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

The crystal structure of the I38T mutant PA endonuclease (2009/H1N1/California) in complex with SJ000988558

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 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, WTD.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, WTD.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.8: 6 residues within 4Å: Chain B: H.61, D.109, E.120, I.121 Ligands: MN.9, WTD.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.61, B:D.109, B:E.120, B:I.121 MN.9: 5 residues within 4Å: Chain B: H.61, E.81, D.109 Ligands: MN.8, WTD.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.81, B:D.109, H2O.2, H2O.2 MN.15: 6 residues within 4Å: Chain C: H.61, D.109, E.120, I.121 Ligands: MN.16, WTD.17 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: MN.15, WTD.17 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.81, C:D.109, H2O.3, H2O.3 MN.22: 6 residues within 4Å: Chain D: H.61, D.109, E.120, I.121 Ligands: MN.23, WTD.24 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:D.109, D:E.120, D:I.121 MN.23: 5 residues within 4Å: Chain D: H.61, E.81, D.109 Ligands: MN.22, WTD.24 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.81, D:D.109, H2O.4, H2O.4 MN.29: 6 residues within 4Å: Chain E: H.61, D.109, E.120, I.121 Ligands: MN.30, WTD.31 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.61, E:D.109, E:E.120, E:I.121 MN.30: 5 residues within 4Å: Chain E: H.61, E.81, D.109 Ligands: MN.29, WTD.31 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.81, E:D.109, H2O.5, H2O.5 MN.36: 6 residues within 4Å: Chain F: H.61, D.109, E.120, I.121 Ligands: MN.37, WTD.38 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.61, F:D.109, F:E.120, F:I.121 MN.37: 5 residues within 4Å: Chain F: H.61, E.81, D.109 Ligands: MN.36, WTD.38 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.81, F:D.109, H2O.7, H2O.7 MN.43: 6 residues within 4Å: Chain G: H.61, D.109, E.120, I.121 Ligands: MN.44, WTD.45 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.61, G:D.109, G:E.120, G:I.121 MN.44: 5 residues within 4Å: Chain G: H.61, E.81, D.109 Ligands: MN.43, WTD.45 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.81, G:D.109, H2O.8, H2O.8 MN.50: 6 residues within 4Å: Chain H: H.61, D.109, E.120, I.121 Ligands: MN.51, WTD.52 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.61, H:D.109, H:E.120, H:I.121 MN.51: 5 residues within 4Å: Chain H: H.61, E.81, D.109 Ligands: MN.50, WTD.52 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.81, H:D.109, H2O.9, H2O.9

8 x WTD: 2-(2,6-difluorophenyl)-5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-6-oxo-3,6-dihydropyrimidine-4-carboxamide(Non-covalent)

WTD.3: 13 residues within 4Å: Chain A: A.40, Y.44, E.46, K.54, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.1, MN.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.44, A:K.54 Hydrogen bonds: A:K.54, A:Y.131, A:K.135 pi-Stacking: A:Y.44 WTD.10: 13 residues within 4Å: Chain B: A.40, Y.44, E.46, K.54, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.8, MN.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.44, B:K.54 Hydrogen bonds: B:K.54, B:Y.131, B:K.135 pi-Stacking: B:Y.44 WTD.17: 13 residues within 4Å: Chain C: A.40, Y.44, E.46, K.54, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.15, MN.16 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.44, C:K.54 Hydrogen bonds: C:K.54, C:Y.131, C:K.135 pi-Stacking: C:Y.44 WTD.24: 13 residues within 4Å: Chain D: A.40, Y.44, E.46, K.54, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.22, MN.23 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:Y.44, D:K.54 Hydrogen bonds: D:K.54, D:Y.131, D:K.135 pi-Stacking: D:Y.44 WTD.31: 13 residues within 4Å: Chain E: A.40, Y.44, E.46, K.54, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.29, MN.30 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:Y.44, E:K.54 Hydrogen bonds: E:K.54, E:K.135 pi-Stacking: E:Y.44 WTD.38: 13 residues within 4Å: Chain F: A.40, Y.44, E.46, K.54, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.36, MN.37 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:Y.44, F:K.54 Hydrogen bonds: F:K.54, F:K.135 pi-Stacking: F:Y.44 WTD.45: 13 residues within 4Å: Chain G: A.40, Y.44, E.46, K.54, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.43, MN.44 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:Y.44, G:K.54 Hydrogen bonds: G:K.54, G:K.135 pi-Stacking: G:Y.44 WTD.52: 13 residues within 4Å: Chain H: A.40, Y.44, E.46, K.54, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.50, MN.51 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:Y.44, H:K.54 Hydrogen bonds: H:K.54, H:E.81, H:K.135 Water bridges: H:D.109 pi-Stacking: H:Y.44

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

QQ4.4: 6 residues within 4Å: Chain A: N.30, M.32, F.66, I.79, E.81, G.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.30 QQ4.11: 6 residues within 4Å: Chain B: N.30, M.32, F.66, I.79, E.81, G.82 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.30 QQ4.18: 6 residues within 4Å: Chain C: N.30, M.32, F.66, I.79, E.81, G.82 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.30 QQ4.25: 6 residues within 4Å: Chain D: N.30, M.32, F.66, I.79, E.81, G.82 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.30 QQ4.32: 6 residues within 4Å: Chain E: N.30, M.32, F.66, I.79, E.81, G.82 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.30 QQ4.39: 6 residues within 4Å: Chain F: N.30, M.32, F.66, I.79, E.81, G.82 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.30 QQ4.46: 6 residues within 4Å: Chain G: N.30, M.32, F.66, I.79, E.81, G.82 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.30 QQ4.53: 6 residues within 4Å: Chain H: N.30, M.32, F.66, I.79, E.81, G.82 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.30

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

SO4.5: 2 residues within 4Å: Chain F: G.18, K.49 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.7: 6 residues within 4Å: Chain A: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain E: G.18, K.49 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain B: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.14: 6 residues within 4Å: Chain B: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain G: G.18, K.49 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain C: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.21: 6 residues within 4Å: Chain C: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain H: G.18, K.49 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain D: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.28: 6 residues within 4Å: Chain D: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain B: G.18, K.49 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain E: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.35: 6 residues within 4Å: Chain E: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain A: G.18, K.49 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain F: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.42: 6 residues within 4Å: Chain F: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.47: 2 residues within 4Å: Chain C: G.18, K.49 Ligand excluded by PLIP SO4.48: 4 residues within 4Å: Chain G: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.49: 6 residues within 4Å: Chain G: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.54: 2 residues within 4Å: Chain D: G.18, K.49 Ligand excluded by PLIP SO4.55: 4 residues within 4Å: Chain H: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.56: 6 residues within 4Å: Chain H: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP

Links

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Citation

Cuypers, M.G. et al., The crystal structure of the I38T mutant PA endonuclease (2009/H1N1/California) in complex with SJ000988558. 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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