SMTL ID : 6whm.1

The crystal structure of the 2009/H1N1/California PA endonuclease wild type bound to DNA oligomer TAGC (cleaved TTAGCATT, 5mM overnight DNA soak)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

1 x DT- DA- DG- DC: DNA (5'-D(P*TP*AP*GP*C)-3')(Non-covalent)

DT-DA-DG-DC.1: 15 residues within 4Å: Chain A: K.54, A.57, I.58, H.61, I.121, G.122, V.123, T.124, R.125, R.126, Y.131, E.134, Q.194, S.195 Ligands: MG.8 Protein-ligand interaction information (PLIP) not available

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: I.79, E.81, G.82, R.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.81 Water bridges: A:I.79, A:I.79 GOL.3: 3 residues within 4Å: Chain A: W.89, N.93, K.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.93, A:N.93

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: H.61, D.109, E.120, I.121 Ligands: MN.5, MG.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.61, A:D.109, A:E.120, A:I.121, H2O.6 MG.8: 7 residues within 4Å: Chain A: H.61, E.81, D.109, E.120 Ligands: DT-DA-DG-DC.1, MG.4, MN.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.109

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

MN.5: 6 residues within 4Å: Chain A: H.61, D.109, E.120, I.121 Ligands: MG.4, MG.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.61, A:D.109, A:E.120, A:I.121, H2O.6

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

SO4.6: 4 residues within 4Å: Chain A: G.72, S.73, R.76, K.114 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.73, A:S.73, A:S.73 Water bridges: A:K.114 Salt bridges: A:R.76, A:K.114 SO4.7: 5 residues within 4Å: Chain A: E.51, T.52, N.53, K.54, S.195 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.51, A:T.52, A:N.53, A:N.53, A:K.54, A:S.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, G. et al., Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism. Nucleic Acids Res. (2021)

Release Date

2021-02-03

Peptides

PA-X protein,Polymerase acidic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PA-X protein,Polymerase acidic protein

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