SMTL ID : 7lp8.1

The crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000983476

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-octamer

Ligands

8 x YAD: (phenylmethyl) (2~{S})-2-[5-oxidanyl-6-oxidanylidene-4-(2-pyridin-4-ylethylcarbamoyl)-1~{H}-pyrimidin-2-yl]pyrrolidine-1-carboxylate(Non-covalent)

YAD.1: 13 residues within 4Å: Chain A: Y.44, E.46, T.58, H.61, E.81, D.109, E.120, I.121, G.122, Y.131, K.135 Ligands: MN.3, MN.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.44, A:Y.44 Hydrogen bonds: A:Y.131, A:Y.131, A:K.135 Water bridges: A:V.123 pi-Cation interactions: A:H.61 YAD.6: 13 residues within 4Å: Chain B: Y.44, E.46, T.58, H.61, E.81, D.109, E.120, I.121, G.122, Y.131, K.135 Ligands: MN.8, MN.9 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.44, B:Y.44 Hydrogen bonds: B:Y.131, B:Y.131, B:K.135 Water bridges: B:V.123 pi-Cation interactions: B:H.61 YAD.11: 13 residues within 4Å: Chain C: Y.44, E.46, T.58, H.61, E.81, D.109, E.120, I.121, G.122, Y.131, K.135 Ligands: MN.13, MN.14 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.44, C:Y.44 Hydrogen bonds: C:Y.131, C:Y.131, C:K.135 Water bridges: C:V.123 pi-Cation interactions: C:H.61 YAD.16: 13 residues within 4Å: Chain D: Y.44, E.46, T.58, H.61, E.81, D.109, E.120, I.121, G.122, Y.131, K.135 Ligands: MN.18, MN.19 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.44, D:Y.44 Hydrogen bonds: D:Y.131, D:Y.131, D:K.135 Water bridges: D:V.123 pi-Cation interactions: D:H.61 YAD.21: 13 residues within 4Å: Chain E: Y.44, E.46, T.58, H.61, E.81, D.109, E.120, I.121, G.122, Y.131, K.135 Ligands: MN.23, MN.24 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:Y.44, E:Y.44 Hydrogen bonds: E:Y.131, E:K.135 Water bridges: E:V.123 pi-Cation interactions: E:H.61 YAD.26: 13 residues within 4Å: Chain F: Y.44, E.46, T.58, H.61, E.81, D.109, E.120, I.121, G.122, Y.131, K.135 Ligands: MN.28, MN.29 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:Y.44, F:Y.44 Hydrogen bonds: F:Y.131, F:K.135 Water bridges: F:V.123 pi-Cation interactions: F:H.61 YAD.31: 13 residues within 4Å: Chain G: Y.44, E.46, T.58, H.61, E.81, D.109, E.120, I.121, G.122, Y.131, K.135 Ligands: MN.33, MN.34 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:Y.44, G:Y.44 Hydrogen bonds: G:Y.131, G:K.135 Water bridges: G:V.123 pi-Cation interactions: G:H.61 YAD.36: 13 residues within 4Å: Chain H: Y.44, E.46, T.58, H.61, E.81, D.109, E.120, I.121, G.122, Y.131, K.135 Ligands: MN.38, MN.39 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:Y.44, H:Y.44 Hydrogen bonds: H:Y.131, H:K.135 Water bridges: H:V.123 pi-Cation interactions: H:H.61

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

QQ4.2: 6 residues within 4Å: Chain A: N.30, M.32, F.66, I.79, E.81, G.82 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.66, A:F.66 QQ4.7: 6 residues within 4Å: Chain B: N.30, M.32, F.66, I.79, E.81, G.82 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.66, B:F.66 QQ4.12: 6 residues within 4Å: Chain C: N.30, M.32, F.66, I.79, E.81, G.82 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.66, C:F.66 QQ4.17: 6 residues within 4Å: Chain D: N.30, M.32, F.66, I.79, E.81, G.82 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.66, D:F.66 QQ4.22: 6 residues within 4Å: Chain E: N.30, M.32, F.66, I.79, E.81, G.82 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.66, E:F.66 QQ4.27: 6 residues within 4Å: Chain F: N.30, M.32, F.66, I.79, E.81, G.82 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:F.66, F:F.66 QQ4.32: 6 residues within 4Å: Chain G: N.30, M.32, F.66, I.79, E.81, G.82 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:F.66, G:F.66 QQ4.37: 6 residues within 4Å: Chain H: N.30, M.32, F.66, I.79, E.81, G.82 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:F.66, H:F.66

