SMTL ID : 7mx0.1

The crystal structure of wild type 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 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.61, A:D.109, A:D.109, A:E.120, A:I.121 MN.2: 6 residues within 4Å: Chain A: E.81, L.107, P.108, D.109 Ligands: MN.1, WTD.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.81, A:D.109 MN.7: 6 residues within 4Å: Chain B: H.61, D.109, E.120, I.121 Ligands: MN.8, WTD.9 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.61, B:D.109, B:D.109, B:E.120, B:I.121 MN.8: 6 residues within 4Å: Chain B: E.81, L.107, P.108, D.109 Ligands: MN.7, WTD.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.81, B:D.109 MN.13: 6 residues within 4Å: Chain C: H.61, D.109, E.120, I.121 Ligands: MN.14, WTD.15 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.61, C:D.109, C:D.109, C:E.120, C:I.121 MN.14: 6 residues within 4Å: Chain C: E.81, L.107, P.108, D.109 Ligands: MN.13, WTD.15 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.81, C:D.109 MN.19: 6 residues within 4Å: Chain D: H.61, D.109, E.120, I.121 Ligands: MN.20, WTD.21 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.61, D:D.109, D:D.109, D:E.120, D:I.121 MN.20: 6 residues within 4Å: Chain D: E.81, L.107, P.108, D.109 Ligands: MN.19, WTD.21 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.81, D:D.109 MN.25: 6 residues within 4Å: Chain E: H.61, D.109, E.120, I.121 Ligands: MN.26, WTD.27 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:H.61, E:D.109, E:D.109, E:E.120, E:I.121 MN.26: 6 residues within 4Å: Chain E: E.81, L.107, P.108, D.109 Ligands: MN.25, WTD.27 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.81, E:D.109 MN.31: 6 residues within 4Å: Chain F: H.61, D.109, E.120, I.121 Ligands: MN.32, WTD.33 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:H.61, F:D.109, F:D.109, F:E.120, F:I.121 MN.32: 6 residues within 4Å: Chain F: E.81, L.107, P.108, D.109 Ligands: MN.31, WTD.33 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.81, F:D.109 MN.37: 6 residues within 4Å: Chain G: H.61, D.109, E.120, I.121 Ligands: MN.38, WTD.39 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:H.61, G:D.109, G:D.109, G:E.120, G:I.121 MN.38: 6 residues within 4Å: Chain G: E.81, L.107, P.108, D.109 Ligands: MN.37, WTD.39 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:E.81, G:D.109 MN.43: 6 residues within 4Å: Chain H: H.61, D.109, E.120, I.121 Ligands: MN.44, WTD.45 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:H.61, H:D.109, H:D.109, H:E.120, H:I.121 MN.44: 6 residues within 4Å: Chain H: E.81, L.107, P.108, D.109 Ligands: MN.43, WTD.45 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:E.81, H:D.109

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, I.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.1, MN.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.58 Hydrogen bonds: A:E.46, A:K.54 pi-Stacking: A:Y.44 WTD.9: 13 residues within 4Å: Chain B: A.40, Y.44, E.46, K.54, I.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.7, MN.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.58 Hydrogen bonds: B:E.46, B:K.54 pi-Stacking: B:Y.44 WTD.15: 13 residues within 4Å: Chain C: A.40, Y.44, E.46, K.54, I.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.13, MN.14 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.58 Hydrogen bonds: C:E.46, C:K.54 pi-Stacking: C:Y.44 WTD.21: 13 residues within 4Å: Chain D: A.40, Y.44, E.46, K.54, I.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.19, MN.20 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.58 Hydrogen bonds: D:E.46, D:K.54 pi-Stacking: D:Y.44 WTD.27: 13 residues within 4Å: Chain E: A.40, Y.44, E.46, K.54, I.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.25, MN.26 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:I.58 Hydrogen bonds: E:K.54, E:Y.131 pi-Stacking: E:Y.44 WTD.33: 13 residues within 4Å: Chain F: A.40, Y.44, E.46, K.54, I.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.31, MN.32 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:I.58 Hydrogen bonds: F:K.54, F:Y.131 pi-Stacking: F:Y.44 WTD.39: 13 residues within 4Å: Chain G: A.40, Y.44, E.46, K.54, I.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.37, MN.38 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:I.58 Hydrogen bonds: G:K.54, G:Y.131 pi-Stacking: G:Y.44 WTD.45: 13 residues within 4Å: Chain H: A.40, Y.44, E.46, K.54, I.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.43, MN.44 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:I.58 Hydrogen bonds: H:K.54, H:E.81, H:Y.131 pi-Stacking: H:Y.44

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

QQ4.4: 7 residues within 4Å: Chain A: N.30, M.32, F.66, I.79, E.81, G.82, R.83 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.66, A:F.66, A:I.79, A:R.83 Hydrogen bonds: A:N.30 QQ4.10: 7 residues within 4Å: Chain B: N.30, M.32, F.66, I.79, E.81, G.82, R.83 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.66, B:F.66, B:I.79, B:R.83 Hydrogen bonds: B:N.30 QQ4.16: 7 residues within 4Å: Chain C: N.30, M.32, F.66, I.79, E.81, G.82, R.83 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.66, C:F.66, C:I.79, C:R.83 Hydrogen bonds: C:N.30 QQ4.22: 7 residues within 4Å: Chain D: N.30, M.32, F.66, I.79, E.81, G.82, R.83 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.66, D:F.66, D:I.79, D:R.83 Hydrogen bonds: D:N.30 QQ4.28: 7 residues within 4Å: Chain E: N.30, M.32, F.66, I.79, E.81, G.82, R.83 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:F.66, E:F.66, E:I.79, E:R.83 Hydrogen bonds: E:N.30 QQ4.34: 7 residues within 4Å: Chain F: N.30, M.32, F.66, I.79, E.81, G.82, R.83 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:F.66, F:F.66, F:I.79, F:R.83 Hydrogen bonds: F:N.30 QQ4.40: 7 residues within 4Å: Chain G: N.30, M.32, F.66, I.79, E.81, G.82, R.83 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:F.66, G:F.66, G:I.79, G:R.83 Hydrogen bonds: G:N.30 QQ4.46: 7 residues within 4Å: Chain H: N.30, M.32, F.66, I.79, E.81, G.82, R.83 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:F.66, H:F.66, H:I.79, H:R.83 Hydrogen bonds: H:N.30

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

SO4.5: 4 residues within 4Å: Chain A: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain B: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain B: E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain C: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.18: 5 residues within 4Å: Chain C: E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain D: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain D: E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain E: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain E: E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain F: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.36: 5 residues within 4Å: Chain F: E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain G: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.42: 5 residues within 4Å: Chain G: E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain H: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.48: 5 residues within 4Å: Chain H: E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cuypers, M.G. et al., The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988558. To Be Published

Release Date

2022-05-18

Peptides

Polymerase acidic protein: 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

Polymerase acidic protein

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