SMTL ID : 8r6v.1

The complex of glycogen phosphorylase with EGCG (epigallocatechin gallate) and caffeine.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

DMS.1: 1 residues within 4Å: Chain A: N.589 Ligand excluded by PLIP DMS.2: 6 residues within 4Å: Chain A: W.61, I.62, Q.65, R.187, T.234 Chain B: V.34 Ligand excluded by PLIP DMS.3: 3 residues within 4Å: Chain A: H.195, W.209, R.345 Ligand excluded by PLIP DMS.4: 7 residues within 4Å: Chain A: Y.197, Q.213, V.215, A.266, I.269, K.288 Ligands: DMS.26 Ligand excluded by PLIP DMS.5: 6 residues within 4Å: Chain A: R.60, N.95, L.96, A.97, R.228, N.230 Ligand excluded by PLIP DMS.6: 4 residues within 4Å: Chain A: Y.547, F.638, L.639, E.640 Ligand excluded by PLIP DMS.7: 5 residues within 4Å: Chain A: E.699, E.700, F.702, F.703, R.780 Ligand excluded by PLIP DMS.8: 8 residues within 4Å: Chain A: R.421, M.422, T.460, I.461, F.462, K.463, D.464, F.465 Ligand excluded by PLIP DMS.9: 5 residues within 4Å: Chain A: I.525, 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: 3 residues within 4Å: Chain A: N.26, H.30, F.31 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: 8 residues within 4Å: Chain A: L.261, D.262, N.264, L.265 Chain B: N.264, L.265, N.268 Ligands: DMS.45 Ligand excluded by PLIP DMS.15: 1 residues within 4Å: Chain A: D.415 Ligand excluded by PLIP DMS.16: 3 residues within 4Å: Chain A: E.790, R.793 Ligands: DMS.29 Ligand excluded by PLIP DMS.17: 3 residues within 4Å: Chain A: T.191, L.216, N.244 Ligand excluded by PLIP DMS.18: 4 residues within 4Å: Chain A: Y.785, P.788, W.791, T.792 Ligand excluded by PLIP DMS.19: 3 residues within 4Å: Chain A: Y.274 Chain B: I.257, Q.258 Ligand excluded by PLIP DMS.20: 3 residues within 4Å: Chain A: H.761, H.762, D.763 Ligand excluded by PLIP DMS.21: 4 residues within 4Å: Chain A: F.279, F.280, E.281, G.282 Ligand excluded by PLIP DMS.22: 7 residues within 4Å: Chain A: H.67, K.71, G.145, V.231, S.824, Q.826, L.828 Ligand excluded by PLIP DMS.23: 5 residues within 4Å: Chain A: R.10, Q.90, E.117, L.488 Ligands: KDH.30 Ligand excluded by PLIP DMS.24: 3 residues within 4Å: Chain A: W.168, H.608 Ligands: DMS.25 Ligand excluded by PLIP DMS.25: 2 residues within 4Å: Chain A: W.168 Ligands: DMS.24 Ligand excluded by PLIP DMS.26: 4 residues within 4Å: Chain A: L.265, N.268, K.288 Ligands: DMS.4 Ligand excluded by PLIP DMS.27: 3 residues within 4Å: Chain A: E.281, G.606 Ligands: CFF.31 Ligand excluded by PLIP DMS.28: 2 residues within 4Å: Chain A: I.452, E.710 Ligand excluded by PLIP DMS.29: 4 residues within 4Å: Chain A: L.784, E.790, M.794 Ligands: DMS.16 Ligand excluded by PLIP DMS.32: 1 residues within 4Å: Chain B: N.589 Ligand excluded by PLIP DMS.33: 6 residues within 4Å: Chain A: V.34 Chain B: W.61, I.62, Q.65, R.187, T.234 Ligand excluded by PLIP DMS.34: 3 residues within 4Å: Chain B: H.195, W.209, R.345 Ligand excluded by PLIP DMS.35: 7 residues within 4Å: Chain B: Y.197, Q.213, V.215, A.266, I.269, K.288 Ligands: DMS.57 Ligand excluded by PLIP DMS.36: 6 residues within 4Å: Chain B: R.60, N.95, L.96, A.97, R.228, N.230 Ligand excluded by PLIP DMS.37: 4 residues within 4Å: Chain B: Y.547, F.638, L.639, E.640 Ligand excluded by PLIP DMS.38: 5 residues within 4Å: Chain B: E.699, E.700, F.702, F.703, R.780 Ligand excluded by