SMTL ID : 7kop.2 (1 other biounit)

The crystal structure of the 2009/H1N1/California PA endonuclease I38T mutant in complex with SJ000988539

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-octamer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: H.61, D.109, E.120, I.121 Ligands: MN.2, WTM.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.61, A:D.109, A:E.120, A:I.121 MN.2: 5 residues within 4Å: Chain A: H.61, E.81, D.109 Ligands: MN.1, WTM.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.6: 6 residues within 4Å: Chain B: H.61, D.109, E.120, I.121 Ligands: MN.7, WTM.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.61, B:D.109, B:E.120, B:I.121 MN.7: 5 residues within 4Å: Chain B: H.61, E.81, D.109 Ligands: MN.6, WTM.8 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.11: 6 residues within 4Å: Chain C: H.61, D.109, E.120, I.121 Ligands: MN.12, WTM.13 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.61, C:D.109, C:E.120, C:I.121 MN.12: 5 residues within 4Å: Chain C: H.61, E.81, D.109 Ligands: MN.11, WTM.13 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.16: 6 residues within 4Å: Chain D: H.61, D.109, E.120, I.121 Ligands: MN.17, WTM.18 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:D.109, D:E.120, D:I.121 MN.17: 5 residues within 4Å: Chain D: H.61, E.81, D.109 Ligands: MN.16, WTM.18 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.81, D:D.109, H2O.6, H2O.6 MN.21: 6 residues within 4Å: Chain E: H.61, D.109, E.120, I.121 Ligands: MN.22, WTM.23 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.61, E:D.109, E:E.120, E:I.121 MN.22: 5 residues within 4Å: Chain E: H.61, E.81, D.109 Ligands: MN.21, WTM.23 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.81, E:D.109, H2O.8, H2O.8 MN.26: 6 residues within 4Å: Chain F: H.61, D.109, E.120, I.121 Ligands: MN.27, WTM.28 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.61, F:D.109, F:E.120, F:I.121 MN.27: 5 residues within 4Å: Chain F: H.61, E.81, D.109 Ligands: MN.26, WTM.28 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.81, F:D.109, H2O.10, H2O.10 MN.31: 6 residues within 4Å: Chain G: H.61, D.109, E.120, I.121 Ligands: MN.32, WTM.33 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.61, G:D.109, G:E.120, G:I.121 MN.32: 5 residues within 4Å: Chain G: H.61, E.81, D.109 Ligands: MN.31, WTM.33 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.81, G:D.109, H2O.11, H2O.12 MN.36: 6 residues within 4Å: Chain H: H.61, D.109, E.120, I.121 Ligands: MN.37, WTM.38 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.61, H:D.109, H:E.120, H:I.121 MN.37: 5 residues within 4Å: Chain H: H.61, E.81, D.109 Ligands: MN.36, WTM.38 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.81, H:D.109, H2O.13, H2O.13

8 x WTM: 2-(2-fluorophenyl)-5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-1,6-dihydropyrimidine-4-carboxamide(Non-covalent)

