SMTL ID : 6wj4.1

The crystal structure of the 2009/H1N1/California PA endonuclease wild type in complex with SJ000986448

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-octamer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.61, D.109, E.120, I.121 Ligands: U3A.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, P.108, D.109 Ligands: U3A.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.81, A:D.109 MN.7: 5 residues within 4Å: Chain B: H.61, D.109, E.120, I.121 Ligands: U3A.9 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, P.108, D.109 Ligands: U3A.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.81, B:D.109 MN.13: 5 residues within 4Å: Chain C: H.61, D.109, E.120, I.121 Ligands: U3A.15 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, P.108, D.109 Ligands: U3A.15 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.81, C:D.109 MN.19: 5 residues within 4Å: Chain D: H.61, D.109, E.120, I.121 Ligands: U3A.21 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, P.108, D.109 Ligands: U3A.21 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.81, D:D.109 MN.25: 5 residues within 4Å: Chain E: H.61, D.109, E.120, I.121 Ligands: U3A.27 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, P.108, D.109 Ligands: U3A.27 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.81, E:D.109 MN.31: 5 residues within 4Å: Chain F: H.61, D.109, E.120, I.121 Ligands: U3A.33 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, P.108, D.109 Ligands: U3A.33 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.81, F:D.109 MN.37: 5 residues within 4Å: Chain G: H.61, D.109, E.120, I.121 Ligands: U3A.39 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, P.108, D.109 Ligands: U3A.39 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:E.81, G:D.109 MN.43: 5 residues within 4Å: Chain H: H.61, D.109, E.120, I.121 Ligands: U3A.45 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, P.108, D.109 Ligands: U3A.45 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:E.81, H:D.109

8 x U3A: 5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-2-[2-(trifluoromethyl)phenyl]-3,6-dihydropyrimidine-4-carboxamide(Non-covalent)

U3A.3: 11 residues within 4Å: Chain A: Y.44, E.46, A.57, I.58, H.61, L.107, D.109, E.120, I.121 Ligands: MN.1, MN.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.44, A:Y.44 Hydrogen bonds: A:Y.131 U3A.9: 11 residues within 4Å: Chain B: Y.44, E.46, A.57, I.58, H.61, L.107, D.109, E.120, I.121 Ligands: MN.7, MN.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.44, B:Y.44 Hydrogen bonds: B:Y.131 U3A.15: 11 residues within 4Å: Chain C: Y.44, E.46, A.57, I.58, H.61, L.107, D.109, E.120, I.121 Ligands: MN.13, MN.14 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.44, C:Y.44 Hydrogen bonds: C:Y.131 U3A.21: 11 residues within 4Å: Chain D: Y.44, E.46, A.57, I.58, H.61, L.107, D.109, E.120, I.121 Ligands: MN.19, MN.20 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.44, D:Y.44 Hydrogen bonds: D:Y.131 U3A.27: 11 residues within 4Å: Chain E: Y.44, E.46, A.57, I.58, H.61, L.107, D.109, E.120, I.121 Ligands: MN.25, MN.26 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.44, E:Y.44 U3A.33: 11 residues within 4Å: Chain F: Y.44, E.46, A.57, I.58, H.61, L.107, D.109, E.120, I.121 Ligands: MN.31, MN.32 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:Y.44, F:Y.44 U3A.39: 11 residues within 4Å: Chain G: Y.44, E.46, A.57, I.58, H.61, L.107, D.109, E.120, I.121 Ligands: MN.37, MN.38 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:Y.44, G:Y.44 U3A.45: 11 residues within 4Å: Chain H: Y.44, E.46, A.57, I.58, H.61, L.107, D.109, E.120, I.121 Ligands: MN.43, MN.44 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:Y.44, H:Y.44 Hydrogen bonds: H:E.81

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

QQ4.4: 5 residues within 4Å: Chain A: M.32, F.66, D.70, I.79, E.81 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.70, A:I.79 QQ4.10: 5 residues within 4Å: Chain B: M.32, F.66, D.70, I.79, E.81 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:D.70, B:I.79 QQ4.16: 5 residues within 4Å: Chain C: M.32, F.66, D.70, I.79, E.81 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:D.70, C:I.79 QQ4.22: 5 residues within 4Å: Chain D: M.32, F.66, D.70, I.79, E.81 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:D.70, D:I.79 QQ4.28: 5 residues within 4Å: Chain E: M.32, F.66, D.70, I.79, E.81 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:D.70, E:I.79 QQ4.34: 5 residues within 4Å: Chain F: M.32, F.66, D.70, I.79, E.81 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:D.70, F:I.79 QQ4.40: 5 residues within 4Å: Chain G: M.32, F.66, D.70, I.79, E.81 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:D.70, G:I.79 QQ4.46: 5 residues within 4Å: Chain H: M.32, F.66, D.70, I.79, E.81 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:D.70, H:I.79

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: 6 residues within 4Å: Chain A: I.50, 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: 6 residues within 4Å: Chain B: I.50, 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: 6 residues within 4Å: Chain C: I.50, 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: 6 residues within 4Å: Chain D: I.50, 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: 6 residues within 4Å: Chain E: I.50, 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: 6 residues within 4Å: Chain F: I.50, 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: 6 residues within 4Å: Chain G: I.50, 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: 6 residues within 4Å: Chain H: I.50, 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

2021-04-14

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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