SMTL ID : 6ya5.1

2009 H1N1 PA Endonuclease in complex with LU2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

MN.1: 7 residues within 4Å: Chain A: H.43, D.91, E.102, I.103, K.117 Ligands: MG.2, LU2.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.43, A:D.91, A:E.102, A:I.103

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: H.43, E.63, D.91 Ligands: MN.1, LU2.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.63, A:D.91, H2O.1, H2O.1, H2O.2

1 x LU2: 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one(Non-covalent)

LU2.3: 16 residues within 4Å: Chain A: A.22, M.23, Y.26, E.28, K.36, I.40, H.43, E.63, D.91, E.102, I.103, Y.113, K.117 Ligands: MN.1, MG.2, DMS.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.26 Hydrogen bonds: A:A.22, A:K.36, A:K.117

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

SO4.4: 2 residues within 4Å: Chain A: Y.26, R.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.26 Salt bridges: A:R.67 SO4.5: 6 residues within 4Å: Chain A: A.22, E.25, E.63, G.64, R.65, R.67 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.25, A:E.63, A:G.64, A:G.64 Water bridges: A:R.67, A:R.67 Salt bridges: A:R.67

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 5 residues within 4Å: Chain A: F.88, E.102, K.117, K.120 Ligands: LU2.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.102

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 4 residues within 4Å: Chain A: M.14, L.18, F.48, R.65 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.65

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 4 residues within 4Å: Chain A: R.153, T.156, R.157, T.160 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.157, A:R.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zima, V. et al., Unraveling the anti-influenza effect of flavonoids: Experimental validation of luteolin and its congeners as potent influenza endonuclease inhibitors. Eur.J.Med.Chem. (2020)

Release Date

2020-09-09

Peptides

Polymerase acidic protein,Polymerase acidic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polymerase acidic protein,Polymerase acidic protein