WTM.3: 14 residues within 4Å: Chain A: A.40, Y.44, E.46, K.54, A.57, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.1, MN.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.44, A:Y.44, A:K.54, A:A.57 Hydrogen bonds: A:Y.131, A:Y.131, A:K.135 WTM.8: 14 residues within 4Å: Chain B: A.40, Y.44, E.46, K.54, A.57, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.6, MN.7 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.44, B:Y.44, B:K.54, B:A.57 Hydrogen bonds: B:Y.131, B:Y.131, B:K.135 WTM.13: 14 residues within 4Å: Chain C: A.40, Y.44, E.46, K.54, A.57, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.11, MN.12 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.44, C:Y.44, C:K.54, C:A.57 Hydrogen bonds: C:Y.131, C:Y.131, C:K.135 WTM.18: 14 residues within 4Å: Chain D: A.40, Y.44, E.46, K.54, A.57, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.16, MN.17 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.44, D:Y.44, D:K.54, D:A.57 Hydrogen bonds: D:Y.131, D:Y.131, D:K.135 WTM.23: 14 residues within 4Å: Chain E: A.40, Y.44, E.46, K.54, A.57, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.21, MN.22 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:Y.44, E:Y.44, E:K.54, E:A.57 Hydrogen bonds: E:Y.131, E:Y.131, E:K.135 WTM.28: 14 residues within 4Å: Chain F: A.40, Y.44, E.46, K.54, A.57, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.26, MN.27 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:Y.44, F:Y.44, F:K.54, F:A.57 Hydrogen bonds: F:Y.131, F:Y.131, F:K.135 WTM.33: 14 residues within 4Å: Chain G: A.40, Y.44, E.46, K.54, A.57, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.31, MN.32 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:Y.44, G:Y.44, G:K.54, G:A.57 Hydrogen bonds: G:Y.131, G:Y.131, G:K.135 WTM.38: 14 residues within 4Å: Chain H: A.40, Y.44, E.46, K.54, A.57, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.36, MN.37 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:Y.44, H:Y.44, H:K.54, H:A.57 Hydrogen bonds: H:Y.131, H:Y.131, H:K.135

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

QQ4.4: 5 residues within 4Å: Chain A: M.32, F.66, I.79, E.81, G.82 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.66 QQ4.9: 5 residues within 4Å: Chain B: M.32, F.66, I.79, E.81, G.82 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.66 QQ4.14: 5 residues within 4Å: Chain C: M.32, F.66, I.79, E.81, G.82 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.66 QQ4.19: 5 residues within 4Å: Chain D: M.32, F.66, I.79, E.81, G.82 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.66 QQ4.24: 5 residues within 4Å: Chain E: M.32, F.66, I.79, E.81, G.82 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:F.66 QQ4.29: 5 residues within 4Å: Chain F: M.32, F.66, I.79, E.81, G.82 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:F.66 QQ4.34: 5 residues within 4Å: Chain G: M.32, F.66, I.79, E.81, G.82 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:F.66 QQ4.39: 5 residues within 4Å: Chain H: M.32, F.66, I.79, E.81, G.82 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:F.66

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

SO4.5: 4 residues within 4Å: Chain A: G.72, S.73, R.76, K.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.73 Water bridges: A:D.165 Salt bridges: A:R.76, A:K.114 SO4.10: 4 residues within 4Å: Chain B: G.72, S.73, R.76, K.114 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.73 Water bridges: B:D.165 Salt bridges: B:R.76, B:K.114 SO4.15: 4 residues within 4Å: Chain C: G.72, S.73, R.76, K.114 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.73 Water bridges: C:D.165 Salt bridges: C:R.76, C:K.114 SO4.20: 4 residues within 4Å: Chain D: G.72, S.73, R.76, K.114 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.73 Water bridges: D:D.165 Salt bridges: D:R.76, D:K.114 SO4.25: 4 residues within 4Å: Chain E: G.72, S.73, R.76, K.114 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.73 Water bridges: E:D.165 Salt bridges: E:R.76, E:K.114 SO4.30: 4 residues within 4Å: Chain F: G.72, S.73, R.76, K.114 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:S.73 Water bridges: F:D.165 Salt bridges: F:R.76, F:K.114 SO4.35: 4 residues within 4Å: Chain G: G.72, S.73, R.76, K.114 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:S.73 Water bridges: G:D.165 Salt bridges: G:R.76, G:K.114 SO4.40: 4 residues within 4Å: Chain H: G.72, S.73, R.76, K.114 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:S.73 Water bridges: H:D.165 Salt bridges: H:R.76, H:K.114

Links

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Citation

Cuypers, M.G. et al., The crystal structure of the 2009/H1N1/California PA endonuclease I38T mutant in complex with SJ000988539. To Be Published

Release Date

2021-11-10

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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