SMTL ID : 7ml8.1

The crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ001023038

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-octamer

Ligands

8 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 5 residues within 4Å: Chain A: T.124, R.125, R.126, Q.194, S.195 6 PLIP interactions: 6 interactions with chain A, Hydrogen bonds: A:T.124, A:T.124, A:R.125, A:Q.194 Salt bridges: A:R.125, A:R.126 GLU.8: 5 residues within 4Å: Chain B: T.124, R.125, R.126, Q.194, S.195 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.124, B:T.124, B:R.125, B:Q.194 Salt bridges: B:R.125, B:R.126 GLU.15: 5 residues within 4Å: Chain C: T.124, R.125, R.126, Q.194, S.195 6 PLIP interactions: 6 interactions with chain C, Hydrogen bonds: C:T.124, C:T.124, C:R.125, C:Q.194 Salt bridges: C:R.125, C:R.126 GLU.22: 5 residues within 4Å: Chain D: T.124, R.125, R.126, Q.194, S.195 6 PLIP interactions: 6 interactions with chain D, Hydrogen bonds: D:T.124, D:T.124, D:R.125, D:Q.194 Salt bridges: D:R.125, D:R.126 GLU.29: 5 residues within 4Å: Chain E: T.124, R.125, R.126, Q.194, S.195 5 PLIP interactions: 5 interactions with chain E, Hydrogen bonds: E:T.124, E:R.125, E:Q.194 Salt bridges: E:R.125, E:R.126 GLU.36: 5 residues within 4Å: Chain F: T.124, R.125, R.126, Q.194, S.195 5 PLIP interactions: 5 interactions with chain F, Hydrogen bonds: F:T.124, F:R.125, F:Q.194 Salt bridges: F:R.125, F:R.126 GLU.43: 5 residues within 4Å: Chain G: T.124, R.125, R.126, Q.194, S.195 5 PLIP interactions: 5 interactions with chain G, Hydrogen bonds: G:T.124, G:R.125, G:Q.194 Salt bridges: G:R.125, G:R.126 GLU.50: 5 residues within 4Å: Chain H: T.124, R.125, R.126, Q.194, S.195 5 PLIP interactions: 5 interactions with chain H, Hydrogen bonds: H:T.124, H:R.125, H:Q.194 Salt bridges: H:R.125, H:R.126

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

ZHJ.2: 16 residues within 4Å: Chain A: A.40, M.41, Y.44, E.46, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, G.122, Y.131 Ligands: MN.4, MN.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.40, A:K.54, A:A.57 Hydrogen bonds: A:T.58, A:Y.131 Water bridges: A:V.123 pi-Stacking: A:Y.44, A:H.61 ZHJ.9: 16 residues within 4Å: Chain B: A.40, M.41, Y.44, E.46, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, G.122, Y.131 Ligands: MN.11, MN.12 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.40, B:K.54, B:A.57 Hydrogen bonds: B:T.58, B:Y.131 Water bridges: B:V.123 pi-Stacking: B:Y.44, B:H.61 ZHJ.16: 16 residues within 4Å: Chain C: A.40, M.41, Y.44, E.46, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, G.122, Y.131 Ligands: MN.18, MN.19 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:A.40, C:K.54, C:A.57 Hydrogen bonds: C:T.58, C:Y.131 Water bridges: C:V.123 pi-Stacking: C:Y.44, C:H.61 ZHJ.23: 16 residues within 4Å: Chain D: A.40, M.41, Y.44, E.46, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, G.122, Y.131 Ligands: MN.25, MN.26 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:A.40, D:K.54, D:A.57 Hydrogen bonds: D:T.58, D:Y.131 Water bridges: D:V.123 pi-Stacking: D:Y.44, D:H.61 ZHJ.30: 16 residues within 4Å: Chain E: A.40, M.41, Y.44, E.46, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, G.122, Y.131 Ligands: MN.32, MN.33 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:A.40, E:K.54, E:A.57 Hydrogen bonds: E:Y.131, E:Y.131 Water bridges: E:V.123 pi-Stacking: E:Y.44, E:H.61 ZHJ.37: 16 residues within 4Å: Chain F: A.40, M.41, Y.44, E.46, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, G.122, Y.131 Ligands: MN.39, MN.40 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:A.40, F:K.54, F:A.57 Hydrogen bonds: F:Y.131, F:Y.131 Water bridges: F:V.123 pi-Stacking: F:Y.44, F:H.61 ZHJ.44: 16 residues within 4Å: Chain G: A.40, M.41, Y.44, E.46, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, G.122, Y.131 Ligands: MN.46, MN.47 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:A.40, G:K.54, G:A.57 Hydrogen bonds: G:Y.131, G:Y.131 Water bridges: G:V.123 pi-Stacking: G:Y.44, G:H.61 ZHJ.51: 16 residues within 4Å: Chain H: A.40, M.41, Y.44, E.46, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, G.122, Y.131 Ligands: MN.53, MN.54 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:A.40, H:K.54, H:A.57 Hydrogen bonds: H:Y.131, H:Y.131 Water bridges: H:V.123 pi-Stacking: H:Y.44, H:H.61

