SMTL ID : 6w7a.1

The crystal structure of the 2009/H1N1/California PA endonuclease mutant E119D bound to DNA oligomer TAGCAT (uncleaved, 5mM overnight DNA soak)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

1 x DT- DA- DG- DC- DA- DT: DNA (5'-D(P*TP*AP*GP*CP*AP*T)-3')(Non-covalent)

DT-DA-DG-DC-DA-DT.1: 22 residues within 4Å: Chain A: A.40, M.41, Y.44, E.46, K.54, A.57, I.58, H.61, W.89, F.106, L.107, I.121, G.122, V.123, T.124, R.125, R.126, Y.131, E.134, Q.194, S.195 Ligands: MN.4 Protein-ligand interaction information (PLIP) not available

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: E.155, Y.162, E.166, R.169, K.173 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.155, A:R.169 Water bridges: A:E.155 GOL.3: 4 residues within 4Å: Chain A: F.66, I.79, E.81, R.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.83 Water bridges: A:I.79, A:I.79

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

MN.4: 5 residues within 4Å: Chain A: H.61, D.109, D.120, I.121 Ligands: DT-DA-DG-DC-DA-DT.1 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.61, A:D.109, A:D.120, A:I.121, H2O.4, H2O.4

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

SO4.5: 4 residues within 4Å: Chain A: G.72, S.73, R.76, K.114 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.73, A:S.73, A:S.73 Salt bridges: A:R.76, A:K.114

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

Protein PA-X,Polymerase acidic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein PA-X,Polymerase acidic protein

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