SMTL ID : 6v56.1

The crystal structure of the 2009 H1N1 PA endonuclease wild type in complex with SJ000985494

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

monomer

Ligands

1 x QPY: benzyl (2S)-2-(4-{[2-(6-amino-9H-purin-9-yl)ethyl]carbamoyl}-5-hydroxy-6-oxo-1,6-dihydropyrimidin-2-yl)pyrrolidine-1-carboxylate(Non-covalent)

QPY.1: 13 residues within 4Å: Chain A: Y.44, E.46, K.54, I.58, H.61, E.81, L.107, D.109, E.120, I.121, Y.131 Ligands: MN.3, MN.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.58, A:I.58, A:H.61 Hydrogen bonds: A:E.46, A:K.54, A:Y.131 Water bridges: A:E.81, A:V.123 pi-Stacking: A:Y.44, A:Y.44

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

QQ4.2: 7 residues within 4Å: Chain A: M.32, L.36, F.66, D.70, I.79, E.81, R.83 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.66, A:F.66, A:D.70, A:I.79, A:R.83

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

MN.3: 6 residues within 4Å: Chain A: H.61, D.109, E.120, I.121 Ligands: QPY.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: QPY.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

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

SO4.5: 6 residues within 4Å: Chain A: I.50, E.51, T.52, N.53, K.54, S.195 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.51, A:E.51, A:N.53, A:N.53, A:K.54, A:S.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cuypers, M.G. et al., The crystal structure of the 2009 H1N1 PA endonuclease mutant I38T in complex with SJ000985494. To Be Published

Release Date

2021-02-10

Peptides

Polymerase acidic protein,Polymerase acidic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polymerase acidic protein,Polymerase acidic protein

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