SMTL ID : 7my5.1

The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988503

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 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, Y5V.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, Y5V.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, Y5V.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, Y5V.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.81, B:D.109, H2O.1, H2O.1 MN.15: 6 residues within 4Å: Chain C: H.61, D.109, E.120, I.121 Ligands: MN.16, Y5V.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, Y5V.17 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.81, C:D.109, H2O.1, H2O.1 MN.22: 6 residues within 4Å: Chain D: H.61, D.109, E.120, I.121 Ligands: MN.23, Y5V.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, Y5V.24 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.81, D:D.109, H2O.2, H2O.2 MN.29: 6 residues within 4Å: Chain E: H.61, D.109, E.120, I.121 Ligands: MN.30, Y5V.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, Y5V.31 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.81, E:D.109, H2O.2, H2O.2 MN.36: 6 residues within 4Å: Chain F: H.61, D.109, E.120, I.121 Ligands: MN.37, Y5V.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, Y5V.38 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.81, F:D.109, H2O.2, H2O.3 MN.43: 6 residues within 4Å: Chain G: H.61, D.109, E.120, I.121 Ligands: MN.44, Y5V.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, Y5V.45 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.81, G:D.109, H2O.3, H2O.3 MN.50: 6 residues within 4Å: Chain H: H.61, D.109, E.120, I.121 Ligands: MN.51, Y5V.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, Y5V.52 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.81, H:D.109, H2O.3, H2O.3

8 x Y5V: 5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-2-(2-methylphenyl)-6-oxo-1,6-dihydropyrimidine-4-carboxamide(Non-covalent)

Y5V.3: 14 residues within 4Å: Chain A: A.40, M.41, 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 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.40, A:Y.44, A:Y.44, A:I.58 Hydrogen bonds: A:E.46, A:Y.131, A:Y.131 Y5V.10: 14 residues within 4Å: Chain B: A.40, M.41, Y.44, E.46, K.54, I.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.8, MN.9 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.40, B:Y.44, B:Y.44, B:I.58 Hydrogen bonds: B:E.46, B:Y.131, B:Y.131 Y5V.17: 14 residues within 4Å: Chain C: A.40, M.41, Y.44, E.46, K.54, I.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.15, MN.16 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.40, C:Y.44, C:Y.44, C:I.58 Hydrogen bonds: C:E.46, C:Y.131, C:Y.131 Y5V.24: 14 residues within 4Å: Chain D: A.40, M.41, Y.44, E.46, K.54, I.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.22, MN.23 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:A.40, D:Y.44, D:Y.44, D:I.58 Hydrogen bonds: D:E.46, D:Y.131, D:Y.131 Y5V.31: 14 residues within 4Å: Chain E: A.40, M.41, Y.44, E.46, K.54, I.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.29, MN.30 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:A.40, E:Y.44, E:Y.44, E:I.58 Hydrogen bonds: E:E.46, E:Y.131, E:Y.131 Y5V.38: 14 residues within 4Å: Chain F: A.40, M.41, Y.44, E.46, K.54, I.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.36, MN.37 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:A.40, F:Y.44, F:Y.44, F:I.58 Hydrogen bonds: F:E.46, F:Y.131, F:Y.131 Y5V.45: 14 residues within 4Å: Chain G: A.40, M.41, 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 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:A.40, G:Y.44, G:Y.44, G:I.58 Hydrogen bonds: G:E.46, G:Y.131, G:Y.131 Y5V.52: 14 residues within 4Å: Chain H: A.40, M.41, Y.44, E.46, K.54, I.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.50, MN.51 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:A.40, H:Y.44, H:Y.44, H:I.58 Hydrogen bonds: H:E.46, H:E.81, H:D.109, H:Y.131, H:Y.131

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 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.66, A:F.66, A:I.79 QQ4.11: 5 residues within 4Å: Chain B: M.32, F.66, I.79, E.81, G.82 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.66, B:F.66, B:I.79 QQ4.18: 5 residues within 4Å: Chain C: M.32, F.66, I.79, E.81, G.82 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.66, C:F.66, C:I.79 QQ4.25: 5 residues within 4Å: Chain D: M.32, F.66, I.79, E.81, G.82 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.66, D:F.66, D:I.79 QQ4.32: 5 residues within 4Å: Chain E: M.32, F.66, I.79, E.81, G.82 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.66, E:F.66, E:I.79 QQ4.39: 5 residues within 4Å: Chain F: M.32, F.66, I.79, E.81, G.82 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:F.66, F:F.66, F:I.79 QQ4.46: 5 residues within 4Å: Chain G: M.32, F.66, I.79, E.81, G.82 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:F.66, G:F.66, G:I.79 QQ4.53: 5 residues within 4Å: Chain H: M.32, F.66, I.79, E.81, G.82 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:F.66, H:F.66, H:I.79

24 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: 3 residues within 4Å: Chain A: Y.162, E.166, R.169 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: I.50, E.51, T.52, N.53, K.54 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain B: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: Y.162, E.166, R.169 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain B: I.50, E.51, T.52, N.53, K.54 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain C: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain C: Y.162, E.166, R.169 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain C: I.50, E.51, T.52, N.53, K.54 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain D: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain D: Y.162, E.166, R.169 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain D: I.50, E.51, T.52, N.53, K.54 Ligand excluded by PLIP SO4.33: 4 residues within 4Å: Chain E: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain E: Y.162, E.166, R.169 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain E: I.50, E.51, T.52, N.53, K.54 Ligand excluded by PLIP SO4.40: 4 residues within 4Å: Chain F: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain F: Y.162, E.166, R.169 Ligand excluded by PLIP SO4.42: 5 residues within 4Å: Chain F: I.50, E.51, T.52, N.53, K.54 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain G: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.48: 3 residues within 4Å: Chain G: Y.162, E.166, R.169 Ligand excluded by PLIP SO4.49: 5 residues within 4Å: Chain G: I.50, E.51, T.52, N.53, K.54 Ligand excluded by PLIP SO4.54: 4 residues within 4Å: Chain H: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.55: 3 residues within 4Å: Chain H: Y.162, E.166, R.169 Ligand excluded by PLIP SO4.56: 5 residues within 4Å: Chain H: I.50, E.51, T.52, N.53, K.54 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 SJ000988503. To Be Published

Release Date

2022-05-25

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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