SMTL ID : 2g9u.1

The crystal structure of glycogen phosphorylase in complex with (3R,4R,5R)-5-hydroxymethyl-1-(3-phenylpropyl)-piperidine-3,4-diol and phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 9 residues within 4Å: Chain A: G.134, G.135, L.136, R.569, Y.573, K.574, E.672, K.680 Ligands: G27.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.135, A:L.136, A:E.672 Water bridges: A:T.676 Salt bridges: A:R.569, A:K.574 PO4.2: 3 residues within 4Å: Chain A: R.242, R.309, R.310 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.242, A:R.242 Salt bridges: A:R.309, A:R.310 PO4.4: 9 residues within 4Å: Chain B: G.134, G.135, L.136, R.569, Y.573, K.574, E.672, K.680 Ligands: G27.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.135, B:L.136, B:Y.573, B:E.672 Water bridges: B:T.676 Salt bridges: B:R.569, B:K.574 PO4.5: 3 residues within 4Å: Chain B: R.242, R.309, R.310 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.242, B:R.242 Salt bridges: B:R.309, B:R.310

2 x G27: (3R,4R,5R)-5-(HYDROXYMETHYL)-1-(3-PHENYLPROPYL)PIPERIDINE-3,4-DIOL(Non-covalent)

G27.3: 18 residues within 4Å: Chain A: G.135, L.136, L.139, H.377, T.378, L.380, A.383, V.455, N.484, R.569, H.571, Y.573, E.672, A.673, S.674, G.675, T.676 Ligands: PO4.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.378, A:L.380, A:A.383, A:Y.573 Hydrogen bonds: A:E.672, A:E.672, A:S.674, A:S.674, A:G.675 Water bridges: A:T.676 pi-Cation interactions: A:R.569 G27.6: 18 residues within 4Å: Chain B: G.135, L.136, L.139, H.377, T.378, L.380, A.383, V.455, N.484, R.569, H.571, Y.573, E.672, A.673, S.674, G.675, T.676 Ligands: PO4.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:T.378, B:L.380, B:A.383, B:Y.573 Hydrogen bonds: B:H.377, B:E.672, B:S.674, B:S.674, B:G.675 Water bridges: B:T.676 pi-Cation interactions: B:R.569

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oikonomakos, N.G. et al., Iminosugars as potential inhibitors of glycogenolysis: structural insights into the molecular basis of glycogen phosphorylase inhibition. J.Med.Chem. (2006)

Release Date

2007-01-16

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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