SMTL ID : 5o50.1

Glycogen Phosphorylase b in complex with 33a

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 14 residues within 4Å: Chain A: G.134, G.135, W.491, V.567, K.568, K.574, Y.648, R.649, V.650, A.653, G.675, T.676, G.677, K.680 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.648, A:V.650, A:K.680 Hydrogen bonds: A:T.676, A:T.676, A:G.677 Water bridges: A:G.135, A:K.568, A:K.568, A:K.574, A:N.678 Salt bridges: A:K.568, A:K.574 PLP.4: 14 residues within 4Å: Chain B: G.134, G.135, W.491, V.567, K.568, K.574, Y.648, R.649, V.650, A.653, G.675, T.676, G.677, K.680 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.648, B:V.650, B:K.680 Hydrogen bonds: B:Y.648, B:T.676, B:T.676, B:G.677 Water bridges: B:G.135, B:K.568, B:K.568, B:K.574, B:N.678 Salt bridges: B:K.568, B:K.574

2 x 9L2: (2~{R},3~{S},4~{R},5~{R},6~{R})-5-azanyl-2-(hydroxymethyl)-6-(4-phenyl-1~{H}-imidazol-2-yl)oxane-3,4-diol(Non-covalent)

9L2.2: 18 residues within 4Å: Chain A: E.88, G.135, L.136, L.139, N.282, N.284, F.285, H.341, H.377, T.378, V.455, N.484, Y.573, E.672, A.673, S.674, G.675, T.676 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.484, A:N.484, A:Y.573, A:E.672, A:E.672, A:A.673, A:S.674, A:G.675 Water bridges: A:L.136, A:T.378, A:K.574, A:T.676 pi-Stacking: A:H.341 9L2.5: 18 residues within 4Å: Chain B: E.88, G.135, L.136, L.139, N.282, N.284, F.285, H.341, H.377, T.378, V.455, N.484, Y.573, E.672, A.673, S.674, G.675, T.676 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:H.377, B:N.484, B:N.484, B:E.672, B:A.673, B:S.674, B:G.675 Water bridges: B:L.136, B:K.574, B:T.676 pi-Stacking: B:H.341

2 x IMP: INOSINIC ACID(Non-covalent)

IMP.3: 7 residues within 4Å: Chain A: Q.71, Q.72, Y.75, R.309, R.310 Chain B: D.42, V.45 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:D.42 Water bridges: A:Q.72 Salt bridges: A:R.309, A:R.310 pi-Stacking: A:Y.75, A:Y.75 IMP.6: 7 residues within 4Å: Chain A: D.42, V.45 Chain B: Q.71, Q.72, Y.75, R.309, R.310 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.42 Water bridges: B:Q.72 Salt bridges: B:R.309, B:R.310 pi-Stacking: B:Y.75, B:Y.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bokor, E. et al., Nanomolar Inhibitors of Glycogen Phosphorylase Based on beta-d-Glucosaminyl Heterocycles: A Combined Synthetic, Enzyme Kinetic, and Protein Crystallography Study. J. Med. Chem. (2017)

Release Date

2017-09-27

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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