SMTL ID : 5ox3.1

Glycogen Phosphorylase in complex with SzB102v

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x B1N: (1S)-1,5-anhydro-1-[3-(4-hydroxyphenyl)-1H-1,2,4-triazol-5-yl]-D-glucitol(Non-covalent)

B1N.1: 19 residues within 4Å: Chain A: E.89, G.136, L.137, L.140, N.283, N.285, F.286, R.293, H.342, H.378, T.379, V.456, N.485, Y.574, E.673, A.674, S.675, G.676, T.677 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.285, A:F.286, A:R.293, A:N.485, A:E.673, A:E.673, A:A.674, A:S.675, A:G.676 Water bridges: A:L.137, A:D.284, A:R.293, A:R.293, A:K.575, A:T.677 pi-Cation interactions: A:H.342 B1N.4: 19 residues within 4Å: Chain B: E.89, G.136, L.137, L.140, N.283, N.285, F.286, R.293, H.342, H.378, T.379, V.456, N.485, Y.574, E.673, A.674, S.675, G.676, T.677 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:N.285, B:F.286, B:R.293, B:H.378, B:N.485, B:E.673, B:A.674, B:S.675, B:G.676 Water bridges: B:L.137, B:D.284, B:R.293, B:R.293, B:K.575, B:T.677 pi-Cation interactions: B:H.342

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

PLP.2: 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:T.677, A:G.678 Water bridges: A:G.136, A:K.569, A:K.569, A:K.575, A:N.679 Salt bridges: A:K.569, A:K.575 PLP.5: 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:T.677, B:G.678 Water bridges: B:G.136, B:K.569, B:K.569, B:K.575, B:N.679 Salt bridges: B:K.569, B:K.575

2 x IMP: INOSINIC ACID(Non-covalent)

IMP.3: 5 residues within 4Å: Chain A: Q.73, Y.76, R.310, R.311 Chain B: V.46 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:R.310, A:R.311 pi-Stacking: A:Y.76, A:Y.76 IMP.6: 5 residues within 4Å: Chain A: V.46 Chain B: Q.73, Y.76, R.310, R.311 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.76 Salt bridges: B:R.310, B:R.311 pi-Stacking: B:Y.76, B:Y.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kyriakis, E. et al., Probing the beta-pocket of the active site of human liver glycogen phosphorylase with 3-(C-beta-d-glucopyranosyl)-5-(4-substituted-phenyl)-1, 2, 4-triazole inhibitors. Bioorg. Chem. (2018)

Release Date

2018-02-28

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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