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

MN.3: 6 residues within 4Å: Chain A: H.61, D.109, E.120, I.121 Ligands: YAD.1, MN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.61, A:D.109, A:E.120, A:I.121 MN.4: 5 residues within 4Å: Chain A: H.61, E.81, D.109 Ligands: YAD.1, MN.3 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: YAD.6, MN.9 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: YAD.6, MN.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.81, B:D.109, H2O.2, H2O.2 MN.13: 6 residues within 4Å: Chain C: H.61, D.109, E.120, I.121 Ligands: YAD.11, MN.14 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: YAD.11, MN.13 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.81, C:D.109, H2O.3, H2O.3 MN.18: 6 residues within 4Å: Chain D: H.61, D.109, E.120, I.121 Ligands: YAD.16, MN.19 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:D.109, D:E.120, D:I.121 MN.19: 5 residues within 4Å: Chain D: H.61, E.81, D.109 Ligands: YAD.16, MN.18 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.81, D:D.109, H2O.4, H2O.4 MN.23: 6 residues within 4Å: Chain E: H.61, D.109, E.120, I.121 Ligands: YAD.21, MN.24 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.61, E:D.109, E:E.120, E:I.121 MN.24: 5 residues within 4Å: Chain E: H.61, E.81, D.109 Ligands: YAD.21, MN.23 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.81, E:D.109, H2O.5, H2O.5 MN.28: 6 residues within 4Å: Chain F: H.61, D.109, E.120, I.121 Ligands: YAD.26, MN.29 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.61, F:D.109, F:E.120, F:I.121 MN.29: 5 residues within 4Å: Chain F: H.61, E.81, D.109 Ligands: YAD.26, MN.28 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.81, F:D.109, H2O.6, H2O.6 MN.33: 6 residues within 4Å: Chain G: H.61, D.109, E.120, I.121 Ligands: YAD.31, MN.34 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.61, G:D.109, G:E.120, G:I.121 MN.34: 5 residues within 4Å: Chain G: H.61, E.81, D.109 Ligands: YAD.31, MN.33 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.81, G:D.109, H2O.7, H2O.8 MN.38: 6 residues within 4Å: Chain H: H.61, D.109, E.120, I.121 Ligands: YAD.36, MN.39 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.61, H:D.109, H:E.120, H:I.121 MN.39: 5 residues within 4Å: Chain H: H.61, E.81, D.109 Ligands: YAD.36, MN.38 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.81, H:D.109, H2O.9, H2O.9

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

SO4.5: 4 residues within 4Å: Chain A: E.51, T.52, N.53, K.54 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.51, A:T.52, A:N.53, A:N.53, A:K.54 SO4.10: 4 residues within 4Å: Chain B: E.51, T.52, N.53, K.54 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.51, B:T.52, B:N.53, B:N.53, B:K.54 SO4.15: 4 residues within 4Å: Chain C: E.51, T.52, N.53, K.54 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.51, C:T.52, C:N.53, C:N.53, C:K.54 SO4.20: 4 residues within 4Å: Chain D: E.51, T.52, N.53, K.54 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.51, D:T.52, D:N.53, D:N.53, D:K.54 SO4.25: 4 residues within 4Å: Chain E: E.51, T.52, N.53, K.54 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:E.51, E:E.51, E:T.52, E:T.52, E:N.53, E:N.53, E:K.54 SO4.30: 4 residues within 4Å: Chain F: E.51, T.52, N.53, K.54 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:E.51, F:E.51, F:T.52, F:T.52, F:N.53, F:N.53, F:K.54 SO4.35: 4 residues within 4Å: Chain G: E.51, T.52, N.53, K.54 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:E.51, G:E.51, G:T.52, G:T.52, G:N.53, G:N.53, G:K.54 SO4.40: 4 residues within 4Å: Chain H: E.51, T.52, N.53, K.54 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:E.51, H:E.51, H:T.52, H:T.52, H:N.53, H:N.53, H:K.54

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 SJ000983476. To Be Published

Release Date

2022-02-16

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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