SMTL ID : 4yua.1

Glycogen phosphorylase in complex with ellagic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 15 residues within 4Å: Chain A: Y.91, G.135, G.136, W.492, V.568, K.569, K.575, Y.649, R.650, V.651, A.654, G.676, T.677, G.678, K.681 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.91, A:Y.649, A:V.651, A:K.681 Hydrogen bonds: A:T.677, A:G.678 Water bridges: A:Y.91, A:G.136, A:K.569, A:K.575, A:K.575, A:N.679 Salt bridges: A:K.569, A:K.575 PLP.3: 15 residues within 4Å: Chain B: Y.91, G.135, G.136, W.492, V.568, K.569, K.575, Y.649, R.650, V.651, A.654, G.676, T.677, G.678, K.681 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.91, B:Y.649, B:V.651, B:K.681 Hydrogen bonds: B:Y.649, B:T.677, B:G.678, B:K.681 Water bridges: B:G.136, B:K.569, B:K.575, B:K.575, B:N.679 Salt bridges: B:K.569, B:K.575

2 x REF: 2,3,7,8-tetrahydroxychromeno[5,4,3-cde]chromene-5,10-dione(Non-covalent)

REF.2: 10 residues within 4Å: Chain A: N.283, D.284, F.286, E.288, E.383, H.572, E.573, A.611, G.613, Y.614 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.286, A:F.286, A:F.286, A:Y.614 Hydrogen bonds: A:N.283, A:E.383, A:H.572, A:E.573, A:G.613 pi-Stacking: A:F.286, A:F.286, A:Y.614 REF.4: 10 residues within 4Å: Chain B: N.283, D.284, F.286, E.288, E.383, H.572, E.573, A.611, G.613, Y.614 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.286, B:F.286, B:F.286, B:Y.614 Hydrogen bonds: B:N.283, B:H.572, B:G.613 pi-Stacking: B:F.286, B:F.286, B:Y.614

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kyriakis, E. et al., Natural flavonoids as antidiabetic agents. The binding of gallic and ellagic acids to glycogen phosphorylase b. Febs Lett. (2015)

Release Date

2015-05-13

Peptides

Glycogen phosphorylase, muscle form: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glycogen phosphorylase, muscle form

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