SMTL ID : 8qmu.1

The complex of Glycogen Phosphorylase with (-)-Epigallocatechin-3-gallate (EGCG).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x KDH: (2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate(Non-covalent)

KDH.1: 11 residues within 4Å: Chain A: E.114, E.115, E.118, K.538, F.539, A.541, Y.542, R.545, E.546, K.649 Ligands: DMS.22 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:E.118, A:K.538, A:A.541, A:Y.542, A:K.649, A:K.649 Hydrogen bonds: A:E.114, A:E.114, A:R.545 Water bridges: A:E.115, A:N.535, A:F.539, A:K.649 Salt bridges: A:R.545 pi-Cation interactions: A:K.538, A:R.545 KDH.25: 11 residues within 4Å: Chain B: E.114, E.115, E.118, K.538, F.539, A.541, Y.542, R.545, E.546, K.649 Ligands: DMS.46 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:E.118, B:K.538, B:A.541, B:Y.542, B:K.649, B:K.649 Hydrogen bonds: B:E.114, B:R.545, B:E.546 Water bridges: B:E.115, B:N.535, B:F.539, B:K.649 Salt bridges: B:R.545 pi-Cation interactions: B:K.538, B:R.545

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

DMS.2: 1 residues within 4Å: Chain A: N.589 Ligand excluded by PLIP DMS.3: 5 residues within 4Å: Chain A: W.61, I.62, Q.65, R.187 Chain B: V.34 Ligand excluded by PLIP DMS.4: 3 residues within 4Å: Chain A: H.195, W.209, R.345 Ligand excluded by PLIP DMS.5: 5 residues within 4Å: Chain A: Q.213, V.215, A.266, I.269, K.288 Ligand excluded by PLIP DMS.6: 5 residues within 4Å: Chain A: R.60, N.95, L.96, R.228, N.230 Ligand excluded by PLIP DMS.7: 4 residues within 4Å: Chain A: Y.547, F.638, L.639, E.640 Ligand excluded by PLIP DMS.8: 5 residues within 4Å: Chain A: E.699, E.700, F.702, F.703, R.780 Ligand excluded by PLIP DMS.9: 6 residues within 4Å: Chain A: I.525, R.526, A.529, P.788, R.789, T.792 Ligand excluded by PLIP DMS.10: 5 residues within 4Å: Chain A: R.513, E.695, E.696, A.697, G.698 Ligand excluded by PLIP DMS.11: 5 residues within 4Å: Chain A: E.20, N.24, D.55, H.56 Chain B: F.31 Ligand excluded by PLIP DMS.12: 2 residues within 4Å: Chain A: R.27, H.30 Ligand excluded by PLIP DMS.13: 5 residues within 4Å: Chain A: E.171 Chain B: F.246, G.255, Y.256, A.259 Ligand excluded by PLIP DMS.14: 7 residues within 4Å: Chain A: L.261, D.262, N.264, L.265 Chain B: L.265, N.268 Ligands: DMS.38 Ligand excluded by PLIP DMS.15: 2 residues within 4Å: Chain A: G.414, D.415 Ligand excluded by PLIP DMS.16: 2 residues within 4Å: Chain A: E.790, R.793 Ligand excluded by PLIP DMS.17: 4 residues within 4Å: Chain A: T.191, L.216, N.244 Ligands: DMS.23 Ligand excluded by PLIP DMS.18: 6 residues within 4Å: Chain A: Y.274, K.283, L.285 Chain B: I.257, Q.258, L.261 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain A: Y.720, H.761, H.762, D.763 Ligand excluded by PLIP DMS.20: 2 residues within 4Å: Chain A: F.280, E.281 Ligand excluded by PLIP DMS.21: 3 residues within 4Å: Chain A: V.39, A.40, T.41 Ligand excluded by PLIP DMS.22: 5 residues within 4Å: Chain A: R.10, Q.90, E.117, L.488 Ligands: KDH.1 Ligand excluded by PLIP DMS.23: 8 residues within 4Å: Chain A: P.188, T.191, L.216, K.241, N.244 Chain B: R.178, Y.179 Ligands: DMS.17 Ligand excluded by PLIP DMS.24: 7 residues within 4Å: Chain A: R.421, T.460, I.461, F.462, K.463, D.464, F.465 Ligand excluded by PLIP DMS.26: 1 residues within 4Å: Chain B: N.589 Ligand excluded by PLIP DMS.27: 5 residues within 4Å: Chain A: V.34 Chain B: W.61, I.62, Q.65, R.187 Ligand excluded by PLIP DMS.28: 3 residues within 4Å: Chain B: H.195, W.209, R.345 Ligand excluded by PLIP DMS.29: 5 residues within 4Å: Chain B: Q.213, V.215, A.266, I.269, K.288 Ligand excluded by PLIP DMS.30: 5 residues within 4Å: Chain B: R.60, N.95, L.96, R.228, N.230 Ligand excluded by PLIP DMS.31: 4 residues within 4Å: Chain B: Y.547, F.638, L.639, E.640 Ligand excluded by PLIP DMS.32: 5 residues within 4Å: Chain B: E.699, E.700, F.702, F.703, R.780 Ligand excluded by PLIP DMS.33: 6 residues within 4Å: Chain B: I.525, R.526, A.529, P.788, R.789, T.792 Ligand excluded by PLIP DMS.34: 5 residues within 4Å: Chain B: R.513, E.695, E.696, A.697, G.698 Ligand excluded by PLIP DMS.35: 5 residues within 4Å: Chain A: F.31 Chain B: E.20, N.24, D.55, H.56 Ligand excluded by PLIP DMS.36: 2 residues within 4Å: Chain B: R.27, H.30 Ligand excluded by PLIP DMS.37: 5 residues within 4Å: Chain A: F.246, G.255, Y.256, A.259 Chain B: E.171 Ligand excluded by PLIP DMS.38: 7 residues within 4Å: Chain A: L.265, N.268 Chain B: L.261, D.262, N.264, L.265 Ligands: DMS.14 Ligand excluded by PLIP DMS.39: 2 residues within 4Å: Chain B: G.414, D.415 Ligand excluded by PLIP DMS.40: 2 residues within 4Å: Chain B: E.790, R.793 Ligand excluded by PLIP DMS.41: 4 residues within 4Å: Chain B: T.191, L.216, N.244 Ligands: DMS.47 Ligand excluded by PLIP DMS.42: 6 residues within 4Å: Chain A: I.257, Q.258, L.261 Chain B: Y.274, K.283, L.285 Ligand excluded by PLIP DMS.43: 4 residues within 4Å: Chain B: Y.720, H.761, H.762, D.763 Ligand excluded by PLIP DMS.44: 2 residues within 4Å: Chain B: F.280, E.281 Ligand excluded by PLIP DMS.45: 3 residues within 4Å: Chain B: V.39, A.40, T.41 Ligand excluded by PLIP DMS.46: 5 residues within 4Å: Chain B: R.10, Q.90, E.117, L.488 Ligands: KDH.25 Ligand excluded by PLIP DMS.47: 8 residues within 4Å: Chain A: R.178, Y.179 Chain B: P.188, T.191, L.216, K.241, N.244 Ligands: DMS.41 Ligand excluded by PLIP DMS.48: 7 residues within 4Å: Chain B: R.421, T.460, I.461, F.462, K.463, D.464, F.465 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alexopoulos, S. et al., Evidence for the Quercetin Binding Site of Glycogen Phosphorylase as a Target for Liver-Isoform-Selective Inhibitors against Glioblastoma: Investigation of Flavanols Epigallocatechin Gallate and Epigallocatechin. J.Agric.Food Chem. (2024)

Release Date

2024-10-30

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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