SMTL ID : 6yve.1

Glycogen phosphorylase b in complex with pelargonidin 3-O-beta-D-glucoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 18 residues within 4Å: Chain A: Y.91, G.135, G.136, R.139, W.492, V.568, K.569, R.570, K.575, Y.649, R.650, V.651, A.654, G.676, T.677, G.678, N.679, K.681 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.91, A:Y.649, A:K.681 Hydrogen bonds: A:V.568, A:T.677, A:T.677, A:G.678 Water bridges: A:G.136, A:K.569, A:K.569, A:K.575, A:K.575, A:N.679 Salt bridges: A:K.569, A:K.575 PLP.4: 18 residues within 4Å: Chain B: Y.91, G.135, G.136, R.139, W.492, V.568, K.569, R.570, K.575, Y.649, R.650, V.651, A.654, G.676, T.677, G.678, N.679, K.681 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.91, B:Y.649, B:K.681 Hydrogen bonds: B:V.568, B:T.677, B:T.677, B:G.678 Water bridges: B:G.136, B:K.569, B:K.569, B:K.575, B:K.575, B:N.679 Salt bridges: B:K.569, B:K.575

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

DMS.2: 7 residues within 4Å: Chain A: L.550, Y.554, V.556, I.644, F.645, L.646, E.647 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.647 pi-Cation interactions: A:Y.554 DMS.5: 7 residues within 4Å: Chain B: L.550, Y.554, V.556, I.644, F.645, L.646, E.647 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.647 pi-Cation interactions: B:Y.554

2 x PUQ: pelargonidin 3-O-beta-D-glucoside(Non-covalent)

PUQ.3: 14 residues within 4Å: Chain A: P.282, N.283, D.284, F.286, E.288, E.383, R.570, H.572, E.573, A.611, G.613, Y.614, H.615, R.771 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.286, A:F.286, A:F.286, A:A.611, A:Y.614, A:Y.614 Hydrogen bonds: A:N.283, A:D.284, A:R.570, A:G.613, A:Y.614, A:Y.614, A:H.615 Water bridges: A:E.573, A:A.611, A:G.613, A:R.771 PUQ.6: 14 residues within 4Å: Chain B: P.282, N.283, D.284, F.286, E.288, E.383, R.570, H.572, E.573, A.611, G.613, Y.614, H.615, R.771 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.286, B:F.286, B:F.286, B:A.611, B:Y.614, B:Y.614 Hydrogen bonds: B:N.283, B:D.284, B:R.570, B:G.613, B:Y.614, B:Y.614, B:H.615 Water bridges: B:E.573, B:A.611, B:G.613, B:R.771

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drakou, C.E. et al., Affinity Crystallography Reveals Binding of Pomegranate Juice Anthocyanins at the Inhibitor Site of Glycogen Phosphorylase: The Contribution of a Sugar Moiety to Potency and Its Implications to the Binding Mode. J.Agric.Food Chem. (2020)

Release Date

2020-11-18

Peptides

Glycogen phosphorylase, muscle form: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

Glycogen phosphorylase, muscle form

Related Entries With Identical Sequence