SMTL ID : 7lm4.1

The crystal structure of the I38T mutant PA Endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988503

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: H.61, D.109, E.120, I.121 Ligands: MN.2, Y5V.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.61, A:D.109, A:E.120, A:I.121 MN.2: 5 residues within 4Å: Chain A: H.61, E.81, D.109 Ligands: MN.1, Y5V.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 Y5V: 5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-2-(2-methylphenyl)-6-oxo-1,6-dihydropyrimidine-4-carboxamide(Non-covalent)

Y5V.3: 15 residues within 4Å: Chain A: A.40, Y.44, E.46, K.54, A.57, T.58, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.1, MN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.40, A:Y.44, A:K.54, A:A.57, A:H.61 Hydrogen bonds: A:Y.131 Water bridges: A:V.123 pi-Stacking: A:Y.44

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

QQ4.4: 5 residues within 4Å: Chain A: M.32, F.66, I.79, E.81, G.82 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.66, A:F.66, A:F.66, A:I.79

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

SO4.5: 4 residues within 4Å: Chain A: G.72, S.73, R.76, K.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.73 Water bridges: A:D.165 Salt bridges: A:R.76, A:K.114 SO4.6: 2 residues within 4Å: Chain A: Y.162, R.169 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.166 Salt bridges: A:R.169 SO4.7: 5 residues within 4Å: Chain A: I.50, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Slavish, P.J. et al., Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential. Eur.J.Med.Chem. (2023)

Release Date

2022-02-09

Peptides

Polymerase acidic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polymerase acidic protein

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