SMTL ID : 7n47.1

The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988514

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 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, 09Y.7 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, 09Y.7 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.10: 6 residues within 4Å: Chain B: H.61, D.109, E.120, I.121 Ligands: MN.11, 09Y.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.61, B:D.109, B:E.120, B:I.121 MN.11: 5 residues within 4Å: Chain B: H.61, E.81, D.109 Ligands: MN.10, 09Y.16 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.19: 6 residues within 4Å: Chain C: H.61, D.109, E.120, I.121 Ligands: MN.20, 09Y.25 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.61, C:D.109, C:E.120, C:I.121 MN.20: 5 residues within 4Å: Chain C: H.61, E.81, D.109 Ligands: MN.19, 09Y.25 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.28: 6 residues within 4Å: Chain D: H.61, D.109, E.120, I.121 Ligands: MN.29, 09Y.34 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:D.109, D:E.120, D:I.121 MN.29: 5 residues within 4Å: Chain D: H.61, E.81, D.109 Ligands: MN.28, 09Y.34 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.37: 6 residues within 4Å: Chain E: H.61, D.109, E.120, I.121 Ligands: MN.38, 09Y.43 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.61, E:D.109, E:E.120, E:I.121 MN.38: 5 residues within 4Å: Chain E: H.61, E.81, D.109 Ligands: MN.37, 09Y.43 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.46: 6 residues within 4Å: Chain F: H.61, D.109, E.120, I.121 Ligands: MN.47, 09Y.52 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.61, F:D.109, F:E.120, F:I.121 MN.47: 5 residues within 4Å: Chain F: H.61, E.81, D.109 Ligands: MN.46, 09Y.52 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.81, F:D.109, H2O.4, H2O.4 MN.55: 6 residues within 4Å: Chain G: H.61, D.109, E.120, I.121 Ligands: MN.56, 09Y.61 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.61, G:D.109, G:E.120, G:I.121 MN.56: 5 residues within 4Å: Chain G: H.61, E.81, D.109 Ligands: MN.55, 09Y.61 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.64: 6 residues within 4Å: Chain H: H.61, D.109, E.120, I.121 Ligands: MN.65, 09Y.70 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.61, H:D.109, H:E.120, H:I.121 MN.65: 5 residues within 4Å: Chain H: H.61, E.81, D.109 Ligands: MN.64, 09Y.70 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.81, H:D.109, H2O.5, H2O.5

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

SO4.3: 4 residues within 4Å: Chain A: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.4: 1 residues within 4Å: Chain A: R.169 Ligand excluded by PLIP SO4.5: 6 residues within 4Å: Chain A: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.8: 7 residues within 4Å: Chain A: N.53, K.54, A.57, R.125, S.195, E.196 Ligands: 09Y.7 Ligand excluded by PLIP SO4.9: 6 residues within 4Å: Chain A: E.78, R.83, V.91 Chain D: T.174, R.175, T.178 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: 1 residues within 4Å: Chain B: R.169 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 SO4.17: 7 residues within 4Å: Chain B: N.53, K.54, A.57, R.125, S.195, E.196 Ligands: 09Y.16 Ligand excluded by PLIP SO4.18: 6 residues within 4Å: Chain B: E.78, R.83, V.91 Chain C: T.174, R.175, T.178 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain C: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.22: 1 residues within 4Å: Chain C: R.169 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain C: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.26: 7 residues within 4Å: Chain C: N.53, K.54, A.57, R.125, S.195, E.196 Ligands: 09Y.25 Ligand excluded by PLIP SO4.27: 6 residues within 4Å: Chain A: T.174, R.175, T.178 Chain C: E.78, R.83, V.91 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain D: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.31: 1 residues within 4Å: Chain D: R.169 Ligand excluded by PLIP SO4.32: 6 residues within 4Å: Chain D: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.35: 7 residues within 4Å: Chain D: N.53, K.54, A.57, R.125, S.195, E.196 Ligands: 09Y.34 Ligand excluded by PLIP SO4.36: 6 residues within 4Å: Chain B: T.174, R.175, T.178 Chain D: E.78, R.83, V.91 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain E: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.40: 1 residues within 4Å: Chain E: R.169 Ligand excluded by PLIP SO4.41: 6 residues within 4Å: Chain E: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.44: 7 residues within 4Å: Chain E: N.53, K.54, A.57, R.125, S.195, E.196 Ligands: 09Y.43 Ligand excluded by PLIP SO4.45: 6 residues within 4Å: Chain E: E.78, R.83, V.91 Chain H: T.174, R.175, T.178 Ligand excluded by PLIP SO4.48: 4 residues within 4Å: Chain F: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.49: 1 residues within 4Å: Chain F: R.169 Ligand excluded by PLIP SO4.50: 6 residues within 4Å: Chain F: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.53: 7 residues within 4Å: Chain F: N.53, K.54, A.57, R.125, S.195, E.196 Ligands: 09Y.52 Ligand excluded by PLIP SO4.54: 6 residues within 4Å: Chain F: E.78, R.83, V.91 Chain G: T.174, R.175, T.178 Ligand excluded by PLIP SO4.57: 4 residues within 4Å: Chain G: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.58: 1 residues within 4Å: Chain G: R.169 Ligand excluded by PLIP SO4.59: 6 residues within 4Å: Chain G: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.62: 7 residues within 4Å: Chain G: N.53, K.54, A.57, R.125, S.195, E.196 Ligands: 09Y.61 Ligand excluded by PLIP SO4.63: 6 residues within 4Å: Chain E: T.174, R.175, T.178 Chain G: E.78, R.83, V.91 Ligand excluded by PLIP SO4.66: 4 residues within 4Å: Chain H: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.67: 1 residues within 4Å: Chain H: R.169 Ligand excluded by PLIP SO4.68: 6 residues within 4Å: Chain H: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.71: 7 residues within 4Å: Chain H: N.53, K.54, A.57, R.125, S.195, E.196 Ligands: 09Y.70 Ligand excluded by PLIP SO4.72: 6 residues within 4Å: Chain F: T.174, R.175, T.178 Chain H: E.78, R.83, V.91 Ligand excluded by PLIP