PLIP DMS.39: 8 residues within 4Å: Chain B: R.421, M.422, T.460, I.461, F.462, K.463, D.464, F.465 Ligand excluded by PLIP DMS.40: 5 residues within 4Å: Chain B: I.525, A.529, P.788, R.789, T.792 Ligand excluded by PLIP DMS.41: 5 residues within 4Å: Chain B: R.513, E.695, E.696, A.697, G.698 Ligand excluded by PLIP DMS.42: 5 residues within 4Å: Chain A: F.31 Chain B: E.20, N.24, D.55, H.56 Ligand excluded by PLIP DMS.43: 3 residues within 4Å: Chain B: N.26, H.30, F.31 Ligand excluded by PLIP DMS.44: 5 residues within 4Å: Chain A: F.246, G.255, Y.256, A.259 Chain B: E.171 Ligand excluded by PLIP DMS.45: 8 residues within 4Å: Chain A: N.264, L.265, N.268 Chain B: L.261, D.262, N.264, L.265 Ligands: DMS.14 Ligand excluded by PLIP DMS.46: 1 residues within 4Å: Chain B: D.415 Ligand excluded by PLIP DMS.47: 3 residues within 4Å: Chain B: E.790, R.793 Ligands: DMS.60 Ligand excluded by PLIP DMS.48: 3 residues within 4Å: Chain B: T.191, L.216, N.244 Ligand excluded by PLIP DMS.49: 4 residues within 4Å: Chain B: Y.785, P.788, W.791, T.792 Ligand excluded by PLIP DMS.50: 3 residues within 4Å: Chain A: I.257, Q.258 Chain B: Y.274 Ligand excluded by PLIP DMS.51: 3 residues within 4Å: Chain B: H.761, H.762, D.763 Ligand excluded by PLIP DMS.52: 4 residues within 4Å: Chain B: F.279, F.280, E.281, G.282 Ligand excluded by PLIP DMS.53: 7 residues within 4Å: Chain B: H.67, K.71, G.145, V.231, S.824, Q.826, L.828 Ligand excluded by PLIP DMS.54: 5 residues within 4Å: Chain B: R.10, Q.90, E.117, L.488 Ligands: KDH.61 Ligand excluded by PLIP DMS.55: 3 residues within 4Å: Chain B: W.168, H.608 Ligands: DMS.56 Ligand excluded by PLIP DMS.56: 2 residues within 4Å: Chain B: W.168 Ligands: DMS.55 Ligand excluded by PLIP DMS.57: 4 residues within 4Å: Chain B: L.265, N.268, K.288 Ligands: DMS.35 Ligand excluded by PLIP DMS.58: 3 residues within 4Å: Chain B: E.281, G.606 Ligands: CFF.62 Ligand excluded by PLIP DMS.59: 2 residues within 4Å: Chain B: I.452, E.710 Ligand excluded by PLIP DMS.60: 4 residues within 4Å: Chain B: L.784, E.790, M.794 Ligands: DMS.47 Ligand excluded by PLIP

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.30: 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.23 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:E.118, A:K.538, A:K.538, A:K.538, A:A.541, A:Y.542 Hydrogen bonds: A:E.114, A:E.114, A:K.649 Water bridges: A:E.115, A:K.538 Salt bridges: A:R.545 pi-Cation interactions: A:K.538, A:R.545 KDH.61: 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.54 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:E.118, B:K.538, B:K.538, B:K.538, B:A.541, B:Y.542 Hydrogen bonds: B:E.114, B:K.649 Water bridges: B:E.115, B:K.538 Salt bridges: B:R.545 pi-Cation interactions: B:K.538, B:R.545

2 x CFF: CAFFEINE(Non-covalent)

CFF.31: 7 residues within 4Å: Chain A: N.276, F.279, H.565, A.604, G.606, Y.607 Ligands: DMS.27 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.608 pi-Stacking: A:F.279, A:F.279, A:Y.607 CFF.62: 7 residues within 4Å: Chain B: N.276, F.279, H.565, A.604, G.606, Y.607 Ligands: DMS.58 5 PLIP interactions: 5 interactions with chain B Water bridges: B:E.376, B:H.608 pi-Stacking: B:F.279, B:F.279, B:Y.607

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

Related Entries With Identical Sequence