SMTL ID : 7mty.1

The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988569

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-octamer

Ligands

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

QQ4.1: 4 residues within 4Å: Chain A: M.32, F.66, I.79, E.81 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.66, A:F.66, A:I.79 QQ4.7: 4 residues within 4Å: Chain B: M.32, F.66, I.79, E.81 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.66, B:F.66, B:I.79 QQ4.13: 4 residues within 4Å: Chain C: M.32, F.66, I.79, E.81 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.66, C:F.66, C:I.79 QQ4.19: 4 residues within 4Å: Chain D: M.32, F.66, I.79, E.81 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.66, D:F.66, D:I.79 QQ4.25: 4 residues within 4Å: Chain E: M.32, F.66, I.79, E.81 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.66, E:F.66, E:I.79 QQ4.31: 4 residues within 4Å: Chain F: M.32, F.66, I.79, E.81 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:F.66, F:F.66, F:I.79 QQ4.37: 4 residues within 4Å: Chain G: M.32, F.66, I.79, E.81 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:F.66, G:F.66, G:I.79 QQ4.43: 4 residues within 4Å: Chain H: M.32, F.66, I.79, E.81 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:F.66, H:F.66, H:I.79

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

MN.2: 6 residues within 4Å: Chain A: H.61, D.109, E.120, I.121 Ligands: MN.3, W5V.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.61, A:D.109, A:E.120, A:I.121 MN.3: 5 residues within 4Å: Chain A: H.61, E.81, D.109 Ligands: MN.2, W5V.4 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, W5V.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, W5V.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.14: 6 residues within 4Å: Chain C: H.61, D.109, E.120, I.121 Ligands: MN.15, W5V.16 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.61, C:D.109, C:E.120, C:I.121 MN.15: 5 residues within 4Å: Chain C: H.61, E.81, D.109 Ligands: MN.14, W5V.16 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.20: 6 residues within 4Å: Chain D: H.61, D.109, E.120, I.121 Ligands: MN.21, W5V.22 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:D.109, D:E.120, D:I.121 MN.21: 5 residues within 4Å: Chain D: H.61, E.81, D.109 Ligands: MN.20, W5V.22 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.26: 6 residues within 4Å: Chain E: H.61, D.109, E.120, I.121 Ligands: MN.27, W5V.28 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.61, E:D.109, E:E.120, E:I.121 MN.27: 5 residues within 4Å: Chain E: H.61, E.81, D.109 Ligands: MN.26, W5V.28 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.32: 6 residues within 4Å: Chain F: H.61, D.109, E.120, I.121 Ligands: MN.33, W5V.34 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.61, F:D.109, F:E.120, F:I.121 MN.33: 5 residues within 4Å: Chain F: H.61, E.81, D.109 Ligands: MN.32, W5V.34 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.81, F:D.109, H2O.2, H2O.2 MN.38: 6 residues within 4Å: Chain G: H.61, D.109, E.120, I.121 Ligands: MN.39, W5V.40 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.61, G:D.109, G:E.120, G:I.121 MN.39: 5 residues within 4Å: Chain G: H.61, E.81, D.109 Ligands: MN.38, W5V.40 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.81, G:D.109, H2O.2, H2O.2 MN.44: 6 residues within 4Å: Chain H: H.61, D.109, E.120, I.121 Ligands: MN.45, W5V.46 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.61, H:D.109, H:E.120, H:I.121 MN.45: 5 residues within 4Å: Chain H: H.61, E.81, D.109 Ligands: MN.44, W5V.46 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 W5V: 2-(2,6-difluorophenyl)-5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-3,6-dihydropyrimidine-4-carboxamide(Non-covalent)

W5V.4: 12 residues within 4Å: Chain A: A.40, E.46, K.54, I.58, H.61, E.81, L.107, D.109, E.120, I.121 Ligands: MN.2, MN.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.54 Hydrogen bonds: A:E.46 pi-Stacking: A:Y.44 W5V.10: 12 residues within 4Å: Chain B: A.40, E.46, K.54, I.58, H.61, E.81, L.107, D.109, E.120, I.121 Ligands: MN.8, MN.9 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.54 Hydrogen bonds: B:E.46 pi-Stacking: B:Y.44 W5V.16: 12 residues within 4Å: Chain C: A.40, E.46, K.54, I.58, H.61, E.81, L.107, D.109, E.120, I.121 Ligands: MN.14, MN.15 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.54 Hydrogen bonds: C:E.46 pi-Stacking: C:Y.44 W5V.22: 12 residues within 4Å: Chain D: A.40, E.46, K.54, I.58, H.61, E.81, L.107, D.109, E.120, I.121 Ligands: MN.20, MN.21 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:K.54 Hydrogen bonds: D:E.46 Water bridges: D:E.81, D:L.107 pi-Stacking: D:Y.44 W5V.28: 12 residues within 4Å: Chain E: A.40, E.46, K.54, I.58, H.61, E.81, L.107, D.109, E.120, I.121 Ligands: MN.26, MN.27 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:K.54 Hydrogen bonds: E:Y.131 pi-Stacking: E:Y.44 W5V.34: 12 residues within 4Å: Chain F: A.40, E.46, K.54, I.58, H.61, E.81, L.107, D.109, E.120, I.121 Ligands: MN.32, MN.33 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:K.54 Hydrogen bonds: F:Y.131 pi-Stacking: F:Y.44 W5V.40: 12 residues within 4Å: Chain G: A.40, E.46, K.54, I.58, H.61, E.81, L.107, D.109, E.120, I.121 Ligands: MN.38, MN.39 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:K.54 Hydrogen bonds: G:Y.131 pi-Stacking: G:Y.44 W5V.46: 12 residues within 4Å: Chain H: A.40, E.46, K.54, I.58, H.61, E.81, L.107, D.109, E.120, I.121 Ligands: MN.44, MN.45 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:K.54 Hydrogen bonds: H:Y.131 Water bridges: H:E.120 pi-Stacking: H:Y.44

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: I.50, E.51, T.52, N.53, K.54 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: I.50, E.51, T.52, N.53, K.54 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: I.50, E.51, T.52, N.53, K.54 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: I.50, E.51, T.52, N.53, K.54 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: I.50, E.51, T.52, N.53, K.54 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: I.50, E.51, T.52, N.53, K.54 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: I.50, E.51, T.52, N.53, K.54 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: I.50, E.51, T.52, N.53, K.54 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Slavish, P.J. et al., Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential. Eur.J.Med.Chem. (2023)

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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