SMTL ID : 7kl3.1

The crystal structure of the 2009/H1N1/California PA endonuclease mutant E119D bound to RNA oligomer AG*CAUC (*uncleaveable bond, -UC disordered)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

1 x A- G: RNA (5'-R(P*AP*GP*CP*A)-3')(Non-covalent)

A-G.1: 10 residues within 4Å: Chain A: Y.44, E.46, K.54, A.57, H.61, E.81, F.106, L.107, D.109 Ligands: RQA.6 Protein-ligand interaction information (PLIP) not available

1 x A: ADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

A.2: 6 residues within 4Å: Chain A: T.124, R.125, R.126, R.193, Q.194 Ligands: RQA.6 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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: Y.162, E.166, R.169 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.166, A:R.169, A:R.169 Water bridges: A:L.164, A:E.166, A:E.166, A:E.166

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

SO4.4: 6 residues within 4Å: Chain A: I.50, E.51, T.52, N.53, K.54, Q.194 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.51, A:E.51, A:T.52, A:N.53, A:N.53, A:K.54 SO4.5: 4 residues within 4Å: Chain A: G.72, S.73, R.76, K.114 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.73, A:S.73 Water bridges: A:G.71, A:S.73, A:S.73, A:R.76, A:D.165 Salt bridges: A:R.76, A:K.114

1 x RQA: 5'-O-sulfocytidine(Non-covalent)

RQA.6: 10 residues within 4Å: Chain A: H.61, I.121, G.122, V.123, R.125, R.126, Y.131, K.138 Ligands: A-G.1, A.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.126, A:Y.131, A:E.134, A:K.138 Water bridges: A:K.138

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein PA-X

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