SMTL ID : 6yem.1

H1N1 2009 PA Endonuclease in complex with Quambalarine B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: H.50, D.98, E.109, I.110 Ligands: MN.2, OOH.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.50, A:D.98, A:I.110, OOH.5 MN.2: 6 residues within 4Å: Chain A: H.50, E.70, D.98, E.109 Ligands: MN.1, OOH.5 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.70, A:D.98, H2O.1, H2O.1, OOH.5

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: Q.16, F.18 Ligand excluded by PLIP

1 x OOH: 3,5,6,8-tetrakis(oxidanyl)-2-pentanoyl-naphthalene-1,4-dione(Non-covalent)

OOH.5: 11 residues within 4Å: Chain A: Y.33, H.50, E.70, D.98, E.109, I.110, G.111, Y.120, K.124 Ligands: MN.1, MN.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.120, A:Y.120, A:K.124 Water bridges: A:V.112 pi-Stacking: A:H.50

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