, H:A.57, H:T.58, H:H.61 Hydrogen bonds: H:D.109, H:K.135 Water bridges: H:D.109 Halogen bonds: H:M.41

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

QQ4.2: 6 residues within 4Å: Chain A: M.32, L.36, F.66, I.79, G.82, R.83 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.66, A:I.79, A:I.79 QQ4.8: 6 residues within 4Å: Chain B: M.32, L.36, F.66, I.79, G.82, R.83 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.66, B:I.79, B:I.79 QQ4.14: 6 residues within 4Å: Chain C: M.32, L.36, F.66, I.79, G.82, R.83 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.66, C:I.79, C:I.79 QQ4.20: 6 residues within 4Å: Chain D: M.32, L.36, F.66, I.79, G.82, R.83 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.66, D:I.79, D:I.79 QQ4.26: 6 residues within 4Å: Chain E: M.32, L.36, F.66, I.79, G.82, R.83 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.66, E:I.79, E:I.79 QQ4.32: 6 residues within 4Å: Chain F: M.32, L.36, F.66, I.79, G.82, R.83 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:F.66, F:I.79, F:I.79 QQ4.38: 6 residues within 4Å: Chain G: M.32, L.36, F.66, I.79, G.82, R.83 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:F.66, G:I.79, G:I.79 QQ4.44: 6 residues within 4Å: Chain H: M.32, L.36, F.66, I.79, G.82, R.83 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:F.66, H:I.79, H:I.79

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

MN.3: 6 residues within 4Å: Chain A: H.61, D.109, E.120, I.121 Ligands: E4Z.1, MN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.61, A:D.109, A:E.120, A:I.121 MN.4: 5 residues within 4Å: Chain A: H.61, E.81, D.109 Ligands: E4Z.1, MN.3 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.9: 6 residues within 4Å: Chain B: H.61, D.109, E.120, I.121 Ligands: E4Z.7, MN.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.61, B:D.109, B:E.120, B:I.121 MN.10: 5 residues within 4Å: Chain B: H.61, E.81, D.109 Ligands: E4Z.7, MN.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.81, B:D.109, H2O.3, H2O.3 MN.15: 6 residues within 4Å: Chain C: H.61, D.109, E.120, I.121 Ligands: E4Z.13, MN.16 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.61, C:D.109, C:E.120, C:I.121 MN.16: 5 residues within 4Å: Chain C: H.61, E.81, D.109 Ligands: E4Z.13, MN.15 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.81, C:D.109, H2O.5, H2O.5 MN.21: 6 residues within 4Å: Chain D: H.61, D.109, E.120, I.121 Ligands: E4Z.19, MN.22 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:D.109, D:E.120, D:I.121 MN.22: 5 residues within 4Å: Chain D: H.61, E.81, D.109 Ligands: E4Z.19, MN.21 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.81, D:D.109, H2O.8, H2O.8 MN.27: 6 residues within 4Å: Chain E: H.61, D.109, E.120, I.121 Ligands: E4Z.25, MN.28 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.61, E:D.109, E:E.120, E:I.121 MN.28: 5 residues within 4Å: Chain E: H.61, E.81, D.109 Ligands: E4Z.25, MN.27 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.81, E:D.109, H2O.10, H2O.10 MN.33: 6 residues within 4Å: Chain F: H.61, D.109, E.120, I.121 Ligands: E4Z.31, MN.34 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.61, F:D.109, F:E.120, F:I.121 MN.34: 5 residues within 4Å: Chain F: H.61, E.81, D.109 Ligands: E4Z.31, MN.33 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.81, F:D.109, H2O.13, H2O.13 MN.39: 6 residues within 4Å: Chain G: H.61, D.109, E.120, I.121 Ligands: E4Z.37, MN.40 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.61, G:D.109, G:E.120, G:I.121 MN.40: 5 residues within 4Å: Chain G: H.61, E.81, D.109 Ligands: E4Z.37, MN.39 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.81, G:D.109, H2O.15, H2O.15 MN.45: 6 residues within 4Å: Chain H: H.61, D.109, E.120, I.121 Ligands: E4Z.43, MN.46 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.61, H:D.109, H:E.120, H:I.121 MN.46: 5 residues within 4Å: Chain H: H.61, E.81, D.109 Ligands: E4Z.43, MN.45 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.81, H:D.109, H2O.17, H2O.17

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

SO4.5: 5 residues within 4Å: Chain A: Y.44, R.85, W.89, L.107 Ligands: E4Z.1 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain B: Y.44, R.85, W.89, L.107 Ligands: E4Z.7 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain B: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain C: Y.44, R.85, W.89, L.107 Ligands: E4Z.13 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain C: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain D: Y.44, R.85, W.89, L.107 Ligands: E4Z.19 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain D: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain E: Y.44, R.85, W.89, L.107 Ligands: E4Z.25 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain E: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain F: Y.44, R.85, W.89, L.107 Ligands: E4Z.31 Ligand excluded by PLIP SO4.36: 4 residues within 4Å: Chain F: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.41: 5 residues within 4Å: Chain G: Y.44, R.85, W.89, L.107 Ligands: E4Z.37 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain G: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.47: 5 residues within 4Å: Chain H: Y.44, R.85, W.89, L.107 Ligands: E4Z.43 Ligand excluded by PLIP SO4.48: 4 residues within 4Å: Chain H: G.72, S.73, R.76, K.114 Ligand excluded by PLIP

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: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

Protein PA-X

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