SMTL ID : 5h5l.1

Structure of prostaglandin synthase D of Nilaparvata lugens

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x GSH: GLUTATHIONE(Non-covalent)

GSH.1: 14 residues within 4Å: Chain A: Y.8, F.9, L.14, W.39, K.43, G.49, Q.50, V.51, P.52, Q.63, S.64, R.99 Chain B: D.97 Ligands: PEG.2 17 PLIP interactions: 2 interactions with chain B, 15 interactions with chain A Hydrogen bonds: B:D.97, A:Q.50, A:V.51, A:V.51, A:Q.63, A:Q.63, A:S.64, A:R.99 Water bridges: B:D.97, A:K.43, A:K.43, A:T.65, A:R.99, A:Y.155, A:Y.155 Hydrophobic interactions: A:L.14 Salt bridges: A:K.43 GSH.3: 13 residues within 4Å: Chain A: D.97 Chain B: Y.8, L.14, W.39, K.43, G.49, Q.50, V.51, P.52, Q.63, S.64, R.99, R.107 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.14 Hydrogen bonds: B:W.39, B:Q.50, B:V.51, B:V.51, B:Q.63, B:Q.63, B:Q.63, B:S.64, B:R.99, B:R.107 Water bridges: B:V.51, B:T.65, A:D.97 Salt bridges: B:K.43

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

PEG.2: 8 residues within 4Å: Chain A: Y.8, G.13, L.14, R.99, I.102, S.103, F.162 Ligands: GSH.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.8, A:R.99, A:R.99 Water bridges: A:S.103

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 2 residues within 4Å: Chain B: F.128, Y.129 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.125 Water bridges: A:K.43, A:K.43, A:K.43 EDO.5: 4 residues within 4Å: Chain B: N.134, D.135, K.138, H.176 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.138 Water bridges: B:N.131, B:N.134, B:N.134 EDO.6: 3 residues within 4Å: Chain B: N.131, K.173, Y.174 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.174 Water bridges: B:N.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamamoto, K. et al., Molecular structure of a prostaglandin D synthase requiring glutathione from the brown planthopper, Nilaparvata lugens. Biochem. Biophys. Res. Commun. (2017)

Release Date

2017-09-20

Peptides

Glutathione s-transferase S2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutathione s-transferase S2