SMTL ID : 7n8f.1

The crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988288

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 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, R3J.4 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, R3J.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.7: 6 residues within 4Å: Chain B: H.61, D.109, E.120, I.121 Ligands: MN.8, R3J.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.61, B:D.109, B:E.120, B:I.121 MN.8: 5 residues within 4Å: Chain B: H.61, E.81, D.109 Ligands: MN.7, R3J.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.13: 6 residues within 4Å: Chain C: H.61, D.109, E.120, I.121 Ligands: MN.14, R3J.16 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.61, C:D.109, C:E.120, C:I.121 MN.14: 5 residues within 4Å: Chain C: H.61, E.81, D.109 Ligands: MN.13, R3J.16 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.81, C:D.109, H2O.2, H2O.2 MN.19: 6 residues within 4Å: Chain D: H.61, D.109, E.120, I.121 Ligands: MN.20, R3J.22 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:D.109, D:E.120, D:I.121 MN.20: 5 residues within 4Å: Chain D: H.61, E.81, D.109 Ligands: MN.19, R3J.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.25: 6 residues within 4Å: Chain E: H.61, D.109, E.120, I.121 Ligands: MN.26, R3J.28 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.61, E:D.109, E:E.120, E:I.121 MN.26: 5 residues within 4Å: Chain E: H.61, E.81, D.109 Ligands: MN.25, R3J.28 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.81, E:D.109, H2O.3, H2O.3 MN.31: 6 residues within 4Å: Chain F: H.61, D.109, E.120, I.121 Ligands: MN.32, R3J.34 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.61, F:D.109, F:E.120, F:I.121 MN.32: 5 residues within 4Å: Chain F: H.61, E.81, D.109 Ligands: MN.31, R3J.34 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.81, F:D.109, H2O.3, H2O.4 MN.37: 6 residues within 4Å: Chain G: H.61, D.109, E.120, I.121 Ligands: MN.38, R3J.40 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.61, G:D.109, G:E.120, G:I.121 MN.38: 5 residues within 4Å: Chain G: H.61, E.81, D.109 Ligands: MN.37, R3J.40 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.81, G:D.109, H2O.4, H2O.4 MN.43: 6 residues within 4Å: Chain H: H.61, D.109, E.120, I.121 Ligands: MN.44, R3J.46 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.61, H:D.109, H:E.120, H:I.121 MN.44: 5 residues within 4Å: Chain H: H.61, E.81, D.109 Ligands: MN.43, R3J.46 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.81, H:D.109, H2O.5, H2O.5

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

QQ4.3: 5 residues within 4Å: Chain A: M.32, F.66, I.79, E.81, R.83 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.66, A:I.79, A:R.83 QQ4.9: 5 residues within 4Å: Chain B: M.32, F.66, I.79, E.81, R.83 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.66, B:I.79, B:R.83 QQ4.15: 5 residues within 4Å: Chain C: M.32, F.66, I.79, E.81, R.83 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.66, C:I.79, C:R.83 QQ4.21: 5 residues within 4Å: Chain D: M.32, F.66, I.79, E.81, R.83 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.66, D:I.79, D:R.83 QQ4.27: 5 residues within 4Å: Chain E: M.32, F.66, I.79, E.81, R.83 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.66, E:I.79, E:R.83 QQ4.33: 5 residues within 4Å: Chain F: M.32, F.66, I.79, E.81, R.83 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:F.66, F:I.79, F:R.83 QQ4.39: 5 residues within 4Å: Chain G: M.32, F.66, I.79, E.81, R.83 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:F.66, G:I.79, G:R.83 QQ4.45: 5 residues within 4Å: Chain H: M.32, F.66, I.79, E.81, R.83 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:F.66, H:I.79, H:R.83

8 x R3J: benzyl [2-(5-hydroxy-4-{[2-(2-methoxypyridin-4-yl)ethyl]carbamoyl}-6-oxo-1,6-dihydropyrimidin-2-yl)propan-2-yl]carbamate(Non-covalent)

R3J.4: 13 residues within 4Å: Chain A: A.40, Y.44, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.1, MN.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.40 Hydrogen bonds: A:K.54, A:Y.131 Water bridges: A:R.125, A:Y.131 pi-Stacking: A:Y.44 R3J.10: 13 residues within 4Å: Chain B: A.40, Y.44, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.7, MN.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.40 Hydrogen bonds: B:K.54, B:Y.131 Water bridges: B:R.125, B:Y.131 pi-Stacking: B:Y.44 R3J.16: 13 residues within 4Å: Chain C: A.40, Y.44, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.13, MN.14 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.40 Hydrogen bonds: C:K.54, C:Y.131 Water bridges: C:R.125, C:Y.131 pi-Stacking: C:Y.44 R3J.22: 13 residues within 4Å: Chain D: A.40, Y.44, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.19, MN.20 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:A.40 Hydrogen bonds: D:K.54, D:E.81, D:E.120, D:Y.131 Water bridges: D:R.125, D:Y.131 pi-Stacking: D:Y.44 R3J.28: 13 residues within 4Å: Chain E: A.40, Y.44, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.25, MN.26 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:A.40 Hydrogen bonds: E:K.54 Water bridges: E:E.120, E:R.125, E:Y.131, E:Y.131 pi-Stacking: E:Y.44 R3J.34: 13 residues within 4Å: Chain F: A.40, Y.44, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.31, MN.32 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:A.40 Hydrogen bonds: F:K.54 Water bridges: F:E.120, F:R.125, F:Y.131, F:Y.131 pi-Stacking: F:Y.44 R3J.40: 13 residues within 4Å: Chain G: A.40, Y.44, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.37, MN.38 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:A.40 Hydrogen bonds: G:K.54 Water bridges: G:E.120, G:R.125, G:Y.131, G:Y.131 pi-Stacking: G:Y.44 R3J.46: 13 residues within 4Å: Chain H: A.40, Y.44, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.43, MN.44 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:A.40 Hydrogen bonds: H:K.54, H:E.120 Water bridges: H:D.109, H:E.120, H:R.125, H:Y.131, H:Y.131 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: 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

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

2022-06-15

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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