SMTL ID : 2prj.1

Binding of N-acetyl-beta-D-glucopyranosylamine to Glycogen Phosphorylase B

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x NBG: N-acetyl-beta-D-glucopyranosylamine(Non-covalent)

NBG.1: 13 residues within 4Å: Chain A: G.135, L.136, N.284, D.339, H.377, T.378, V.455, N.484, Y.573, E.672, A.673, S.674, G.675 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:H.377, A:T.378 Hydrogen bonds: A:N.284, A:N.284, A:H.377, A:E.672, A:E.672, A:S.674, A:G.675, A:G.675 Water bridges: A:L.136, A:A.673, A:A.673, A:T.676, A:T.676 NBG.4: 13 residues within 4Å: Chain B: G.135, L.136, N.284, D.339, H.377, T.378, V.455, N.484, Y.573, E.672, A.673, S.674, G.675 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:H.377, B:T.378 Hydrogen bonds: B:N.284, B:N.284, B:H.377, B:H.377, B:E.672, B:S.674, B:G.675, B:G.675 Water bridges: B:L.136, B:A.673, B:A.673, B:T.676, B:T.676

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

PLP.2: 13 residues within 4Å: Chain A: G.134, G.135, W.491, K.568, K.574, Y.648, R.649, V.650, A.653, G.675, T.676, G.677, K.680 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.648, A:K.680 Hydrogen bonds: A:T.676, A:T.676, A:T.676, A:G.677 Water bridges: A:G.135, A:K.568, A:K.574, A:K.574, A:G.675, A:N.678, A:N.678 Salt bridges: A:K.568, A:K.574 PLP.5: 13 residues within 4Å: Chain B: G.134, G.135, W.491, K.568, K.574, Y.648, R.649, V.650, A.653, G.675, T.676, G.677, K.680 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.648, 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.574, B:K.574, B:G.675, B:N.678, B:N.678 Salt bridges: B:K.568, B:K.574

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, 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 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.72, A:D.42 Water bridges: B:Y.155 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

Oikonomakos, N.G. et al., N-acetyl-beta-D-glucopyranosylamine: a potent T-state inhibitor of glycogen phosphorylase. A comparison with alpha-D-glucose. Protein Sci. (1995)

Release Date

1998-12-16

Peptides

GLYCOGEN PHOSPHORYLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GLYCOGEN PHOSPHORYLASE

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