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

QQ4.3: 5 residues within 4Å: Chain A: N.30, M.32, I.33, F.66, I.79 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.33, A:F.66, A:F.66, A:F.66, A:I.79 QQ4.10: 5 residues within 4Å: Chain B: N.30, M.32, I.33, F.66, I.79 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.33, B:F.66, B:F.66, B:F.66, B:I.79 QQ4.17: 5 residues within 4Å: Chain C: N.30, M.32, I.33, F.66, I.79 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.33, C:F.66, C:F.66, C:F.66, C:I.79 QQ4.24: 5 residues within 4Å: Chain D: N.30, M.32, I.33, F.66, I.79 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.33, D:F.66, D:F.66, D:F.66, D:I.79 QQ4.31: 5 residues within 4Å: Chain E: N.30, M.32, I.33, F.66, I.79 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:I.33, E:F.66, E:F.66, E:F.66, E:I.79 QQ4.38: 5 residues within 4Å: Chain F: N.30, M.32, I.33, F.66, I.79 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:I.33, F:F.66, F:F.66, F:F.66, F:I.79 QQ4.45: 5 residues within 4Å: Chain G: N.30, M.32, I.33, F.66, I.79 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:I.33, G:F.66, G:F.66, G:F.66, G:I.79 QQ4.52: 5 residues within 4Å: Chain H: N.30, M.32, I.33, F.66, I.79 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:I.33, H:F.66, H:F.66, H:F.66, H:I.79

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

MN.4: 5 residues within 4Å: Chain A: H.61, D.109, E.120, I.121 Ligands: ZHJ.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.61, A:D.109, A:E.120, A:I.121 MN.5: 5 residues within 4Å: Chain A: E.81, L.107, P.108, D.109 Ligands: ZHJ.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.109, H2O.1 MN.11: 5 residues within 4Å: Chain B: H.61, D.109, E.120, I.121 Ligands: ZHJ.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.61, B:D.109, B:E.120, B:I.121 MN.12: 5 residues within 4Å: Chain B: E.81, L.107, P.108, D.109 Ligands: ZHJ.9 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.109, H2O.1 MN.18: 5 residues within 4Å: Chain C: H.61, D.109, E.120, I.121 Ligands: ZHJ.16 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.61, C:D.109, C:E.120, C:I.121 MN.19: 5 residues within 4Å: Chain C: E.81, L.107, P.108, D.109 Ligands: ZHJ.16 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.109, H2O.2 MN.25: 5 residues within 4Å: Chain D: H.61, D.109, E.120, I.121 Ligands: ZHJ.23 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:D.109, D:E.120, D:I.121 MN.26: 5 residues within 4Å: Chain D: E.81, L.107, P.108, D.109 Ligands: ZHJ.23 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.109, H2O.3 MN.32: 5 residues within 4Å: Chain E: H.61, D.109, E.120, I.121 Ligands: ZHJ.30 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.61, E:D.109, E:E.120, E:I.121 MN.33: 5 residues within 4Å: Chain E: E.81, L.107, P.108, D.109 Ligands: ZHJ.30 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.109, H2O.4 MN.39: 5 residues within 4Å: Chain F: H.61, D.109, E.120, I.121 Ligands: ZHJ.37 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.61, F:D.109, F:E.120, F:I.121 MN.40: 5 residues within 4Å: Chain F: E.81, L.107, P.108, D.109 Ligands: ZHJ.37 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.109, H2O.5 MN.46: 5 residues within 4Å: Chain G: H.61, D.109, E.120, I.121 Ligands: ZHJ.44 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.61, G:D.109, G:E.120, G:I.121 MN.47: 5 residues within 4Å: Chain G: E.81, L.107, P.108, D.109 Ligands: ZHJ.44 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.109, H2O.5 MN.53: 5 residues within 4Å: Chain H: H.61, D.109, E.120, I.121 Ligands: ZHJ.51 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.61, H:D.109, H:E.120, H:I.121 MN.54: 5 residues within 4Å: Chain H: E.81, L.107, P.108, D.109 Ligands: ZHJ.51 2 PLIP interactions: 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.109, H2O.6

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

SO4.6: 6 residues within 4Å: Chain A: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.13: 6 residues within 4Å: Chain B: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.20: 6 residues within 4Å: Chain C: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain C: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.27: 6 residues within 4Å: Chain D: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain D: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.34: 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 E: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.41: 6 residues within 4Å: Chain F: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain F: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.48: 6 residues within 4Å: Chain G: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.49: 4 residues within 4Å: Chain G: G.72, S.73, R.76, K.114 Ligand excluded by PLIP SO4.55: 6 residues within 4Å: Chain H: I.50, E.51, T.52, N.53, K.54, S.195 Ligand excluded by PLIP SO4.56: 4 residues within 4Å: Chain H: G.72, S.73, R.76, K.114 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cuypers, M.G. et al., The crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with St Jude compound AC067-19. To Be Published

Release Date

2021-10-27

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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