SMTL ID : 8r53.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.1: 12 residues within 4Å: Chain A: G.129, L.130, L.133, N.278, H.371, V.449, N.478, Y.567, E.666, A.667, S.668, G.669 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.129, A:L.130, A:N.278, A:N.278, A:N.478, A:N.478, A:E.666, A:E.666, A:A.667, A:S.668, A:S.668, A:G.669 Water bridges: A:D.277, A:D.277, A:T.670 Salt bridges: A:H.371 GLC.29: 12 residues within 4Å: Chain B: G.129, L.130, L.133, N.278, H.371, V.449, N.478, Y.567, E.666, A.667, S.668, G.669 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:G.129, B:L.130, B:N.278, B:N.278, B:H.371, B:N.478, B:N.478, B:Y.567, B:E.666, B:A.667, B:S.668, B:S.668, B:G.669 Water bridges: B:D.277, B:D.277, B:T.670 Salt bridges: B:H.371

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

DMS.2: 1 residues within 4Å: Chain A: N.589 Ligand excluded by PLIP DMS.3: 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.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: F.196, Q.213, V.215, A.266, 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: 3 residues within 4Å: Chain A: N.26, 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.42 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: 3 residues within 4Å: Chain A: T.191, L.216, N.244 Ligand excluded by PLIP DMS.18: 5 residues within 4Å: Chain A: Y.274, K.283, L.285 Chain B: I.257, Q.258 Ligand excluded by PLIP DMS.19: 5 residues within 4Å: Chain A: Y.720, H.761, H.762, D.763, R.764 Ligand excluded by PLIP DMS.20: 3 residues within 4Å: Chain A: F.280, E.281, G.282 Ligand excluded by PLIP DMS.21: 6 residues within 4Å: Chain A: H.67, K.71, G.145, S.824, Q.826, L.828 Ligand excluded by PLIP DMS.22: 6 residues within 4Å: Chain A: R.10, Q.90, E.99, E.114, E.117 Ligands: KDH.28 Ligand excluded by PLIP DMS.23: 6 residues within 4Å: Chain A: T.143, Y.227, N.229, S.507, R.825, R.827 Ligand excluded by PLIP DMS.24: 3 residues within 4Å: Chain A: F.412, E.467, L.468 Ligand excluded by PLIP DMS.25: 2 residues within 4Å: Chain A: I.452, E.710 Ligand excluded by PLIP DMS.26: 5 residues within 4Å: Chain A: A.498, E.499, R.500, I.501, G.502 Ligand excluded by PLIP DMS.27: 6 residues within 4Å: Chain A: Y.726, I.736, E.737, S.740, V.756, M.760 Ligand excluded by PLIP DMS.30: 1 residues within 4Å: Chain B: N.589 Ligand excluded by PLIP DMS.31: 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.32: 3 residues within 4Å: Chain B: H.195, W.209, R.345 Ligand excluded by PLIP DMS.33: 5 residues within 4Å: Chain B: F.196, Q.213, V.215, A.266, K.288 Ligand excluded by PLIP DMS.34: 5 residues within 4Å: Chain B: R.60, N.95, L.96, R.228, N.230 Ligand excluded by PLIP DMS.35: 4 residues within 4Å: Chain B: Y.547, F.638, L.639, E.640 Ligand excluded by PLIP DMS.36: 5 residues within 4Å: Chain B: E.699, E.700, F.702, F.703, R.780 Ligand excluded by PLIP DMS.37: 6 residues within 4Å: Chain B: I.525, R.526, A.529, P.788, R.789, T.792 Ligand excluded by PLIP DMS.38: 5 residues within 4Å: Chain B: R.513, E.695, E.696, A.697, G.698 Ligand excluded by PLIP DMS.39: 5 residues within 4Å: Chain A: F.31 Chain B: E.20, N.24, D.55, H.56 Ligand excluded by PLIP DMS.40: 3 residues within 4Å: Chain B: N.26, R.27, H.30 Ligand excluded by PLIP DMS.41: 5 residues within 4Å: Chain A: F.246, G.255, Y.256, A.259 Chain B: E.171 Ligand excluded by PLIP DMS.42: 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.43: 2 residues within 4Å: Chain B: G.414, D.415 Ligand excluded by PLIP DMS.44: 2 residues within 4Å: Chain B: E.790, R.793 Ligand excluded by PLIP DMS.45: 3 residues within 4Å: Chain B: T.191, L.216, N.244 Ligand excluded by PLIP DMS.46: 5 residues within 4Å: Chain A: I.257, Q.258 Chain B: Y.274, K.283, L.285 Ligand excluded by PLIP DMS.47: 5 residues within 4Å: Chain B: Y.720, H.761, H.762, D.763, R.764 Ligand excluded by PLIP DMS.48: 3 residues within 4Å: Chain B: F.280, E.281, G.282 Ligand excluded by PLIP DMS.49: 6 residues within 4Å: Chain B: H.67, K.71, G.145, S.824, Q.826, L.828 Ligand excluded by PLIP DMS.50: 6 residues within 4Å: Chain B: R.10, Q.90, E.99, E.114, E.117 Ligands: KDH.56 Ligand excluded by PLIP DMS.51: 6 residues within 4Å: Chain B: T.143, Y.227, N.229, S.507, R.825, R.827 Ligand excluded by PLIP DMS.52: 3 residues within 4Å: Chain B: F.412, E.467, L.468 Ligand excluded by PLIP DMS.53: 2 residues within 4Å: Chain B: I.452, E.710 Ligand excluded by PLIP DMS.54: 5 residues within 4Å: Chain B: A.498, E.499, R.500, I.501, G.502 Ligand excluded by PLIP DMS.55: 6 residues within 4Å: Chain B: Y.726, I.736, E.737, S.740, V.756, M.760 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.28: 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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:E.118, A:K.538, 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 Salt bridges: A:R.545 pi-Cation interactions: A:K.538, A:R.545 KDH.56: 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.50 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:E.118, B:K.538, B:K.538, B:A.541, B:Y.542, B:K.649, B:K.649 Hydrogen bonds: B:E.114, B:R.545 Salt bridges: B:R.545 pi-Cation interactions: B:K.538, B:R.545

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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