SMTL ID : 7onf.1

The binding of p-coumaroyl glucose to glycogen phosphorylase reveals the relationship between structural data and effects on cell metabolome

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 15 residues within 4Å: Chain A: Y.79, G.123, G.124, W.480, V.556, K.557, K.563, Y.637, R.638, V.639, A.642, G.664, T.665, G.666, K.669 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.79, A:Y.637, A:V.639, A:K.669 Hydrogen bonds: A:T.665, A:G.666 Water bridges: A:Y.79, A:G.124, A:K.557, A:K.563, A:K.563, A:N.667, A:N.667 Salt bridges: A:K.557, A:K.563 PLP.4: 15 residues within 4Å: Chain B: Y.79, G.123, G.124, W.480, V.556, K.557, K.563, Y.637, R.638, V.639, A.642, G.664, T.665, G.666, K.669 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.79, B:Y.637, B:V.639, B:K.669 Hydrogen bonds: B:Y.637, B:T.665, B:G.666 Water bridges: B:G.124, B:K.557, B:K.563, B:K.563, B:N.667, B:N.667 Salt bridges: B:K.557, B:K.563

2 x IMP: INOSINIC ACID(Non-covalent)

IMP.2: 6 residues within 4Å: Chain A: Q.60, Y.64, R.298, R.299 Chain B: D.31, V.34 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:D.31 Water bridges: B:D.31, A:R.298, A:R.298 Salt bridges: A:R.298, A:R.299 pi-Stacking: A:Y.64, A:Y.64 IMP.5: 6 residues within 4Å: Chain A: D.31, V.34 Chain B: Q.60, Y.64, R.298, R.299 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Water bridges: B:R.298, B:R.298 Salt bridges: B:R.298, B:R.299 pi-Stacking: B:Y.64, B:Y.64 Hydrogen bonds: A:D.31

2 x VKK: p-coumaroyl glucose(Non-covalent)

VKK.3: 18 residues within 4Å: Chain A: E.77, G.124, L.125, L.128, N.271, D.272, N.273, F.274, R.281, H.330, H.366, V.444, N.473, Y.562, E.661, A.662, S.663, G.664 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.125 Hydrogen bonds: A:G.124, A:L.125, A:N.273, A:F.274, A:N.473, A:N.473, A:E.661, A:E.661, A:A.662, A:S.663, A:G.664 Water bridges: A:G.126, A:E.276, A:R.281, A:T.665 Salt bridges: A:H.366 pi-Cation interactions: A:H.330 VKK.6: 18 residues within 4Å: Chain B: E.77, G.124, L.125, L.128, N.271, D.272, N.273, F.274, R.281, H.330, H.366, V.444, N.473, Y.562, E.661, A.662, S.663, G.664 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.125 Hydrogen bonds: B:G.124, B:L.125, B:N.273, B:F.274, B:N.473, B:N.473, B:E.661, B:A.662, B:S.663, B:G.664 Water bridges: B:G.126, B:E.276, B:R.281, B:Y.562, B:T.665 Salt bridges: B:H.366 pi-Cation interactions: B:H.330

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsagkarakou, A.S. et al., Structure activity relationship of the binding of p-coumaroyl glucose to glycogen phosphorylase and its effect on hepatic cell metabolic pathways. Eur J Med Chem Rep (2021)

Release Date

2022-04-06

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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