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

QQ4.6: 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 QQ4.15: 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 QQ4.24: 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 QQ4.33: 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 QQ4.42: 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 QQ4.51: 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 QQ4.60: 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 QQ4.69: 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

8 x 09Y: 5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-2-(2-methylphenyl)-6-oxo-1,6-dihydropyrimidine-4-carboxamide(Non-covalent)

09Y.7: 14 residues within 4Å: Chain A: A.40, Y.44, K.54, I.58, H.61, E.81, L.107, D.109, E.120, I.121, Y.131 Ligands: MN.1, MN.2, SO4.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.40, A:Y.44, A:Y.44, A:K.54 Water bridges: A:V.123 09Y.16: 14 residues within 4Å: Chain B: A.40, Y.44, K.54, I.58, H.61, E.81, L.107, D.109, E.120, I.121, Y.131 Ligands: MN.10, MN.11, SO4.17 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.40, B:Y.44, B:Y.44, B:K.54 Water bridges: B:V.123 09Y.25: 14 residues within 4Å: Chain C: A.40, Y.44, K.54, I.58, H.61, E.81, L.107, D.109, E.120, I.121, Y.131 Ligands: MN.19, MN.20, SO4.26 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.40, C:Y.44, C:Y.44, C:K.54 Water bridges: C:V.123 09Y.34: 14 residues within 4Å: Chain D: A.40, Y.44, K.54, I.58, H.61, E.81, L.107, D.109, E.120, I.121, Y.131 Ligands: MN.28, MN.29, SO4.35 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:A.40, D:Y.44, D:Y.44, D:K.54 Hydrogen bonds: D:E.120, D:I.121 Water bridges: D:D.109, D:V.123 09Y.43: 14 residues within 4Å: Chain E: A.40, Y.44, K.54, I.58, H.61, E.81, L.107, D.109, E.120, I.121, Y.131 Ligands: MN.37, MN.38, SO4.44 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:A.40, E:Y.44, E:Y.44, E:K.54 Hydrogen bonds: E:Y.131 Water bridges: E:V.123 09Y.52: 14 residues within 4Å: Chain F: A.40, Y.44, K.54, I.58, H.61, E.81, L.107, D.109, E.120, I.121, Y.131 Ligands: MN.46, MN.47, SO4.53 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:A.40, F:Y.44, F:Y.44, F:K.54 Hydrogen bonds: F:Y.131 Water bridges: F:V.123 09Y.61: 14 residues within 4Å: Chain G: A.40, Y.44, K.54, I.58, H.61, E.81, L.107, D.109, E.120, I.121, Y.131 Ligands: MN.55, MN.56, SO4.62 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:A.40, G:Y.44, G:Y.44, G:K.54 Hydrogen bonds: G:Y.131 Water bridges: G:V.123 09Y.70: 14 residues within 4Å: Chain H: A.40, Y.44, K.54, I.58, H.61, E.81, L.107, D.109, E.120, I.121, Y.131 Ligands: MN.64, MN.65, SO4.71 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:A.40, H:Y.44, H:Y.44, H:K.54 Hydrogen bonds: H:E.81, H:I.121, H:Y.131 Water bridges: H:V.123

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

2022-06-08

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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